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1

Mutation analysis and embryonic expression of the HLXB9 Currarino syndrome gene.  

PubMed Central

The HLXB9 homeobox gene was recently identified as a locus for autosomal dominant Currarino syndrome, also known as hereditary sacral agenesis (HSA). This gene specifies a 403-amino acid protein containing a homeodomain preceded by a very highly conserved 82-amino acid domain of unknown function; the remainder of the protein is not well conserved. Here we report an extensive mutation survey that has identified mutations in the HLXB9 gene in 20 of 21 patients tested with familial Currarino syndrome. Mutations were also detected in two of seven sporadic Currarino syndrome patients; the remainder could be explained by undetected mosaicism for an HLXB9 mutation or by genetic heterogeneity in the sporadic patients. Of the mutations identified in the 22 index patients, 19 were intragenic and included 11 mutations that could lead to the introduction of a premature termination codon. The other eight mutations were missense mutations that were significantly clustered in the homeodomain, resulting, in each patient, in nonconservative substitution of a highly conserved amino acid. All of the intragenic mutations were associated with comparable phenotypes. The only genotype-phenotype correlation appeared to be the occurrence of developmental delay in the case of three patients with microdeletions. HLXB9 expression was analyzed during early human development in a period spanning Carnegie stages 12-21. Signal was detected in the basal plate of the spinal cord and hindbrain and in the pharynx, esophagus, stomach, and pancreas. Significant spatial and temporal expression differences were evident when compared with expression of the mouse Hlxb9 gene, which may partly explain the significant human-mouse differences in mutant phenotype.

Hagan, D M; Ross, A J; Strachan, T; Lynch, S A; Ruiz-Perez, V; Wang, Y M; Scambler, P; Custard, E; Reardon, W; Hassan, S; Nixon, P; Papapetrou, C; Winter, R M; Edwards, Y; Morrison, K; Barrow, M; Cordier-Alex, M P; Correia, P; Galvin-Parton, P A; Gaskill, S; Gaskin, K J; Garcia-Minaur, S; Gereige, R; Hayward, R; Homfray, T

2000-01-01

2

Population Differences in the Polyalanine Domain and 6 New Mutations in HLXB9 in Patients with Currarino Syndrome  

Microsoft Academic Search

Background: The combination of partial absence of the sacrum, anorectal anomalies, and presacral mass consti- tutes Currarino syndrome (CS), which is associated with mutations in HLXB9. Methods: We analyzed 5 CS families and 6 sporadic cases for HLXB9 mutations by direct sequencing. Poten- tially pathologic expansions of HLXB9 GCC repeats were analyzed in patients, 4 general populations (Chi- nese, Japanese,

Man-ting So; Danny Ko-chun Lau; Thomas Yuk-yu Leon; Zheng-wei Yuan; Wei-song Cai; Vincent Chi-hang Lui; Ming Fu; Jo-Anne Herbrick; Long Li; Jacqueline Pierre-Louis; Kirk Aleck; Ernest van Heurn; Stephen W. Scherer; Paul Kwong-hang Tam

3

The embryonic transcription factor Hlxb9 is a menin interacting partner that controls pancreatic ?-cell proliferation and the expression of insulin regulators.  

PubMed

The multiple endocrine neoplasia type 1 (MEN1) syndrome is caused by germline mutations in the MEN1 gene encoding menin, with tissue-specific tumors of the parathyroids, anterior pituitary, and enteropancreatic endocrine tissues. Also, 30-40% of sporadic pancreatic endocrine tumors show somatic MEN1 gene inactivation. Although menin is expressed in all cell types of the pancreas, mouse models with loss of menin in either pancreatic ?-cells, or ?-cells, or total pancreas develop ?-cell-specific endocrine tumors (insulinomas). Loss of widely expressed tumor suppressor genes may produce tissue-specific tumors by reactivating one or more embryonic-specific differentiation factors. Therefore, we determined the effect of menin overexpression or knockdown on the expression of ?-cell differentiation factors in a mouse ?-cell line (MIN6). We show that the ?-cell differentiation factor Hlxb9 is posttranscriptionally upregulated upon menin knockdown, and it interacts with menin. Hlxb9 reduces cell proliferation and causes apoptosis in the presence of menin, and it regulates genes that modulate insulin level. Thus, upon menin loss or from other causes, dysregulation of Hlxb9 predicts a possible combined mechanism for ?-cell proliferation and insulin production in insulinomas. These observations help to understand how a ubiquitously expressed protein such as menin might control tissue-specific tumorigenesis. Also, our findings identify Hlxb9 as an important factor for ?-cell proliferation and insulin regulation. PMID:23419452

Shi, Kerong; Parekh, Vaishali I; Roy, Swarnava; Desai, Shruti S; Agarwal, Sunita K

2013-02-18

4

VACTERL/caudal regression/Currarino syndrome-like malformations in mice with mutation in the proprotein convertase Pcsk5.  

PubMed

We have identified an ethylnitrosourea (ENU)-induced recessive mouse mutation (Vcc) with a pleiotropic phenotype that includes cardiac, tracheoesophageal, anorectal, anteroposterior patterning defects, exomphalos, hindlimb hypoplasia, a presacral mass, renal and palatal agenesis, and pulmonary hypoplasia. It results from a C470R mutation in the proprotein convertase PCSK5 (PC5/6). Compound mutants (Pcsk5(Vcc/null)) completely recapitulate the Pcsk5(Vcc/Vcc) phenotype, as does an epiblast-specific conditional deletion of Pcsk5. The C470R mutation ablates a disulfide bond in the P domain, and blocks export from the endoplasmic reticulum and proprotein convertase activity. We show that GDF11 is cleaved and activated by PCSK5A, but not by PCSK5A-C470R, and that Gdf11-deficient embryos, in addition to having anteroposterior patterning defects and renal and palatal agenesis, also have a presacral mass, anorectal malformation, and exomphalos. Pcsk5 mutation results in abnormal expression of several paralogous Hox genes (Hoxa, Hoxc, and Hoxd), and of Mnx1 (Hlxb9). These include known Gdf11 targets, and are necessary for caudal embryo development. We identified nonsynonymous mutations in PCSK5 in patients with VACTERL (vertebral, anorectal, cardiac, tracheoesophageal, renal, limb malformation OMIM 192350) and caudal regression syndrome, the phenotypic features of which resemble the mouse mutation. We propose that Pcsk5, at least in part via GDF11, coordinately regulates caudal Hox paralogs, to control anteroposterior patterning, nephrogenesis, skeletal, and anorectal development. PMID:18519639

Szumska, Dorota; Pieles, Guido; Essalmani, Rachid; Bilski, Michal; Mesnard, Daniel; Kaur, Kulvinder; Franklyn, Angela; El Omari, Kamel; Jefferis, Joanna; Bentham, Jamie; Taylor, Jennifer M; Schneider, Jurgen E; Arnold, Sebastian J; Johnson, Paul; Tymowska-Lalanne, Zuzanna; Stammers, Dave; Clarke, Kieran; Neubauer, Stefan; Morris, Andrew; Brown, Steve D; Shaw-Smith, Charles; Cama, Armando; Capra, Valeria; Ragoussis, Jiannis; Constam, Daniel; Seidah, Nabil G; Prat, Annik; Bhattacharya, Shoumo

2008-06-01

5

IDH1 mutation identified in human melanoma  

PubMed Central

Isocitrate dehydrogenase 1 (IDH1) and isocitrate dehydrogenase 2 (IDH2) are enzymes which convert isocitrate to ?-ketoglutarate while reducing nicotinamide adenine dinucleotide phosphate (NADP+ to NADPH). IDH1/2 were recently identified as mutated in a large percentage of progressive gliomas. These mutations occur at IDH1R132 or the homologous IDH2R172. Melanomas share some genetic features with IDH1/2-mutated gliomas, such as frequent TP53 mutation. We sought to test whether melanoma is associated with IDH1/2 mutations. 78 human melanoma samples were analyzed for IDH1R132 and IDH2R172 mutation status. A somatic, heterozygous IDH1 c.C394T (p.R132C) mutation was identified in one human melanoma metastasis to the lung. Having identified this mutation in one metastasis, we sought to test the hypothesis that certain selective pressures in the brain environment may specifically favor the cell growth or survival of tumor cells with mutations in IDH1/2, regardless of primary tumor site. To address this, we analyzed IDH1R132 and IDH2R172 mutation status 53 metastatic brain tumors, including 9 melanoma metastases. Results revealed no mutations in any samples. This lack of mutations would suggest that mutations in IDH1R132 or IDH2R172 may be necessary for the formation of tumors in a cell-lineage dependent manner, with a particularly strong selective pressure for mutations in progressive gliomas; this also suggests the lack of a particular selective pressure for growth in brain tissue in general. Studies on the cell-lineages of tumors with IDH1/2 mutations may help clarify the role of these mutations in the development of brain tumors.

Lopez, Giselle Y.; Reitman, Zachary J.; Solomon, David; Waldman, Todd; Bigner, Darell D.; McLendon, Roger E.; Samuels, Yardena; Yan, Hai

2010-01-01

6

A microarray approach for identifying mutated genes  

Microsoft Academic Search

This study was performed to evaluate if microarray technology can identify genes using their transcriptionally defective mutant alleles. Three barley (Hordeum vulgare L.) mutant strains, xantha-h57, xantha-f27 and xantha-g28, with mutations in the genes encoding the three subunits of the chlorophyll biosynthetic enzyme magnesium chelatase, were used in a reconstruction experiment. The mutation xantha-h57 prevents transcription of Xantha-h mRNA. Microarrays

Shakhira Zakhrabekova; C. Gamini Kannangara; Diter von Wettstein; Mats Hansson

2002-01-01

7

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma  

SciTech Connect

We characterized the mutational landscape of melanoma, the form of skin cancer with the highest mortality rate, by sequencing the exomes of 147 melanomas. Sun-exposed melanomas had markedly more ultraviolet (UV)-like C>T somatic mutations compared to sun-shielded acral, mucosal and uveal melanomas. Among the newly identified cancer genes was PPP6C, encoding a serine/threonine phosphatase, which harbored mutations that clustered in the active site in 12% of sun-exposed melanomas, exclusively in tumors with mutations in BRAF or NRAS. Notably, we identified a recurrent UV-signature, an activating mutation in RAC1 in 9.2% of sun-exposed melanomas. This activating mutation, the third most frequent in our cohort of sun-exposed melanoma after those of BRAF and NRAS, changes Pro29 to serine (RAC1{sup P29S}) in the highly conserved switch I domain. Crystal structures, and biochemical and functional studies of RAC1{sup P29S} showed that the alteration releases the conformational restraint conferred by the conserved proline, causes an increased binding of the protein to downstream effectors, and promotes melanocyte proliferation and migration. These findings raise the possibility that pharmacological inhibition of downstream effectors of RAC1 signaling could be of therapeutic benefit.

Krauthammer, Michael; Kong, Yong; Ha, Byung Hak; Evans, Perry; Bacchiocchi, Antonella; McCusker, James P.; Cheng, Elaine; Davis, Matthew J.; Goh, Gerald; Choi, Murim; Ariyan, Stephan; Narayan, Deepak; Dutton-Regester, Ken; Capatana, Ana; Holman, Edna C.; Bosenberg, Marcus; Sznol, Mario; Kluger, Harriet M.; Brash, Douglas E.; Stern, David F.; Materin, Miguel A.; Lo, Roger S.; Mane, Shrikant; Ma, Shuangge; Kidd, Kenneth K.; Hayward, Nicholas K.; Lifton, Richard P.; Schlessinger, Joseph; Boggon, Titus J.; Halaban, Ruth (Yale-MED); (UCLA); (Queens)

2012-10-11

8

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma.  

PubMed

Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide and has no effective treatment, yet the molecular basis of hepatocarcinogenesis remains largely unknown. Here we report findings from a whole-genome sequencing (WGS) study of 88 matched HCC tumor/normal pairs, 81 of which are Hepatitis B virus (HBV) positive, seeking to identify genetically altered genes and pathways implicated in HBV-associated HCC. We find beta-catenin to be the most frequently mutated oncogene (15.9%) and TP53 the most frequently mutated tumor suppressor (35.2%). The Wnt/beta-catenin and JAK/STAT pathways, altered in 62.5% and 45.5% of cases, respectively, are likely to act as two major oncogenic drivers in HCC. This study also identifies several prevalent and potentially actionable mutations, including activating mutations of Janus kinase 1 (JAK1), in 9.1% of patients and provides a path toward therapeutic intervention of the disease. PMID:23788652

Kan, Zhengyan; Zheng, Hancheng; Liu, Xiao; Li, Shuyu; Barber, Thomas D; Gong, Zhuolin; Gao, Huan; Hao, Ke; Willard, Melinda D; Xu, Jiangchun; Hauptschein, Robert; Rejto, Paul A; Fernandez, Julio; Wang, Guan; Zhang, Qinghui; Wang, Bo; Chen, Ronghua; Wang, Jian; Lee, Nikki P; Zhou, Wei; Lin, Zhao; Peng, Zhiyu; Yi, Kang; Chen, Shengpei; Li, Lin; Fan, Xiaomei; Yang, Jie; Ye, Rui; Ju, Jia; Wang, Kai; Estrella, Heather; Deng, Shibing; Wei, Ping; Qiu, Ming; Wulur, Isabella H; Liu, Jiangang; Ehsani, Mariam E; Zhang, Chunsheng; Loboda, Andrey; Sung, Wing Kin; Aggarwal, Amit; Poon, Ronnie T; Fan, Sheung Tat; Wang, Jun; Hardwick, James; Reinhard, Christoph; Dai, Hongyue; Li, Yingrui; Luk, John M; Mao, Mao

2013-06-20

9

Human-specific nonsense mutations identified by genome sequence comparisons  

Microsoft Academic Search

The comparative study of the human and chimpanzee genomes may shed light on the genetic ingredients for the evolution of the\\u000a unique traits of humans. Here, we present a simple procedure to identify human-specific nonsense mutations that might have\\u000a arisen since the human–chimpanzee divergence. The procedure involves collecting orthologous sequences in which a stop codon\\u000a of the human sequence is

Yoonsoo Hahn; Byungkook Lee

2006-01-01

10

Exome Sequencing Identifies ZNF644 Mutations in High Myopia  

PubMed Central

Myopia is the most common ocular disorder worldwide, and high myopia in particular is one of the leading causes of blindness. Genetic factors play a critical role in the development of myopia, especially high myopia. Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders. Here we show a successful application of exome sequencing to identify a gene for an autosomal dominant disorder, and we have identified a gene potentially responsible for high myopia in a monogenic form. We captured exomes of two affected individuals from a Han Chinese family with high myopia and performed sequencing analysis by a second-generation sequencer with a mean coverage of 30× and sufficient depth to call variants at ?97% of each targeted exome. The shared genetic variants of these two affected individuals in the family being studied were filtered against the 1000 Genomes Project and the dbSNP131 database. A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644) was identified as being related to the phenotype of this family. After we performed sequencing analysis of the exons in the ZNF644 gene in 300 sporadic cases of high myopia, we identified an additional five mutations (I587V, R680G, C699Y, 3?UTR+12 C>G, and 3?UTR+592 G>A) in 11 different patients. All these mutations were absent in 600 normal controls. The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE). Given that ZNF644 is predicted to be a transcription factor that may regulate genes involved in eye development, mutation may cause the axial elongation of eyeball found in high myopia patients. Our results suggest that ZNF644 might be a causal gene for high myopia in a monogenic form.

Zhang, Dingding; Zhang, Hao; Li, Yuanfeng; Lu, Fang; Liu, Xiaoqi; He, Fei; Gong, Bo; Cai, Li; Li, Ruiqiang; Liao, Shihuang; Ma, Shi; Lin, He; Cheng, Jing; Zheng, Hancheng; Shan, Ying; Chen, Bin; Hu, Jianbin; Jin, Xin; Zhao, Peiquan; Chen, Yiye; Zhang, Yong; Lin, Ying; Li, Xi; Fan, Yingchuan; Yang, Huanming; Wang, Jun; Yang, Zhenglin

2011-01-01

11

Newly identified CHO ERCC3/XPB mutations and phenotype characterization.  

PubMed

Nucleotide excision repair (NER) is a complex multistage process involving many interacting gene products to repair a wide range of DNA lesions. Genetic defects in NER cause human hereditary diseases including xeroderma pigmentosum (XP), Cockayne syndrome (CS), trichothiodystrophy and a combined XP/CS overlapping symptom. One key gene product associated with all these disorders is the excision repair cross-complementing 3/xeroderma pigmentosum B (ERCC3/XPB) DNA helicase, a subunit of the transcription factor IIH complex. ERCC3 is involved in initiation of basal transcription and global genome repair as well as in transcription-coupled repair (TCR). The hamster ERCC3 gene shows high degree of homology with the human ERCC3/XPB gene. We identified new mutations in the Chinese hamster ovary cell ERCC3 gene and characterized the role of hamster ERCC3 protein in DNA repair of ultraviolet (UV)-induced and oxidative DNA damage. All but one newly described mutations are located in the protein C-terminal region around the last intron-exon boundary. Due to protein truncations or frameshifts, they lack amino acid Ser751, phosphorylation of which prevents the 5' incision of the UV-induced lesion during NER. Thus, despite the various locations of the mutations, their phenotypes are similar. All ercc3 mutants are extremely sensitive to UV-C light and lack recovery of RNA synthesis (RRS), confirming a defect in TCR of UV-induced damage. Their limited global genome NER capacity averages approximately 8%. We detected modest sensitivity of ercc3 mutants to the photosensitizer Ro19-8022, which primarily introduces 8-oxoguanine lesions into DNA. Ro19-8022-induced damage interfered with RRS, and some of the ercc3 mutants had delayed kinetics. All ercc3 mutants showed efficient base excision repair (BER). Thus, the positions of the mutations have no effect on the sensitivity to, and repair of, Ro19-8022-induced DNA damage, suggesting that the ERCC3 protein is not involved in BER. PMID:19942596

Rybanská, Ivana; Gursky, Ján; Fasková, Miriam; Salazar, Edmund P; Kimlícková-Polakovicová, Erika; Kleibl, Karol; Thompson, Larry H; Pirsel, Miroslav

2009-11-25

12

PORCN mutations and variants identified in patients with focal dermal hypoplasia through diagnostic gene sequencing.  

PubMed

Focal dermal hypoplasia (FDH) is an X-linked dominant disorder caused by mutations in the gene PORCN, which encodes a protein required for the secretion and signaling of Wnt proteins. While deletions are responsible for a small percentage of FDH-causing mutations, the vast majority of mutations are single-nucleotide substitutions or small deletions or insertions that can be identified by sequence analysis. In 2007, we implemented a PORCN gene sequencing test for individuals with a clinical diagnosis of FDH. To date, we have detected 12 novel PORCN mutations and 6 previously reported mutations in 53 such unrelated patients. The pathogenic PORCN mutations included nine nonsense mutations, three missense mutations, one small deletion, two small duplications, and three splice-site mutations. Of these mutations, two were found in affected men and were mosaic; one of these was found in three other affected women. The remaining 16 mutations were found only in women. All the mutations detected in women were presumed heterozygous. In addition to the disease-causing mutations, eight nucleotide variants of unknown significance were identified. Further characterization of these variants suggests that four of them are pathogenic mutations. These findings add to the heterogeneity of mutations in the PORCN gene that cause FDH. PMID:20854095

Fernandes, Priscilla H; Wen, Shu; Sutton, Vernon Reid; Ward, Patricia A; Van den Veyver, Ignatia B; Fang, Ping

2010-09-20

13

Cancer Risk Estimates for BRCA1 Mutation Carriers Identified in a Risk Evaluation Program  

Microsoft Academic Search

Background: Increasing numbers of BRCA1 mutation car- riers are being identified in cancer risk evaluation programs. However, no estimates of cancer risk specific to a clinic- based population of mutation carriers are available. These data are clinically relevant, because estimates based on fami- lies ascertained for linkage studies may overestimate cancer risk in mutation carriers, and population-based series may underestimate

Marcia S. Brose; Timothy R. Rebbeck; Kathleen A. Calzone; Jill E. Stopfer; Katherine L. Nathanson; Barbara L. Weber

14

New mutations identified in the ocular albinism type 1 gene  

Microsoft Academic Search

As the most common form of ocular albinism, ocular albinism type I (OA1) is an X-linked disorder that has an estimated prevalence of about 1:50,000. We searched for mutations through the human genome sequence draft by direct sequencing on eighteen patients with OA1, both within the coding region and in a thousand base pairs upstream of its start site. Here,

Cristin Roma; Paola Ferrante; Ombretta Guardiola; Andrea Ballabio; Massimo Zollo

2007-01-01

15

Identifying Mutations in Duplicated Functions in Saccharomyces cererrisiae: Recessive Mutations in HMGCoA Reductase Genes  

Microsoft Academic Search

The two yeast genes for 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, HMGl and HMG2, each encode a functional isozyme. Although cells bearing null mutations in both genes are inviable, cells bearing a null mutation in either gene are viable. This paper describes a method of screening for recessive mutations in the HMGl gene, the gene encoding the majority of HMG-CoA reductase activity

Michael E. Basson; Robert L. Moore; Jules O'Rear; Jasper Rine

16

High Throughput Genotyping in Osteosarcoma Identifies Multiple Mutations in PIK3CA and other Oncogenes  

PubMed Central

Background Identification of new genes that are mutated in osteosarcomas is critical to developing a better understanding of the molecular pathogenesis of this disease and discovering new targets for therapeutic development. Methods We identified somatic non-synonymous coding mutations in oncogenes associated with human cancers and hotspot mutations from tumor suppressor genes that were either well-described in literature or seen multiple times in human cancer sequencing efforts. We then systematically characterized 961 mutations in 89 genes across 98 osteosarcoma tumor samples and cell lines. All identified mutations were replicated on an independent platform using homogeneous mass extend MALDI-TOF (Sequenom hME Genotyping). Results We identified 14 mutations in at least one osteosarcoma tumor sample or cell line. Some of the genetic changes identified were in tumor suppressor genes previously known to be altered in osteosarcoma: p53 (R273H, R273C, and Y163C) and RB1 (E137*). Notably, we identified multiple mutations in PIK3CA (H1047R, E545K, and H701P) which have never previously been observed in osteosarcoma. Additionally, we observed mutations in KRAS (G12S), CUBN (I3189V, seen in two separate tumor samples), CDH1 (A617T, seen in two separate tumor samples), CTNNB1 (N287S), and FSCB (S775L). Conclusion We performed the largest mutational profiling of osteosarcoma to date and identified for the first time several mutations involving the PI3 kinase pathway – adding osteosarcoma on to the growing list of malignancies with PI3 kinase mutations. Additionally, we initiated a mutational map detailing DNA sequence changes across a variety of osteosarcoma subtypes and offered new candidates for therapeutic targeting.

Choy, Edwin; Hornicek, Francis; MacConaill, Laura; Harmon, David; Tariq, Zeeshan; Garraway, Levi; Duan, Zhenfeng

2011-01-01

17

Functional Characterization and Targeted Correction of ATM Mutations Identified in Japanese Patients with Ataxia-Telangiectasia  

PubMed Central

A recent challenge for investigators studying the progressive neurological disease ataxia-telangiectasia (A-T) is to identify mutations whose effects might be alleviated by mutation-targeted therapies. We studied ATM mutations in eight families of Japanese A-T patients (JPAT) and were able to identify all 16 mutations. The probands were compound heterozygotes in seven families, and one (JPAT2) was homozygous for a frameshift mutation. All mutations - four frameshift, two nonsense, four large genomic deletions, and six affecting splicing - were novel except for c.748C>T found in family JPAT6 and c.2639?384A>G found in family JPAT11/12. Using an established lymphoblastoid cell line (LCL) of patient JPAT11, ATM protein was restored to levels approaching wildtype by exposure to an antisense morpholino oligonucleotide designed to correct a pseudoexon splicing mutation. In addition, in an LCL from patient JPAT8/9, a heterozygous carrier of a nonsense mutation, ATM levels could also be partially restored by exposure to readthrough compounds (RTC): an aminoglycoside, G418, and a novel small molecule identified in our laboratory, RTC13. Taken together, our results suggest that screening and functional characterization of the various sorts of mutations affecting the ATM gene can lead to better identification of A-T patients who are most likely to benefit from rapidly developing mutation-targeted therapeutic technologies.

Nakamura, Kotoka; Du, Liutao; Tunuguntla, Rashmi; Fike, Francesca; Cavalieri, Simona; Morio, Tomohiro; Mizutani, Shuki; Brusco, Alfredo; Gatti, Richard A

2011-01-01

18

Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators.  

PubMed

Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. We sequenced and analyzed the whole genomes of 27 HCCs, 25 of which were associated with hepatitis B or C virus infections, including two sets of multicentric tumors. Although no common somatic mutations were identified in the multicentric tumor pairs, their whole-genome substitution patterns were similar, suggesting that these tumors developed from independent mutations, although their shared etiological backgrounds may have strongly influenced their somatic mutation patterns. Statistical and functional analyses yielded a list of recurrently mutated genes. Multiple chromatin regulators, including ARID1A, ARID1B, ARID2, MLL and MLL3, were mutated in ?50% of the tumors. Hepatitis B virus genome integration in the TERT locus was frequently observed in a high clonal proportion. Our whole-genome sequencing analysis of HCCs identified the influence of etiological background on somatic mutation patterns and subsequent carcinogenesis, as well as recurrent mutations in chromatin regulators in HCCs. PMID:22634756

Fujimoto, Akihiro; Totoki, Yasushi; Abe, Tetsuo; Boroevich, Keith A; Hosoda, Fumie; Nguyen, Ha Hai; Aoki, Masayuki; Hosono, Naoya; Kubo, Michiaki; Miya, Fuyuki; Arai, Yasuhito; Takahashi, Hiroyuki; Shirakihara, Takuya; Nagasaki, Masao; Shibuya, Tetsuo; Nakano, Kaoru; Watanabe-Makino, Kumiko; Tanaka, Hiroko; Nakamura, Hiromi; Kusuda, Jun; Ojima, Hidenori; Shimada, Kazuaki; Okusaka, Takuji; Ueno, Masaki; Shigekawa, Yoshinobu; Kawakami, Yoshiiku; Arihiro, Koji; Ohdan, Hideki; Gotoh, Kunihito; Ishikawa, Osamu; Ariizumi, Shun-Ichi; Yamamoto, Masakazu; Yamada, Terumasa; Chayama, Kazuaki; Kosuge, Tomoo; Yamaue, Hiroki; Kamatani, Naoyuki; Miyano, Satoru; Nakagama, Hitoshi; Nakamura, Yusuke; Tsunoda, Tatsuhiko; Shibata, Tatsuhiro; Nakagawa, Hidewaki

2012-05-27

19

CREB3L2-PPARg Fusion Mutation Identifies a Thyroid Signaling Pathway Regulated by Intramembrane Proteolysis  

Microsoft Academic Search

The discovery of gene fusion mutations, particularly in leukemia, has consistently identified new cancer pathways and led to molecular diagnostic assays and molecular-targeted chemotherapies for cancer patients. Here, we report our discovery of a novel CREB3L2-PPARg fusion mutation in thyroid carcinoma with t(3;7)(p25;q34), showing that a family of somatic PPARg fusion mutations exist in thyroid cancer. The CREB3L2-PPARg fusion encodes

Lingchun Zeng; Victoria Rehrmann; Seema Deshpande; Maria Tretiakova; Edwin L. Kaplan; Ingo Leibiger; Barbara Leibiger; Ulla Enberg; Catharina Larsson; Todd G. Kroll

20

Yale team identifies successful combination drug therapies for melanoma mutations  

Cancer.gov

Yale Cancer Center researchers have identified several effective combinations of therapies that inhibit melanomas driven by two of the most formidable cancer genes. Some combinations include cholesterol-lowering statin drugs. The study appears in the journal Cancer Discovery. The Yale scientists were seeking to overcome the problems of resistance and partial response to single-drug cancer therapy in patients with melanoma.

21

Alteration of Four Identified K^+ Currents in Drosophila Muscle by Mutations in eag  

Microsoft Academic Search

Voltage-clamp analysis of Drosophila larval muscle revealed that ether a go-go (eag) mutations affected all identified potassium currents, including those specifically eliminated by mutations in the Shaker or slowpoke gene. Together with DNA sequence analysis, the results suggest that the eag locus encodes a subunit common to different potassium channels. Thus, combinatorial assembly of polypeptides from different genes may contribute

Yi Zhong; Chun-Fang Wu

1991-01-01

22

A high-throughput panel for identifying clinically relevant mutation profiles in melanoma.  

PubMed

Success with molecular-based targeted drugs in the treatment of cancer has ignited extensive research efforts within the field of personalized therapeutics. However, successful application of such therapies is dependent on the presence or absence of mutations within the patient's tumor that can confer clinical efficacy or drug resistance. Building on these findings, we developed a high-throughput mutation panel for the identification of frequently occurring and clinically relevant mutations in melanoma. An extensive literature search and interrogation of the Catalogue of Somatic Mutations in Cancer database identified more than 1,000 melanoma mutations. Applying a filtering strategy to focus on mutations amenable to the development of targeted drugs, we initially screened 120 known mutations in 271 samples using the Sequenom MassARRAY system. A total of 252 mutations were detected in 17 genes, the highest frequency occurred in BRAF (n = 154, 57%), NRAS (n = 55, 20%), CDK4 (n = 8, 3%), PTK2B (n = 7, 2.5%), and ERBB4 (n = 5, 2%). Based on this initial discovery screen, a total of 46 assays interrogating 39 mutations in 20 genes were designed to develop a melanoma-specific panel. These assays were distributed in multiplexes over 8 wells using strict assay design parameters optimized for sensitive mutation detection. The final melanoma-specific mutation panel is a cost effective, sensitive, high-throughput approach for identifying mutations of clinical relevance to molecular-based therapeutics for the treatment of melanoma. When used in a clinical research setting, the panel may rapidly and accurately identify potentially effective treatment strategies using novel or existing molecularly targeted drugs. PMID:22383533

Dutton-Regester, Ken; Irwin, Darryl; Hunt, Priscilla; Aoude, Lauren G; Tembe, Varsha; Pupo, Gulietta M; Lanagan, Cathy; Carter, Candace D; O'Connor, Linda; O'Rourke, Michael; Scolyer, Richard A; Mann, Graham J; Schmidt, Christopher W; Herington, Adrian; Hayward, Nicholas K

2012-03-01

23

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.  

PubMed

Chronic lymphocytic leukaemia (CLL), the most frequent leukaemia in adults in Western countries, is a heterogeneous disease with variable clinical presentation and evolution. Two major molecular subtypes can be distinguished, characterized respectively by a high or low number of somatic hypermutations in the variable region of immunoglobulin genes. The molecular changes leading to the pathogenesis of the disease are still poorly understood. Here we performed whole-genome sequencing of four cases of CLL and identified 46 somatic mutations that potentially affect gene function. Further analysis of these mutations in 363 patients with CLL identified four genes that are recurrently mutated: notch 1 (NOTCH1), exportin 1 (XPO1), myeloid differentiation primary response gene 88 (MYD88) and kelch-like 6 (KLHL6). Mutations in MYD88 and KLHL6 are predominant in cases of CLL with mutated immunoglobulin genes, whereas NOTCH1 and XPO1 mutations are mainly detected in patients with unmutated immunoglobulins. The patterns of somatic mutation, supported by functional and clinical analyses, strongly indicate that the recurrent NOTCH1, MYD88 and XPO1 mutations are oncogenic changes that contribute to the clinical evolution of the disease. To our knowledge, this is the first comprehensive analysis of CLL combining whole-genome sequencing with clinical characteristics and clinical outcomes. It highlights the usefulness of this approach for the identification of clinically relevant mutations in cancer. PMID:21642962

Puente, Xose S; Pinyol, Magda; Quesada, Víctor; Conde, Laura; Ordóñez, Gonzalo R; Villamor, Neus; Escaramis, Georgia; Jares, Pedro; Beà, Sílvia; González-Díaz, Marcos; Bassaganyas, Laia; Baumann, Tycho; Juan, Manel; López-Guerra, Mónica; Colomer, Dolors; Tubío, José M C; López, Cristina; Navarro, Alba; Tornador, Cristian; Aymerich, Marta; Rozman, María; Hernández, Jesús M; Puente, Diana A; Freije, José M P; Velasco, Gloria; Gutiérrez-Fernández, Ana; Costa, Dolors; Carrió, Anna; Guijarro, Sara; Enjuanes, Anna; Hernández, Lluís; Yagüe, Jordi; Nicolás, Pilar; Romeo-Casabona, Carlos M; Himmelbauer, Heinz; Castillo, Ester; Dohm, Juliane C; de Sanjosé, Silvia; Piris, Miguel A; de Alava, Enrique; San Miguel, Jesús; Royo, Romina; Gelpí, Josep L; Torrents, David; Orozco, Modesto; Pisano, David G; Valencia, Alfonso; Guigó, Roderic; Bayés, Mónica; Heath, Simon; Gut, Marta; Klatt, Peter; Marshall, John; Raine, Keiran; Stebbings, Lucy A; Futreal, P Andrew; Stratton, Michael R; Campbell, Peter J; Gut, Ivo; López-Guillermo, Armando; Estivill, Xavier; Montserrat, Emili; López-Otín, Carlos; Campo, Elías

2011-06-05

24

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia  

PubMed Central

Chronic lymphocytic leukaemia (CLL), the most frequent leukaemia in adults in Western countries, is a heterogeneous disease with variable clinical presentation and evolution1,2. Two major molecular subtypes can be distinguished, characterized respectively by a high or low number of somatic hypermutations in the variable region of immunoglobulin genes3,4. The molecular changes leading to the pathogenesis of the disease are still poorly understood. Here we performed whole-genome sequencing of four cases of CLL and identified 46 somatic mutations that potentially affect gene function. Further analysis of these mutations in 363 patients with CLL identified four genes that are recurrently mutated: notch 1 (NOTCH1), exportin 1 (XPO1), myeloid differentiation primary response gene 88 (MYD88) and kelch-like 6 (KLHL6). Mutations in MYD88 and KLHL6 are predominant in cases of CLL with mutated immunoglobulin genes, whereas NOTCH1 and XPO1 mutations are mainly detected in patients with unmutated immunoglobulins. The patterns of somatic mutation, supported by functional and clinical analyses, strongly indicate that the recurrent NOTCH1, MYD88 and XPO1 mutations are oncogenic changes that contribute to the clinical evolution of the disease. To our knowledge, this is the first comprehensive analysis of CLL combining whole-genome sequencing with clinical characteristics and clinical outcomes. It highlights the usefulness of this approach for the identification of clinically relevant mutations in cancer.

Puente, Xose S.; Pinyol, Magda; Quesada, Victor; Conde, Laura; Ordonez, Gonzalo R.; Villamor, Neus; Escaramis, Georgia; Jares, Pedro; Bea, Silvia; Gonzalez-Diaz, Marcos; Bassaganyas, Laia; Baumann, Tycho; Juan, Manel; Lopez-Guerra, Monica; Colomer, Dolors; Tubio, Jose M. C.; Lopez, Cristina; Navarro, Alba; Tornador, Cristian; Aymerich, Marta; Rozman, Maria; Hernandez, Jesus M.; Puente, Diana A.; Freije, Jose M. P.; Velasco, Gloria; Gutierrez-Fernandez, Ana; Costa, Dolors; Carrio, Anna; Guijarro, Sara; Enjuanes, Anna; Hernandez, Lluis; Yague, Jordi; Nicolas, Pilar; Romeo-Casabona, Carlos M.; Himmelbauer, Heinz; Castillo, Ester; Dohm, Juliane C.; de Sanjose, Silvia; Piris, Miguel A.; de Alava, Enrique; Miguel, Jesus San; Royo, Romina; Gelpi, Josep L.; Torrents, David; Orozco, Modesto; Pisano, David G.; Valencia, Alfonso; Guigo, Roderic; Bayes, Monica; Heath, Simon; Gut, Marta; Klatt, Peter; Marshall, John; Raine, Keiran; Stebbings, Lucy A.; Futreal, P. Andrew; Stratton, Michael R.; Campbell, Peter J.; Gut, Ivo; Lopez-Guillermo, Armando; Estivill, Xavier; Montserrat, Emili; Lopez-Otin, Carlos; Campo, Elias

2012-01-01

25

Two novel mutations of the MYBPC3 gene identified in Chinese families with hypertrophic cardiomyopathy  

PubMed Central

BACKGROUND: Hypertrophic cardiomyopathy (HCM) is one of the most common genetic cardiovascular disorders. Mutations in the MYBPC3 gene are one of the most frequent genetic causes of HCM. OBJECTIVES: To screen MYBPC3 gene mutations in Chinese patients with HCM, and analyze the correlation between the genotype and the phenotype. METHODS: The 35 exons of the MYBPC3 gene were amplified by polymerase chain reaction in the 11 consecutive unrelated Chinese pedigrees. The sequences of the products were analyzed and the mutation sites were determined. The clinical data of genotype-positive families were collected, and the correlation between genotype and phenotype was analyzed. RESULTS: Two mutations of the MYBPC3 gene were confirmed among 11 pedigrees. A frameshift mutation (Pro459fs) was identified in exon 17 in family H8, and a splice mutation (IVS5+5G?C) was identified in intron 5 in family H3. These two mutations were first identified in Chinese patients with familial HCM and were absent in 110 chromosomes of healthy controls. Seven known polymorphisms were found in the cohort. CONCLUSIONS: Compared with what was reported abroad, the MYBPC3 gene is a common pathogenic gene responsible for HCM in Chinese patients, and the phenotypes of these two mutations in their respective families may have their own clinical characteristics.

Lin, Jia; Zheng, Dong-Dong; Tao, Qin; Yang, Jun-Hua; Jiang, Wen-Ping; Yang, Xiang-Jun; Song, Jian-Ping; Jiang, Ting-Bo; Li, Xun

2010-01-01

26

Exome Sequencing Identifies FUS Mutations as a Cause of Essential Tremor  

PubMed Central

Essential tremor (ET) is a common neurodegenerative disorder that is characterized by a postural or motion tremor. Despite a strong genetic basis, a gene with rare pathogenic mutations that cause ET has not yet been reported. We used exome sequencing to implement a simple approach to control for misdiagnosis of ET, as well as phenocopies involving sporadic and senile ET cases. We studied a large ET-affected family and identified a FUS p.Gln290? mutation as the cause of ET in this family. Further screening of 270 ET cases identified two additional rare missense FUS variants. Functional considerations suggest that the pathogenic effects of ET-specific FUS mutations are different from the effects observed when FUS is mutated in amyotrophic lateral sclerosis cases; we have shown that the ET FUS nonsense mutation is degraded by the nonsense-mediated-decay pathway, whereas amyotrophic lateral sclerosis FUS mutant transcripts are not.

Merner, Nancy D.; Girard, Simon L.; Catoire, Helene; Bourassa, Cynthia V.; Belzil, Veronique V.; Riviere, Jean-Baptiste; Hince, Pascale; Levert, Annie; Dionne-Laporte, Alexandre; Spiegelman, Dan; Noreau, Anne; Diab, Sabrina; Szuto, Anna; Fournier, Helene; Raelson, John; Belouchi, Majid; Panisset, Michel; Cossette, Patrick; Dupre, Nicolas; Bernard, Genevieve; Chouinard, Sylvain; Dion, Patrick A.; Rouleau, Guy A.

2012-01-01

27

Novel mutant-enriched Sequencing Identified High Frequency of PIK3CA Mutations in Pharyngeal Cancer  

PubMed Central

We previously reported four PIK3CA mutations in 38 head and neck cancer samples; three of which were identified in six pharyngeal cancer samples. To determine the mutation frequency of PIK3CA in pharyngeal cancer, we studied 24 additional cases of pharyngeal squamous cell carcinoma in this study. Using both direct genomic DNA sequencing and novel mutant-enriched sequencing methods developed specifically for the three hot-spot mutations (H1047R, E545K and E452K) of PIK3CA, we detected five mutations of PIK3CA in the 24 pharyngeal cancers (20.8%). Three of the five mutations had been missed by the conventional sequencing method and were subsequently detected by novel mutant-enriched sequencing methods. We showed that the mutant-enriched sequencing method for the H1047R hot-spot mutation can identify the mutation in a mixed population of mutant and wild-type DNA sequences at 1:360 ratios. These novel mutant-enriched sequencing methods allow the detection of the PIK3CA hot-spot mutations in clinical specimens which often contain limited tumor tissues (i.e. biopsy specimens). The data further supports that oncogenic PIK3CA may play a critical role in pharyngeal carcinogenesis, and the mutant-enriched sequencing methods for PIK3CA are sensitive and reliable ways to detect PIK3CA mutations in clinical samples. Because PIK3CA and its pathway are potential targets for chemotherapy and radiation therapy, and frequent somatic mutation of PIK3CA has been identified in many human cancer types (e.g. breast cancer, colorectal cancer), the abilities to detect PIK3CA mutations with enhanced sensitivities have great potential impacts on target therapies for many cancer types.

Qiu, Wanglong; Tong, Guo-Xia; Manolidis, Spiros; Close, Lanny G.; Assaad, Adel M.; Su, Gloria H.

2009-01-01

28

Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype.  

PubMed

Among acute myeloid leukemia (AML) patients with a normal karyotype (CN-AML), NPM1 and CEBPA mutations define World Health Organization 2008 provisional entities accounting for approximately 60% of patients, but the remaining 40% are molecularly poorly characterized. Using whole-exome sequencing of one CN-AML patient lacking mutations in NPM1, CEBPA, FLT3-ITD, IDH1, and MLL-PTD, we newly identified a clonal somatic mutation in BCOR (BCL6 corepressor), a gene located on chromosome Xp11.4. Further analyses of 553 AML patients showed that BCOR mutations occurred in 3.8% of unselected CN-AML patients and represented a substantial fraction (17.1%) of CN-AML patients showing the same genotype as the AML index patient subjected to whole-exome sequencing. BCOR somatic mutations were: (1) disruptive events similar to the germline BCOR mutations causing the oculo-facio-cardio-dental genetic syndrome; (2) associated with decreased BCOR mRNA levels, absence of full-length BCOR, and absent or low expression of a truncated BCOR protein; (3) virtually mutually exclusive with NPM1 mutations; and (4) frequently associated with DNMT3A mutations, suggesting cooperativity among these genetic alterations. Finally, BCOR mutations tended to be associated with an inferior outcome in a cohort of 422 CN-AML patients (25.6% vs 56.7% overall survival at 2 years; P = .032). Our results for the first time implicate BCOR in CN-AML pathogenesis. PMID:22012066

Grossmann, Vera; Tiacci, Enrico; Holmes, Antony B; Kohlmann, Alexander; Martelli, Maria Paola; Kern, Wolfgang; Spanhol-Rosseto, Ariele; Klein, Hans-Ulrich; Dugas, Martin; Schindela, Sonja; Trifonov, Vladimir; Schnittger, Susanne; Haferlach, Claudia; Bassan, Renato; Wells, Victoria A; Spinelli, Orietta; Chan, Joseph; Rossi, Roberta; Baldoni, Stefano; De Carolis, Luca; Goetze, Katharina; Serve, Hubert; Peceny, Rudolf; Kreuzer, Karl-Anton; Oruzio, Daniel; Specchia, Giorgina; Di Raimondo, Francesco; Fabbiano, Francesco; Sborgia, Marco; Liso, Arcangelo; Farinelli, Laurent; Rambaldi, Alessandro; Pasqualucci, Laura; Rabadan, Raul; Haferlach, Torsten; Falini, Brunangelo

2011-10-19

29

Triangulation of the human, chimpanzee, and Neanderthal genome sequences identifies potentially compensated mutations.  

PubMed

Triangulation of the human, chimpanzee, and Neanderthal genome sequences with respect to 44,348 disease-causing or disease-associated missense mutations and 1,712 putative regulatory mutations listed in the Human Gene Mutation Database was employed to identify genetic variants that are apparently pathogenic in humans but which may represent a "compensated" wild-type state in at least one of the other two species. Of 122 such "potentially compensated mutations" (PCMs) identified, 88 were deemed "ancestral" on the basis that the reported wild-type Neanderthal nucleotide was identical to that of the chimpanzee. Another 33 PCMs were deemed to be "derived" in that the Neanderthal wild-type nucleotide matched the human but not the chimpanzee wild-type. For the remaining PCM, all three wild-type states were found to differ. Whereas a derived PCM would require compensation only in the chimpanzee, ancestral PCMs are useful as a means to identify sites of possible adaptive differences between modern humans on the one hand, and Neanderthals and chimpanzees on the other. Ancestral PCMs considered to be disease-causing in humans were identified in two Neanderthal genes (DUOX2, MAMLD1). Because the underlying mutations are known to give rise to recessive conditions in human, it is possible that they may also have been of pathological significance in Neanderthals. Hum Mutat 31:1-8, 2010. © 2010 Wiley-Liss, Inc. PMID:21064102

Zhang, Guojie; Pei, Zhang; Krawczak, Michael; Ball, Edward V; Mort, Matthew; Kehrer-Sawatzki, Hildegard; Cooper, David N

2010-12-01

30

Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma.  

PubMed

Synonymous mutations, which do not alter the protein sequence, have been shown to affect protein function [Sauna ZE, Kimchi-Sarfaty C (2011) Nat Rev Genet 12(10):683-691]. However, synonymous mutations are rarely investigated in the cancer genomics field. We used whole-genome and -exome sequencing to identify somatic mutations in 29 melanoma samples. Validation of one synonymous somatic mutation in BCL2L12 in 285 samples identified 12 cases that harbored the recurrent F17F mutation. This mutation led to increased BCL2L12 mRNA and protein levels because of differential targeting of WT and mutant BCL2L12 by hsa-miR-671-5p. Protein made from mutant BCL2L12 transcript bound p53, inhibited UV-induced apoptosis more efficiently than WT BCL2L12, and reduced endogenous p53 target gene transcription. This report shows selection of a recurrent somatic synonymous mutation in cancer. Our data indicate that silent alterations have a role to play in human cancer, emphasizing the importance of their investigation in future cancer genome studies. PMID:23901115

Gartner, Jared J; Parker, Stephen C J; Prickett, Todd D; Dutton-Regester, Ken; Stitzel, Michael L; Lin, Jimmy C; Davis, Sean; Simhadri, Vijaya L; Jha, Sujata; Katagiri, Nobuko; Gotea, Valer; Teer, Jamie K; Wei, Xiaomu; Morken, Mario A; Bhanot, Umesh K; Chen, Guo; Elnitski, Laura L; Davies, Michael A; Gershenwald, Jeffrey E; Carter, Hannah; Karchin, Rachel; Robinson, William; Robinson, Steven; Rosenberg, Steven A; Collins, Francis S; Parmigiani, Giovanni; Komar, Anton A; Kimchi-Sarfaty, Chava; Hayward, Nicholas K; Margulies, Elliott H; Samuels, Yardena

2013-07-30

31

Mutational screening of PARKIN identified a 3' UTR variant (rs62637702) associated with Parkinson's disease.  

PubMed

PRKN mutations have been linked to Parkinson's disease (PD). Most of the mutational screenings have focused on the coding exons. The 3' untranslated region (UTR) could also harbor functionally relevant nucleotide changes. We performed a mutational screening of PRKN in a cohort of early-onset PD patients (n?=?235) from Spain. We found 16 mutations (five new): 16 patients (7 %) carried two mutations and only one mutation was found in 28 (12 %). Patients with two mutations had significantly lower mean age (30?±?9 years) compared to patients with one (40?±?7) or no mutation (42?±?7). We found a total of 15 nucleotide variants (three new) in the 3' UTR region. The frequency of carriers of the rare rs62637702 G allele (*94A/G) was significantly lower among the patients compared to healthy controls (n?=?418) (0.03 vs. 0.004; p?identified functional variant. PMID:23275044

de Mena, Lorena; Samaranch, L Luís; Coto, Eliecer; Cardo, Lucía F; Ribacoba, René; Lorenzo-Betancor, Oswaldo; Pastor, Pau; Wang, Li; Irigoyen, Jaione; Mata, Ignacio F; Díaz, Marta; Moris, Germán; Menéndez, Manuel; Corao, Ana I; Lorenzo, Elena; Alvarez, Victoria

2012-12-30

32

Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancer  

Microsoft Academic Search

The identification of tumor-suppressor genes in solid tumors by classical cancer genetics methods is difficult and slow. We combined nonsense-mediated RNA decay microarrays1 and array-based comparative genomic hybridization2,3 for the genome-wide identification of genes with biallelic inactivation involving nonsense mutations and loss of the wild-type allele. This approach enabled us to identify previously unknown mutations in the receptor tyrosine kinase

Pia Huusko; Damaris Ponciano-Jackson; Maija Wolf; Jeff A Kiefer; David O Azorsa; Sukru Tuzmen; Don Weaver; Christiane Robbins; Tracy Moses; Minna Allinen; Sampsa Hautaniemi; Yidong Chen; Abdel Elkahloun; Mark Basik; G Steven Bova; Lukas Bubendorf; Alessandro Lugli; Guido Sauter; Johanna Schleutker; Hilmi Ozcelik; Sabine Elowe; Tony Pawson; Jeffrey M Trent; John D Carpten; Olli-P Kallioniemi; Spyro Mousses

2004-01-01

33

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations  

PubMed Central

Evidence for the etiology of autism spectrum disorders (ASD) has consistently pointed to a strong genetic component complicated by substantial locus heterogeneity1,2. We sequenced the exomes of 20 sporadic cases of ASD and their parents, reasoning that these families would be enriched for de novo mutations of major effect. We identified 21 de novo mutations, of which 11 were protein-altering. Protein-altering mutations were significantly enriched for changes at highly conserved residues. We identified potentially causative de novo events in 4/20 probands, particularly among more severely affected individuals, in FOXP1, GRIN2B, SCN1A, and LAMC3. In the FOXP1 mutation carrier, we also observed a rare inherited CNTNAP2 mutation and provide functional support for a multihit model for disease risk3. Our results demonstrate that trio-based exome sequencing is a powerful approach for identifying novel candidate genes for ASD and suggest that de novo mutations may contribute substantially to the genetic risk for ASD.

O'Roak, Brian J.; Deriziotis, Pelagia; Lee, Choli; Vives, Laura; Schwartz, Jerrod J.; Girirajan, Santhosh; Karakoc, Emre; MacKenzie, Alexandra P.; Ng, Sarah B.; Baker, Carl; Rieder, Mark J.; Nickerson, Deborah A.; Bernier, Raphael; Fisher, Simon E.; Shendure, Jay; Eichler, Evan E.

2011-01-01

34

New Mutations in Chronic Lymphocytic Leukemia Identified by Target Enrichment and Deep Sequencing  

PubMed Central

Chronic lymphocytic leukemia (CLL) is a heterogeneous disease without a well-defined genetic alteration responsible for the onset of the disease. Several lines of evidence coincide in identifying stimulatory and growth signals delivered by B-cell receptor (BCR), and co-receptors together with NFkB pathway, as being the driving force in B-cell survival in CLL. However, the molecular mechanism responsible for this activation has not been identified. Based on the hypothesis that BCR activation may depend on somatic mutations of the BCR and related pathways we have performed a complete mutational screening of 301 selected genes associated with BCR signaling and related pathways using massive parallel sequencing technology in 10 CLL cases. Four mutated genes in coding regions (KRAS, SMARCA2, NFKBIE and PRKD3) have been confirmed by capillary sequencing. In conclusion, this study identifies new genes mutated in CLL, all of them in cases with progressive disease, and demonstrates that next-generation sequencing technologies applied to selected genes or pathways of interest are powerful tools for identifying novel mutational changes.

Gzlez-Pena, Daniel; Lopez, Mar; Herreros, Beatriz; Menezes, Juliane; Gomez-Lozano, Natalia; Carro, Angel; Grana, Osvaldo; Pisano, David G.; Dominguez, Orlando; Garcia-Marco, Jose A.; Piris, Miguel A.; Sanchez-Beato, Margarita

2012-01-01

35

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer.  

PubMed

Small-cell lung cancer (SCLC) is an aggressive lung tumor subtype with poor prognosis. We sequenced 29 SCLC exomes, 2 genomes and 15 transcriptomes and found an extremely high mutation rate of 7.4±1 protein-changing mutations per million base pairs. Therefore, we conducted integrated analyses of the various data sets to identify pathogenetically relevant mutated genes. In all cases, we found evidence for inactivation of TP53 and RB1 and identified recurrent mutations in the CREBBP, EP300 and MLL genes that encode histone modifiers. Furthermore, we observed mutations in PTEN, SLIT2 and EPHA7, as well as focal amplifications of the FGFR1 tyrosine kinase gene. Finally, we detected many of the alterations found in humans in SCLC tumors from Tp53 and Rb1 double knockout mice. Our study implicates histone modification as a major feature of SCLC, reveals potentially therapeutically tractable genomic alterations and provides a generalizable framework for the identification of biologically relevant genes in the context of high mutational background. PMID:22941188

Peifer, Martin; Fernández-Cuesta, Lynnette; Sos, Martin L; George, Julie; Seidel, Danila; Kasper, Lawryn H; Plenker, Dennis; Leenders, Frauke; Sun, Ruping; Zander, Thomas; Menon, Roopika; Koker, Mirjam; Dahmen, Ilona; Müller, Christian; Di Cerbo, Vincenzo; Schildhaus, Hans-Ulrich; Altmüller, Janine; Baessmann, Ingelore; Becker, Christian; de Wilde, Bram; Vandesompele, Jo; Böhm, Diana; Ansén, Sascha; Gabler, Franziska; Wilkening, Ines; Heynck, Stefanie; Heuckmann, Johannes M; Lu, Xin; Carter, Scott L; Cibulskis, Kristian; Banerji, Shantanu; Getz, Gad; Park, Kwon-Sik; Rauh, Daniel; Grütter, Christian; Fischer, Matthias; Pasqualucci, Laura; Wright, Gavin; Wainer, Zoe; Russell, Prudence; Petersen, Iver; Chen, Yuan; Stoelben, Erich; Ludwig, Corinna; Schnabel, Philipp; Hoffmann, Hans; Muley, Thomas; Brockmann, Michael; Engel-Riedel, Walburga; Muscarella, Lucia A; Fazio, Vito M; Groen, Harry; Timens, Wim; Sietsma, Hannie; Thunnissen, Erik; Smit, Egbert; Heideman, Daniëlle A M; Snijders, Peter J F; Cappuzzo, Federico; Ligorio, Claudia; Damiani, Stefania; Field, John; Solberg, Steinar; Brustugun, Odd Terje; Lund-Iversen, Marius; Sänger, Jörg; Clement, Joachim H; Soltermann, Alex; Moch, Holger; Weder, Walter; Solomon, Benjamin; Soria, Jean-Charles; Validire, Pierre; Besse, Benjamin; Brambilla, Elisabeth; Brambilla, Christian; Lantuejoul, Sylvie; Lorimier, Philippe; Schneider, Peter M; Hallek, Michael; Pao, William; Meyerson, Matthew; Sage, Julien; Shendure, Jay; Schneider, Robert; Büttner, Reinhard; Wolf, Jürgen; Nürnberg, Peter; Perner, Sven; Heukamp, Lukas C; Brindle, Paul K; Haas, Stefan; Thomas, Roman K

2012-09-02

36

New Quantitative Method to Identify NPM1 Mutations in Acute Myeloid Leukaemia.  

PubMed

Somatic mutations in the NPM1 gene, which encodes for nucleophosmin, have been reported to be the most frequent genetic abnormalities found in acute myeloid leukaemia (AML). Their identification and quantification remain crucial for the patients' residual disease monitoring. We investigated a new method that could represent a novel reliable alternative to sequencing for its identification. This method was based on high-resolution melting analysis in order to detect mutated patients and on an allele-specific oligonucleotide real-time quantitative polymerase chain reaction (ASO-RQ-PCR) for the identification and quantification of the transcripts carrying NPM1 mutations (NPM1m). Few patients carrying known NPM1m enabled us to set up a table with the different primers' ?CT values, identifying a profile for each mutation type. We then analysed a series of 337 AML patients' samples for NPM1 mutational status characterization and confirmed the ASO-RQ-PCR results by direct sequencing. We identified some mutations in 86 samples, and the results were fully correlated in 100% of the 36 sequenced samples. We also detected other rare NPM1m in two samples, that we confirmed by direct sequencing. This highly specific method provides a novel quick, useful, and costless tool, easy to use in routine practice. PMID:23691328

Huet, Sarah; Jallades, Laurent; Charlot, Carole; Chabane, Kaddour; Nicolini, Franck E; Michallet, Mauricette; Magaud, Jean-Pierre; Hayette, Sandrine

2013-04-09

37

Whole-genome sequencing identifies recurrent somatic NOTCH2 mutations in splenic marginal zone lymphoma  

PubMed Central

Splenic marginal zone lymphoma (SMZL), the most common primary lymphoma of spleen, is poorly understood at the genetic level. In this study, using whole-genome DNA sequencing (WGS) and confirmation by Sanger sequencing, we observed mutations identified in several genes not previously known to be recurrently altered in SMZL. In particular, we identified recurrent somatic gain-of-function mutations in NOTCH2, a gene encoding a protein required for marginal zone B cell development, in 25 of 99 (?25%) cases of SMZL and in 1 of 19 (?5%) cases of nonsplenic MZLs. These mutations clustered near the C-terminal proline/glutamate/serine/threonine (PEST)-rich domain, resulting in protein truncation or, rarely, were nonsynonymous substitutions affecting the extracellular heterodimerization domain (HD). NOTCH2 mutations were not present in other B cell lymphomas and leukemias, such as chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL; n = 15), mantle cell lymphoma (MCL; n = 15), low-grade follicular lymphoma (FL; n = 44), hairy cell leukemia (HCL; n = 15), and reactive lymphoid hyperplasia (n = 14). NOTCH2 mutations were associated with adverse clinical outcomes (relapse, histological transformation, and/or death) among SMZL patients (P = 0.002). These results suggest that NOTCH2 mutations play a role in the pathogenesis and progression of SMZL and are associated with a poor prognosis.

Kiel, Mark J.; Velusamy, Thirunavukkarasu; Betz, Bryan L.; Zhao, Lili; Weigelin, Helmut G.; Chiang, Mark Y.; Huebner-Chan, David R.; Bailey, Nathanael G.; Yang, David T.; Bhagat, Govind; Miranda, Roberto N.; Bahler, David W.; Medeiros, L. Jeffrey; Lim, Megan S.

2012-01-01

38

Whole-genome sequencing identifies recurrent somatic NOTCH2 mutations in splenic marginal zone lymphoma.  

PubMed

Splenic marginal zone lymphoma (SMZL), the most common primary lymphoma of spleen, is poorly understood at the genetic level. In this study, using whole-genome DNA sequencing (WGS) and confirmation by Sanger sequencing, we observed mutations identified in several genes not previously known to be recurrently altered in SMZL. In particular, we identified recurrent somatic gain-of-function mutations in NOTCH2, a gene encoding a protein required for marginal zone B cell development, in 25 of 99 (?25%) cases of SMZL and in 1 of 19 (?5%) cases of nonsplenic MZLs. These mutations clustered near the C-terminal proline/glutamate/serine/threonine (PEST)-rich domain, resulting in protein truncation or, rarely, were nonsynonymous substitutions affecting the extracellular heterodimerization domain (HD). NOTCH2 mutations were not present in other B cell lymphomas and leukemias, such as chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL; n = 15), mantle cell lymphoma (MCL; n = 15), low-grade follicular lymphoma (FL; n = 44), hairy cell leukemia (HCL; n = 15), and reactive lymphoid hyperplasia (n = 14). NOTCH2 mutations were associated with adverse clinical outcomes (relapse, histological transformation, and/or death) among SMZL patients (P = 0.002). These results suggest that NOTCH2 mutations play a role in the pathogenesis and progression of SMZL and are associated with a poor prognosis. PMID:22891276

Kiel, Mark J; Velusamy, Thirunavukkarasu; Betz, Bryan L; Zhao, Lili; Weigelin, Helmut G; Chiang, Mark Y; Huebner-Chan, David R; Bailey, Nathanael G; Yang, David T; Bhagat, Govind; Miranda, Roberto N; Bahler, David W; Medeiros, L Jeffrey; Lim, Megan S; Elenitoba-Johnson, Kojo S J

2012-08-13

39

Characterization of three XPG-defective patients identifies three missense mutations that impair repair and transcription.  

PubMed

Only 16 XPG-defective patients with 20 different mutations have been described. The current hypothesis is that missense mutations impair repair (xeroderma pigmentosum (XP) symptoms), whereas truncating mutations impair both repair and transcription (XP and Cockayne syndrome (CS) symptoms). We identified three cell lines of XPG-defective patients (XP40GO, XP72MA, and XP165MA). Patients' fibroblasts showed a reduced post-UVC cell survival. The reduced repair capability, assessed by host cell reactivation, could be complemented by XPG cDNA. XPG mRNA expression of XP165MA, XP72MA, and XP40GO was 83%, 97%, and 82.5%, respectively, compared with normal fibroblasts. XP165MA was homozygous for a p.G805R mutation; XP72MA and XP40GO were both compound heterozygous (p.W814S and p.E727X, and p.L778P and p.Q150X, respectively). Allele-specific complementation analysis of these five mutations revealed that p.L778P and p.W814S retained considerable residual repair activity. In line with the severe XP/CS phenotypes of XP72MA and XP165MA, even the missense mutations failed to interact with the transcription factor IIH subunits XPD and to some extent cdk7 in coimmunoprecipitation assays. Immunofluorescence techniques revealed that the mutations destabilized early recruitment of XP proteins to localized photodamage and delayed their redistribution in vivo. Thus, we identified three XPG missense mutations in the I-region of XPG that impaired repair and transcription and resulted in severe XP/CS. PMID:23370536

Schäfer, Annika; Schubert, Steffen; Gratchev, Alexei; Seebode, Christina; Apel, Antje; Laspe, Petra; Hofmann, Lars; Ohlenbusch, Andreas; Mori, Toshio; Kobayashi, Nobuhiko; Schürer, Anke; Schön, Michael P; Emmert, Steffen

2013-01-31

40

Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity.  

PubMed

The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a 5-year survival rate of ~15%, the identification of new therapeutic targets for EAC is greatly important. We analyze the mutation spectra from whole-exome sequencing of 149 EAC tumor-normal pairs, 15 of which have also been subjected to whole-genome sequencing. We identify a mutational signature defined by a high prevalence of A>C transversions at AA dinucleotides. Statistical analysis of exome data identified 26 significantly mutated genes. Of these genes, five (TP53, CDKN2A, SMAD4, ARID1A and PIK3CA) have previously been implicated in EAC. The new significantly mutated genes include chromatin-modifying factors and candidate contributors SPG20, TLR4, ELMO1 and DOCK2. Functional analyses of EAC-derived mutations in ELMO1 identifies increased cellular invasion. Therefore, we suggest the potential activation of the RAC1 pathway as a contributor to EAC tumorigenesis. PMID:23525077

Dulak, Austin M; Stojanov, Petar; Peng, Shouyong; Lawrence, Michael S; Fox, Cameron; Stewart, Chip; Bandla, Santhoshi; Imamura, Yu; Schumacher, Steven E; Shefler, Erica; McKenna, Aaron; Carter, Scott L; Cibulskis, Kristian; Sivachenko, Andrey; Saksena, Gordon; Voet, Douglas; Ramos, Alex H; Auclair, Daniel; Thompson, Kristin; Sougnez, Carrie; Onofrio, Robert C; Guiducci, Candace; Beroukhim, Rameen; Zhou, Zhongren; Lin, Lin; Lin, Jules; Reddy, Rishindra; Chang, Andrew; Landrenau, Rodney; Pennathur, Arjun; Ogino, Shuji; Luketich, James D; Golub, Todd R; Gabriel, Stacey B; Lander, Eric S; Beer, David G; Godfrey, Tony E; Getz, Gad; Bass, Adam J

2013-03-24

41

Exome sequencing identifies mitochondrial alanyl-tRNA synthetase mutations in infantile mitochondrial cardiomyopathy.  

PubMed

Infantile cardiomyopathies are devastating fatal disorders of the neonatal period or the first year of life. Mitochondrial dysfunction is a common cause of this group of diseases, but the underlying gene defects have been characterized in only a minority of cases, because tissue specificity of the manifestation hampers functional cloning and the heterogeneity of causative factors hinders collection of informative family materials. We sequenced the exome of a patient who died at the age of 10 months of hypertrophic mitochondrial cardiomyopathy with combined cardiac respiratory chain complex I and IV deficiency. Rigorous data analysis allowed us to identify a homozygous missense mutation in AARS2, which we showed to encode the mitochondrial alanyl-tRNA synthetase (mtAlaRS). Two siblings from another family, both of whom died perinatally of hypertrophic cardiomyopathy, had the same mutation, compound heterozygous with another missense mutation. Protein structure modeling of mtAlaRS suggested that one of the mutations affected a unique tRNA recognition site in the editing domain, leading to incorrect tRNA aminoacylation, whereas the second mutation severely disturbed the catalytic function, preventing tRNA aminoacylation. We show here that mutations in AARS2 cause perinatal or infantile cardiomyopathy with near-total combined mitochondrial respiratory chain deficiency in the heart. Our results indicate that exome sequencing is a powerful tool for identifying mutations in single patients and allows recognition of the genetic background in single-gene disorders of variable clinical manifestation and tissue-specific disease. Furthermore, we show that mitochondrial disorders extend to prenatal life and are an important cause of early infantile cardiac failure. PMID:21549344

Götz, Alexandra; Tyynismaa, Henna; Euro, Liliya; Ellonen, Pekka; Hyötyläinen, Tuulia; Ojala, Tiina; Hämäläinen, Riikka H; Tommiska, Johanna; Raivio, Taneli; Oresic, Matej; Karikoski, Riitta; Tammela, Outi; Simola, Kalle O J; Paetau, Anders; Tyni, Tiina; Suomalainen, Anu

2011-05-05

42

Exome Sequencing Identifies Mitochondrial Alanyl-tRNA Synthetase Mutations in Infantile Mitochondrial Cardiomyopathy  

PubMed Central

Infantile cardiomyopathies are devastating fatal disorders of the neonatal period or the first year of life. Mitochondrial dysfunction is a common cause of this group of diseases, but the underlying gene defects have been characterized in only a minority of cases, because tissue specificity of the manifestation hampers functional cloning and the heterogeneity of causative factors hinders collection of informative family materials. We sequenced the exome of a patient who died at the age of 10 months of hypertrophic mitochondrial cardiomyopathy with combined cardiac respiratory chain complex I and IV deficiency. Rigorous data analysis allowed us to identify a homozygous missense mutation in AARS2, which we showed to encode the mitochondrial alanyl-tRNA synthetase (mtAlaRS). Two siblings from another family, both of whom died perinatally of hypertrophic cardiomyopathy, had the same mutation, compound heterozygous with another missense mutation. Protein structure modeling of mtAlaRS suggested that one of the mutations affected a unique tRNA recognition site in the editing domain, leading to incorrect tRNA aminoacylation, whereas the second mutation severely disturbed the catalytic function, preventing tRNA aminoacylation. We show here that mutations in AARS2 cause perinatal or infantile cardiomyopathy with near-total combined mitochondrial respiratory chain deficiency in the heart. Our results indicate that exome sequencing is a powerful tool for identifying mutations in single patients and allows recognition of the genetic background in single-gene disorders of variable clinical manifestation and tissue-specific disease. Furthermore, we show that mitochondrial disorders extend to prenatal life and are an important cause of early infantile cardiac failure.

Gotz, Alexandra; Tyynismaa, Henna; Euro, Liliya; Ellonen, Pekka; Hyotylainen, Tuulia; Ojala, Tiina; Hamalainen, Riikka H.; Tommiska, Johanna; Raivio, Taneli; Oresic, Matej; Karikoski, Riitta; Tammela, Outi; Simola, Kalle O.J.; Paetau, Anders; Tyni, Tiina; Suomalainen, Anu

2011-01-01

43

Screening of 38 genes identifies mutations in 62% of families with nonsyndromic deafness in Turkey.  

PubMed

More than 60% of prelingual deafness is genetic in origin, and of these up to 95% are monogenic autosomal recessive traits. Causal mutations have been identified in 1 of 38 different genes in a subset of patients with nonsyndromic autosomal recessive deafness. In this study, we screened 49 unrelated Turkish families with at least three affected children born to consanguineous parents. Probands from all families were negative for mutations in the GJB2 gene, two large deletions in the GJB6 gene, and the 1555A>G substitution in the mitochondrial DNA MTRNR1 gene. Each family was subsequently screened via autozygosity mapping with genomewide single-nucleotide polymorphism arrays. If the phenotype cosegregated with a haplotype flanking one of the 38 genes, mutation analysis of the gene was performed. We identified 22 different autozygous mutations in 11 genes, other than GJB2, in 26 of 49 families, which overall explains deafness in 62% of families. Relative frequencies of genes following GJB2 were MYO15A (9.9%), TMIE (6.6%), TMC1 (6.6%), OTOF (5.0%), CDH23 (3.3%), MYO7A (3.3%), SLC26A4 (1.7%), PCDH15 (1.7%), LRTOMT (1.7%), SERPINB6 (1.7%), and TMPRSS3 (1.7%). Nineteen of 22 mutations are reported for the first time in this study. Unknown rare genes for deafness appear to be present in the remaining 23 families. PMID:21117948

Duman, Duygu; Sirmaci, Asli; Cengiz, F Basak; Ozdag, Hilal; Tekin, Mustafa

2010-11-30

44

A novel UBIAD1 mutation identified in a Chinese family with Schnyder crystalline corneal dystrophy  

PubMed Central

Purpose To identify the molecular defect causing Schnyder crystalline corneal dystrophy (SCCD) in a Chinese family with bilateral corneal abnormalities. Methods The Chinese SCCD family was subjected to a complete ophthalmic examination that included slit-lamp examination and slit-lamp photography to assess and document the crystalline deposits and arcus lipoides. In vivo laser scanning confocal microscopy and Fourier-domain OCT were also performed on both eyes of SCCD patients. Blood samples were taken for subsequent genetic analysis. The two coding exons of the UbiA prenyltransferase domain-containing protein 1 (UBIAD1) gene were screened for mutations by direct sequencing. Results We report on a novel heterozygous mutation of UBIAD1, G98S, in two patients with SCCD. The identified molecular defect cosegregates with the disease and is not found in 50 unaffected individuals. Morphological evaluation on SCCD by in vivo laser scanning confocal microscopy and Fourier-domain OCT highlighted pathological observations at the level of Bowman’s membrane and anterior stroma. Conclusion The newly identified mutation expands the spectrum of mutations in UBIAD1 that may cause pathological corneal cholesterol deposition. Observations by in vivo laser scanning confocal microscopy and Fourier-domain OCT were consistent with the previous histopathologic descriptions of SCCD.

Liu, Chun; Xu, Junmin; Wang, Liya

2009-01-01

45

Functional Analysis of Novel Sonic Hedgehog Gene Mutations Identified in Basal Cell Carcinomas from Xeroderma Pigmentosum Patients  

Microsoft Academic Search

Altered sonic hedgehog (SHH) signaling is crucial in the development of basal cell carcinomas (BCC), the most common human cancer. Mutations in SHH signal transducers, PATCHED and SMOOTHENED, have already been identified, but SHH mutations are extremely rare; only 1 was detected in 74 sporadic BCCs. We present data showing unique SHH mutations in BCCs from repair-deficient, skin cancer-prone xeroderma

Sophie Couve; Marc Le Bret; Elisabeth Traiffort; Sophie Queille; Josee Coulombe; Bakar Bouadjar; Marie Francoise Avril; Martial Ruat; Alain Sarasin; Leela Daya-Grosjean

2004-01-01

46

Functional analysis of BMP4 mutations identified in pediatric CAKUT patients.  

PubMed

Human congenital anomalies of the kidney and urinary tract (CAKUT) represent the major causes of chronic renal failure (CRF) in children. This set of disorders comprises renal agenesis, hypoplasia, dysplastic or double kidneys, and/or malformations of the ureter. It has recently been shown that mutations in several genes, among them BMP4, are associated with hereditary renal developmental diseases. In BMP4, we formerly identified three missense mutations (S91C, T116S, N150K) in five pediatric CAKUT patients. These BMP4 mutations were subsequently studied in a cellular expression system, and here we present functional data demonstrating a lower level of messenger RNA (mRNA) abundance in Bmp4 mutants that indicates a possible negative feedback of the mutants on their own mRNA expression and/or stability. Furthermore, we describe the formation of alternative protein complexes induced by the S91C-BMP4 mutation, which results in perinuclear endoplasmic reticulum (ER) accumulation and enhanced lysosomal degradation of Bmp4. This work further supports the role of mutations in BMP4 for abnormalities of human kidney development. PMID:19685083

Tabatabaeifar, Mansoureh; Schlingmann, Karl-Peter; Litwin, Mieczyslaw; Emre, Sevinc; Bakkaloglu, Aysin; Mehls, Otto; Antignac, Corinne; Schaefer, Franz; Weber, Stefanie

2009-08-14

47

Mutations in multidomain protein MEGF8 identify a Carpenter syndrome subtype associated with defective lateralization.  

PubMed

Carpenter syndrome is an autosomal-recessive multiple-congenital-malformation disorder characterized by multisuture craniosynostosis and polysyndactyly of the hands and feet; many other clinical features occur, and the most frequent include obesity, umbilical hernia, cryptorchidism, and congenital heart disease. Mutations of RAB23, encoding a small GTPase that regulates vesicular transport, are present in the majority of cases. Here, we describe a disorder caused by mutations in multiple epidermal-growth-factor-like-domains 8 (MEGF8), which exhibits substantial clinical overlap with Carpenter syndrome but is frequently associated with abnormal left-right patterning. We describe five affected individuals with similar dysmorphic facies, and three of them had either complete situs inversus, dextrocardia, or transposition of the great arteries; similar cardiac abnormalities were previously identified in a mouse mutant for the orthologous Megf8. The mutant alleles comprise one nonsense, three missense, and two splice-site mutations; we demonstrate in zebrafish that, in contrast to the wild-type protein, the proteins containing all three missense alterations provide only weak rescue of an early gastrulation phenotype induced by Megf8 knockdown. We conclude that mutations in MEGF8 cause a Carpenter syndrome subtype frequently associated with defective left-right patterning, probably through perturbation of signaling by hedgehog and nodal family members. We did not observe any subject with biallelic loss-of function mutations, suggesting that some residual MEGF8 function might be necessary for survival and might influence the phenotypes observed. PMID:23063620

Twigg, Stephen R F; Lloyd, Deborah; Jenkins, Dagan; Elçioglu, Nursel E; Cooper, Christopher D O; Al-Sannaa, Nouriya; Annagür, Ali; Gillessen-Kaesbach, Gabriele; Hüning, Irina; Knight, Samantha J L; Goodship, Judith A; Keavney, Bernard D; Beales, Philip L; Gileadi, Opher; McGowan, Simon J; Wilkie, Andrew O M

2012-10-11

48

Two novel SRY missense mutations reducing DNA binding identified in XY females and their mosaic fathers  

SciTech Connect

Two novel mutations in the sex-determining gene SRY were identified by screening DNA from 30 sex-reversed XY females by using the SSCP assay. Both point mutations lead to an amino acid substitution in the DNA-binding high-mobility-group domain of the SRY protein. The first mutation, changing a serine at position 91 to glycine, was found in a sporadic case. The second mutation, leading to replacement of a highly conserved proline at position 125 with leucine, is shared by three members of the same family, two sisters and a half sister having the same father. The mutant SRY proteins showed reduced DNA-binding ability in a gel-shift assay. Analysis of lymphocyte DNA from the respective fathers revealed that they carry both the wild-type and the mutant version of the SRY gene. The fact that both fathers transmitted the mutant SRY copy to their offspring implies that they are mosaic for the SRY gene in testis as well as in blood, as a result of a mutation during early embryonic development. 30 refs., 5 figs.

Schmitt-Ney, M.; Scherer, G. [Univ. of Freiburg (Germany); Thiele, H.; KaltwaBer, P. [Universitaet Halle-Wittenberg (Italy); Bardoni, B.; Cisternino, M. [Univ. of Pavia (Italy)

1995-04-01

49

Whole exome sequencing reveals uncommon mutations in the recently identified Fanconi anemia gene SLX4/FANCP.  

PubMed

Fanconi anemia (FA) is a rare genetic disorder characterized by congenital malformations, progressive bone marrow failure (BMF), and susceptibility to malignancies. FA is caused by biallelic or hemizygous mutations in one of 15 known FA genes, whose products are involved in the FA/BRCA DNA damage response pathway. Here, we report on a patient with previously unknown mutations of the most recently identified FA gene, SLX4/FANCP. Whole exome sequencing (WES) revealed a nonsense mutation and an unusual splice site mutation resulting in the partial replacement of exonic with intronic bases, thereby removing a nuclear localization signal. Immunoblotting detected no residual SLX4 protein, which was consistent with abrogated interactions with XPF/ERCC1 and MUS81/EME1. This cellular finding did not result in a more severe clinical phenotype than that of previously reported FA-P patients. Our study additionally exemplifies the versatility of WES for the detection of mutations in heterogenic disorders such as FA. PMID:23033263

Schuster, Beatrice; Knies, Kerstin; Stoepker, Chantal; Velleuer, Eunike; Friedl, Richard; Gottwald-Mühlhauser, Birgit; de Winter, Johan P; Schindler, Detlev

2012-10-16

50

Genes critical for muscle development and function in Caenorhabditis elegans identified through lethal mutations  

PubMed Central

By taking advantage of a lethal phenotype characteristic of Caenorhabditis elegans embryos that fail to move, we have identified 13 genes required for muscle assembly and function and discovered a new lethal class of alleles for three previously known muscle-affecting genes. By staining mutant embryos for myosin and actin we have recognized five distinct classes of genes: mutations in four genes disrupt the assembly of thick and thin filaments into the myofilament lattice as well as the polarized location of these components to the sarcolemma. Mutations in another three genes also disrupt thick and thin filament assembly, but allow proper polarization of lattice components based on the myosin heavy chain isoform that we analyzed. Another two classes of genes are defined by mutations with principal effects on thick or thin filament assembly into the lattice, but not both. The final class includes three genes in which mutations cause relatively minor defects in lattice assembly. Failure of certain mutants to stain with antibodies to specific muscle cell antigens suggest that two genes associated with severe disruptions of myofilament lattice assembly may code for components of the basement membrane and the sarcolemma that are concentrated where dense bodies (Z- line analogs) and M-lines attach to the cell membrane. Similar evidence suggests that one of the genes associated with mild effects on lattice assembly may code for tropomyosin. Many of the newly identified genes are likely to play critical roles in muscle development and function.

1994-01-01

51

Newly identified milder phenotype of peroxisome biogenesis disorder caused by mutated PEX3 gene.  

PubMed

We identified the first patient with infantile Refsum disease (IRD), a milder phenotype of peroxisome biogenesis disorder (PBD) caused by a mutated PEX3, and investigated the clinical, molecular and cellular characterization in this patient. The patient presented psychomotor regression, late-onset leukodystrophy, peripheral neuropathy, hearing impairment, a renal cyst, and renal hypertension and survived until the age of 36. Furthermore, fibroblasts from the patient indicated a mosaic pattern of catalase-positive particles (peroxisomes) and numerous peroxisomal membrane structures. Molecular analysis was homozygous for the D347Y mutation and reduced gene expression of PEX3 which encodes a peroxisomal membrane protein, pex3p, involved in peroxisome assembly at the early stage of peroxisomal membrane vesicle formation, therefore, patients with a mutated PEX3 gene have been reported to have only a severe phenotype of Zellweger syndrome and no or less peroxisomal remnant membrane structure. This is not only a newly identified milder PBD caused by a mutated PEX3 gene but also the first report of a Japanese patient with IRD who had not been diagnosed until over 30years of age, which suggests there must be more variant PBD in patients with degenerative neurologic disorder, and to bring them to light is necessary. PMID:23245813

Matsui, Shuji; Funahashi, Masuko; Honda, Ayako; Shimozawa, Nobuyuki

2012-12-14

52

Functional studies of a novel Germline p53 splicing mutation identified in a patient with Li-Fraumeni-Like syndrome.  

PubMed

Most p53 mutations identified in Li-Fraumeni syndrome (LFS) are missense mutations; splicing mutations have rarely been reported. A novel splicing p53 mutation was identified in a patient with Li-Fraumeni-like syndrome (LFL). Usually, p53 missense mutants identified in LFS and cancer cells function as dominant negative mutations interfering with wild-type p53 function. However, the mechanism by which p53 haploinsufficiency causes carcinogenesis is not well characterized. In this study, we describe a novel splicing mutation that results in the loss-of-function of p53. These findings suggest a linkage between the loss-of-function type p53 mutation and a LFL phenotype. © 2012 Wiley Periodicals, Inc. PMID:22495821

Piao, Jinhua; Sakurai, Naoto; Iwamoto, Shotaro; Nishioka, Junji; Nakatani, Kaname; Komada, Yoshihiro; Mizutani, Shuki; Takagi, Masatoshi

2012-04-11

53

Mitochondrial cardiomyopathies: how to identify candidate pathogenic mutations by mitochondrial DNA sequencing, MITOMASTER and phylogeny  

PubMed Central

Pathogenic mitochondrial DNA (mtDNA) mutations leading to mitochondrial dysfunction can cause cardiomyopathy and heart failure. Owing to a high mutation rate, mtDNA defects may occur at any nucleotide in its 16?569?bp sequence. Complete mtDNA sequencing may detect pathogenic mutations, which can be difficult to interpret because of normal ethnic/geographic-associated haplogroup variation. Our goal is to show how to identify candidate mtDNA mutations by sorting out polymorphisms using readily available online tools. The purpose of this approach is to help investigators in prioritizing mtDNA variants for functional analysis to establish pathogenicity. We analyzed complete mtDNA sequences from 29 Italian patients with mitochondrial cardiomyopathy or suspected disease. Using MITOMASTER and PhyloTree, we characterized 593 substitution variants by haplogroup and allele frequencies to identify all novel, non-haplogroup-associated variants. MITOMASTER permitted determination of each variant's location, amino acid change and evolutionary conservation. We found that 98% of variants were common or rare, haplogroup-associated variants, and thus unlikely to be primary cause in 80% of cases. Six variants were novel, non-haplogroup variants and thus possible contributors to disease etiology. Two with the greatest pathogenic potential were heteroplasmic, nonsynonymous variants: m.15132T>C in MT-CYB for a patient with hypertrophic dilated cardiomyopathy and m.6570G>T in MT-CO1 for a patient with myopathy. In summary, we have used our automated information system, MITOMASTER, to make a preliminary distinction between normal mtDNA variation and pathogenic mutations in patient samples; this fast and easy approach allowed us to select the variants for traditional analysis to establish pathogenicity.

Zaragoza, Michael V; Brandon, Martin C; Diegoli, Marta; Arbustini, Eloisa; Wallace, Douglas C

2011-01-01

54

Mitochondrial cardiomyopathies: how to identify candidate pathogenic mutations by mitochondrial DNA sequencing, MITOMASTER and phylogeny.  

PubMed

Pathogenic mitochondrial DNA (mtDNA) mutations leading to mitochondrial dysfunction can cause cardiomyopathy and heart failure. Owing to a high mutation rate, mtDNA defects may occur at any nucleotide in its 16?569?bp sequence. Complete mtDNA sequencing may detect pathogenic mutations, which can be difficult to interpret because of normal ethnic/geographic-associated haplogroup variation. Our goal is to show how to identify candidate mtDNA mutations by sorting out polymorphisms using readily available online tools. The purpose of this approach is to help investigators in prioritizing mtDNA variants for functional analysis to establish pathogenicity. We analyzed complete mtDNA sequences from 29 Italian patients with mitochondrial cardiomyopathy or suspected disease. Using MITOMASTER and PhyloTree, we characterized 593 substitution variants by haplogroup and allele frequencies to identify all novel, non-haplogroup-associated variants. MITOMASTER permitted determination of each variant's location, amino acid change and evolutionary conservation. We found that 98% of variants were common or rare, haplogroup-associated variants, and thus unlikely to be primary cause in 80% of cases. Six variants were novel, non-haplogroup variants and thus possible contributors to disease etiology. Two with the greatest pathogenic potential were heteroplasmic, nonsynonymous variants: m.15132T>C in MT-CYB for a patient with hypertrophic dilated cardiomyopathy and m.6570G>T in MT-CO1 for a patient with myopathy. In summary, we have used our automated information system, MITOMASTER, to make a preliminary distinction between normal mtDNA variation and pathogenic mutations in patient samples; this fast and easy approach allowed us to select the variants for traditional analysis to establish pathogenicity. PMID:20978534

Zaragoza, Michael V; Brandon, Martin C; Diegoli, Marta; Arbustini, Eloisa; Wallace, Douglas C

2010-10-27

55

A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation  

PubMed Central

Transcription factor (TF) regulation is often post-translational. TF modifications such as reversible phosphorylation and missense mutations, which can act independent of TF expression level, are overlooked by differential expression analysis. Using bovine Piedmontese myostatin mutants as proof-of-concept, we propose a new algorithm that correctly identifies the gene containing the causal mutation from microarray data alone. The myostatin mutation releases the brakes on Piedmontese muscle growth by translating a dysfunctional protein. Compared to a less muscular non-mutant breed we find that myostatin is not differentially expressed at any of ten developmental time points. Despite this challenge, the algorithm identifies the myostatin ‘smoking gun’ through a coordinated, simultaneous, weighted integration of three sources of microarray information: transcript abundance, differential expression, and differential wiring. By asking the novel question “which regulator is cumulatively most differentially wired to the abundant most differentially expressed genes?” it yields the correct answer, “myostatin”. Our new approach identifies causal regulatory changes by globally contrasting co-expression network dynamics. The entirely data-driven ‘weighting’ procedure emphasises regulatory movement relative to the phenotypically relevant part of the network. In contrast to other published methods that compare co-expression networks, significance testing is not used to eliminate connections.

Dalrymple, Brian P.

2009-01-01

56

Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis  

PubMed Central

Although ubiquitination plays a critical role in virtually all cellular processes, mechanistic details of ubiquitin (Ub) transfer are still being defined. To identify the molecular determinants within E3 ligases that modulate activity, we scored each member of a library of nearly 100,000 protein variants of the murine ubiquitination factor E4B (Ube4b) U-box domain for auto-ubiquitination activity in the presence of the E2 UbcH5c. This assay identified mutations that enhance activity both in vitro and in cellular p53 degradation assays. The activity-enhancing mutations fall into two distinct mechanistic classes: One increases the U-box:E2-binding affinity, and the other allosterically stimulates the formation of catalytically active conformations of the E2?Ub conjugate. The same mutations enhance E3 activity in the presence of another E2, Ube2w, implying a common allosteric mechanism, and therefore the general applicability of our observations to other E3s. A comparison of the E3 activity with the two different E2s identified an additional variant that exhibits E3:E2 specificity. Our results highlight the general utility of high-throughput mutagenesis in delineating the molecular basis of enzyme activity.

Starita, Lea M.; Pruneda, Jonathan N.; Lo, Russell S.; Fowler, Douglas M.; Kim, Helen J.; Hiatt, Joseph B.; Shendure, Jay; Brzovic, Peter S.; Fields, Stanley; Klevit, Rachel E.

2013-01-01

57

Novel and recurrent EMD mutations in patients with Emery–Dreifuss muscular dystrophy, identify exon 2 as a mutation hot spot  

Microsoft Academic Search

Emery–Dreifuss muscular dystrophy (EDMD) is a neuromuscular disorder exhibiting a cardiomyopathy with cardiac conduction defects. X-linked EDMD arises from mutations in the EMD gene, which encodes for a nuclear membrane protein termed emerin. In this study, we describe novel and recurrent EMD mutations identified in 18 probands and three carriers from a cohort of 255 North American patients referred for

Charlotte A Brown; Juergen Scharner; Kevin Felice; Matthew N Meriggioli; Mark Tarnopolsky; Matthew Bower; Peter S Zammit; Jerry R Mendell; Juliet A Ellis

2011-01-01

58

Mutations in human interferon gamma affecting inclusion body formation identified by a general immunochemical screen.  

PubMed

High level expression of the gene for human interferon-gamma (HuIFN-gamma) in E. coli JM101 cultured at 37 degrees C results in the distribution of over 90 percent of the total accumulated gene product into inclusion bodies (IBs). We have identified mutations throughout the molecule that alter the distribution between the soluble and inclusion body fractions without greatly affecting total expression level. Some mutants retain high biological activity but are localized almost entirely in the soluble fraction. Mutations affecting IB distribution as well as stability to intracellular proteolysis were detected by immunochemical screens and verified by gel assays. Immunochemical screens such as those employed here may allow identification of folding and stability mutants in heterologously expressed proteins when there is no other basis for selection or screening. These results also suggest that one solution to production problems arising from IB formation may be to identify mutations in the target protein that favor expression of soluble protein while retaining biological activity. PMID:1367633

Wetzel, R; Perry, L J; Veilleux, C

1991-08-01

59

Exome Sequencing Identifies Truncating Mutations in Human SERPINF1 in Autosomal-Recessive Osteogenesis Imperfecta  

PubMed Central

Osteogenesis imperfecta (OI) is a heterogeneous genetic disorder characterized by bone fragility and susceptibility to fractures after minimal trauma. After mutations in all known OI genes had been excluded by Sanger sequencing, we applied next-generation sequencing to analyze the exome of a single individual who has a severe form of the disease and whose parents are second cousins. A total of 26,922 variations from the human reference genome sequence were subjected to several filtering steps. In addition, we extracted the genotypes of all dbSNP130-annotated SNPs from the exome sequencing data and used these 299,494 genotypes as markers for the genome-wide identification of homozygous regions. A single homozygous truncating mutation, affecting SERPINF1 on chromosome 17p13.3, that was embedded into a homozygous stretch of 2.99 Mb remained. The mutation was also homozygous in the affected brother of the index patient. Subsequently, we identified homozygosity for two different truncating SERPINF1 mutations in two unrelated patients with OI and parental consanguinity. All four individuals with SERPINF1 mutations have severe OI. Fractures of long bones and severe vertebral compression fractures with resulting deformities were observed as early as the first year of life in these individuals. Collagen analyses with cultured dermal fibroblasts displayed no evidence for impaired collagen folding, posttranslational modification, or secretion. SERPINF1 encodes pigment epithelium-derived factor (PEDF), a secreted glycoprotein of the serpin superfamily. PEDF is a multifunctional protein and one of the strongest inhibitors of angiogenesis currently known in humans. Our data provide genetic evidence for PEDF involvement in human bone homeostasis.

Becker, Jutta; Semler, Oliver; Gilissen, Christian; Li, Yun; Bolz, Hanno Jorn; Giunta, Cecilia; Bergmann, Carsten; Rohrbach, Marianne; Koerber, Friederike; Zimmermann, Katharina; de Vries, Petra; Wirth, Brunhilde; Schoenau, Eckhard; Wollnik, Bernd; Veltman, Joris A.; Hoischen, Alexander; Netzer, Christian

2011-01-01

60

DNA ligase IV mutations identified in patients exhibiting developmental delay and immunodeficiency.  

PubMed

DNA ligase IV functions in DNA nonhomologous end-joining and V(D)J recombination. Four patients with features including immunodeficiency and developmental and growth delay were found to have mutations in the gene encoding DNA ligase IV (LIG4). Their clinical phenotype closely resembles the DNA damage response disorder, Nijmegen breakage syndrome (NBS). Some of the mutations identified in the patients directly disrupt the ligase domain while others impair the interaction between DNA ligase IV and Xrcc-4. Cell lines from the patients show pronounced radiosensitivity. Unlike NBS cell lines, they show normal cell cycle checkpoint responses but impaired DNA double-strand break rejoining. An unexpected V(D)J recombination phenotype is observed involving a small decrease in rejoining frequency coupled with elevated imprecision at signal junctions. PMID:11779494

O'Driscoll, M; Cerosaletti, K M; Girard, P M; Dai, Y; Stumm, M; Kysela, B; Hirsch, B; Gennery, A; Palmer, S E; Seidel, J; Gatti, R A; Varon, R; Oettinger, M A; Neitzel, H; Jeggo, P A; Concannon, P

2001-12-01

61

Zygotic Lethal Mutations with Maternal Effect Phenotypes in Drosophila Melanogaster. II. Loci on the Second and Third Chromosomes Identified by P-Element-Induced Mutations  

PubMed Central

Screens for zygotic lethal mutations that are associated with specific maternal effect lethal phenotypes have only been conducted for the X chromosome. To identify loci on the autosomes, which represent four-fifths of the Drosophila genome, we have used the autosomal ``FLP-DFS'' technique to screen a collection of 496 P element-induced mutations established by the Berkeley Drosophila Genome Project. We have identified 64 new loci whose gene products are required for proper egg formation or normal embryonic development.

Perrimon, N.; Lanjuin, A.; Arnold, C.; Noll, E.

1996-01-01

62

Targeted exome sequencing identified novel USH2A mutations in Usher syndrome families.  

PubMed

Usher syndrome (USH) is a leading cause of deaf-blindness in autosomal recessive trait. Phenotypic and genetic heterogeneities in USH make molecular diagnosis much difficult. This is a pilot study aiming to develop an approach based on next-generation sequencing to determine the genetic defects in patients with USH or allied diseases precisely and effectively. Eight affected patients and twelve unaffected relatives from five unrelated Chinese USH families, including 2 pseudo-dominant ones, were recruited. A total of 144 known genes of inherited retinal diseases were selected for deep exome resequencing. Through systematic data analysis using established bioinformatics pipeline and segregation analysis, a number of genetic variants were released. Eleven mutations, eight of them were novel, in the USH2A gene were identified. Biparental mutations in USH2A were revealed in 2 families with pseudo-dominant inheritance. A proband was found to have triple mutations, two of them were supposed to locate in the same chromosome. In conclusion, this study revealed the genetic defects in the USH2A gene and demonstrated the robustness of targeted exome sequencing to precisely and rapidly determine genetic defects. The methodology provides a reliable strategy for routine gene diagnosis of USH. PMID:23737954

Huang, Xiu-Feng; Xiang, Ping; Chen, Jie; Xing, Dong-Jun; Huang, Na; Min, Qingjie; Gu, Feng; Tong, Yi; Pang, Chi-Pui; Qu, Jia; Jin, Zi-Bing

2013-05-30

63

Exome sequencing identifies rare deleterious mutations in DNA repair genes FANCC and BLM as potential breast cancer susceptibility alleles.  

PubMed

Despite intensive efforts using linkage and candidate gene approaches, the genetic etiology for the majority of families with a multi-generational breast cancer predisposition is unknown. In this study, we used whole-exome sequencing of thirty-three individuals from 15 breast cancer families to identify potential predisposing genes. Our analysis identified families with heterozygous, deleterious mutations in the DNA repair genes FANCC and BLM, which are responsible for the autosomal recessive disorders Fanconi Anemia and Bloom syndrome. In total, screening of all exons in these genes in 438 breast cancer families identified three with truncating mutations in FANCC and two with truncating mutations in BLM. Additional screening of FANCC mutation hotspot exons identified one pathogenic mutation among an additional 957 breast cancer families. Importantly, none of the deleterious mutations were identified among 464 healthy controls and are not reported in the 1,000 Genomes data. Given the rarity of Fanconi Anemia and Bloom syndrome disorders among Caucasian populations, the finding of multiple deleterious mutations in these critical DNA repair genes among high-risk breast cancer families is intriguing and suggestive of a predisposing role. Our data demonstrate the utility of intra-family exome-sequencing approaches to uncover cancer predisposition genes, but highlight the major challenge of definitively validating candidates where the incidence of sporadic disease is high, germline mutations are not fully penetrant, and individual predisposition genes may only account for a tiny proportion of breast cancer families. PMID:23028338

Thompson, Ella R; Doyle, Maria A; Ryland, Georgina L; Rowley, Simone M; Choong, David Y H; Tothill, Richard W; Thorne, Heather; Barnes, Daniel R; Li, Jason; Ellul, Jason; Philip, Gayle K; Antill, Yoland C; James, Paul A; Trainer, Alison H; Mitchell, Gillian; Campbell, Ian G

2012-09-27

64

Exome Sequencing Identifies Rare Deleterious Mutations in DNA Repair Genes FANCC and BLM as Potential Breast Cancer Susceptibility Alleles  

PubMed Central

Despite intensive efforts using linkage and candidate gene approaches, the genetic etiology for the majority of families with a multi-generational breast cancer predisposition is unknown. In this study, we used whole-exome sequencing of thirty-three individuals from 15 breast cancer families to identify potential predisposing genes. Our analysis identified families with heterozygous, deleterious mutations in the DNA repair genes FANCC and BLM, which are responsible for the autosomal recessive disorders Fanconi Anemia and Bloom syndrome. In total, screening of all exons in these genes in 438 breast cancer families identified three with truncating mutations in FANCC and two with truncating mutations in BLM. Additional screening of FANCC mutation hotspot exons identified one pathogenic mutation among an additional 957 breast cancer families. Importantly, none of the deleterious mutations were identified among 464 healthy controls and are not reported in the 1,000 Genomes data. Given the rarity of Fanconi Anemia and Bloom syndrome disorders among Caucasian populations, the finding of multiple deleterious mutations in these critical DNA repair genes among high-risk breast cancer families is intriguing and suggestive of a predisposing role. Our data demonstrate the utility of intra-family exome-sequencing approaches to uncover cancer predisposition genes, but highlight the major challenge of definitively validating candidates where the incidence of sporadic disease is high, germline mutations are not fully penetrant, and individual predisposition genes may only account for a tiny proportion of breast cancer families.

Thompson, Ella R.; Doyle, Maria A.; Ryland, Georgina L.; Rowley, Simone M.; Choong, David Y. H.; Tothill, Richard W.; Thorne, Heather; Barnes, Daniel R.; Li, Jason; Ellul, Jason; Philip, Gayle K.; Antill, Yoland C.; James, Paul A.; Trainer, Alison H.; Mitchell, Gillian; Campbell, Ian G.

2012-01-01

65

DNA Methylome of Familial Breast Cancer Identifies Distinct Profiles Defined by Mutation Status  

PubMed Central

It is now understood that epigenetic alterations occur frequently in sporadic breast carcinogenesis, but little is known about the epigenetic alterations associated with familial breast tumors. We performed genome-wide DNA-methylation profiling on familial breast cancers (n = 33) to identify patterns of methylation specific to the different mutation groups (BRCA1, BRCA2, and BRCAx) or intrinsic subtypes of breast cancer (basal, luminal A, luminal B, HER2-amplified, and normal-like). We used methylated DNA immunoprecipitation (MeDIP) on Affymetrix promoter chips to interrogate methylation profiles across 25,500 distinct transcripts. Using a support vector machine classification algorithm, we demonstrated that genome-wide methylation profiles predicted tumor mutation status with estimated error rates of 19% (BRCA1), 31% (BRCA2), and 36% (BRCAx) but did not accurately predict the intrinsic subtypes defined by gene expression. Furthermore, using unsupervised hierarchical clustering, we identified a distinct subgroup of BRCAx tumors defined by methylation profiles. We validated these findings in the 33 tumors in the test set, as well as in an independent validation set of 47 formalin-fixed, paraffin-embedded familial breast tumors, by pyrosequencing and Epityper. Finally, gene-expression profiling and SNP CGH array previously performed on the same samples allowed full integration of methylation, gene-expression, and copy-number data sets, revealing frequent hypermethylation of genes that also displayed loss of heterozygosity, as well as of genes that show copy-number gains, providing a potential mechanism for expression dosage compensation. Together, these data show that methylation profiles for familial breast cancers are defined by the mutation status and are distinct from the intrinsic subtypes.

Flanagan, James M.; Cocciardi, Sibylle; Waddell, Nic; Johnstone, Cameron N.; Marsh, Anna; Henderson, Stephen; Simpson, Peter; da Silva, Leonard; Khanna, Kumkum; Lakhani, Sunil; Boshoff, Chris; Chenevix-Trench, Georgia

2010-01-01

66

Sequencing ASMT Identifies Rare Mutations in Chinese Han Patients with Autism  

PubMed Central

Melatonin is involved in the regulation of circadian and seasonal rhythms and immune function. Prior research reported low melatonin levels in autism spectrum disorders (ASD). ASMT located in pseudo-autosomal region 1 encodes the last enzyme of the melatonin biosynthesis pathway. A previous study reported an association between ASD and single nucleotide polymorphisms (SNPs) rs4446909 and rs5989681 located in the promoter of ASMT. Furthermore, rare deleterious mutations were identified in a subset of patients. To investigate the association between ASMT and autism, we sequenced all ASMT exons and its neighboring region in 398 Chinese Han individuals with autism and 437 healthy controls. Although our study did not detect significant differences of genotypic distribution and allele frequencies of the common SNPs in ASMT between patients with autism and healthy controls, we identified new rare coding mutations of ASMT. Among these rare variants, 4 were exclusively detected in patients with autism including a stop mutation (p.R115W, p.V166I, p.V179G, and p.W257X). These four coding variants were observed in 6 of 398 (1.51%) patients with autism and none in 437 controls (Chi-Square test, Continuity Correction p?=?0.032, two-sided). Functional prediction of impact of amino acid showed that p.R115W might affect protein function. These results indicate that ASMT might be a susceptibility gene for autism. Further studies in larger samples are needed to better understand the degree of variation in this gene as well as to understand the biochemical and clinical impacts of ASMT/melatonin deficiency.

Wang, Lifang; Li, Jun; Ruan, Yanyan; Lu, Tianlan; Liu, Chenxing; Jia, Meixiang; Yue, Weihua; Liu, Jing; Bourgeron, Thomas; Zhang, Dai

2013-01-01

67

A novel splice site mutation of the MEN1 gene identified in a patient with primary hyperparathyroidism.  

PubMed

Heterozygous germline mutation of the tumor suppressor gene MEN1 is responsible for multiple endocrine neoplasia type 1 (MEN1), a familial cancer syndrome characterized by pituitary, parathyroid and enteropancreatic tumors. Various mutations have been identified throughout the entire gene region in patients with MEN1 and its incomplete forms often manifested as familial isolated hyperparathyroidism and apparently sporadic parathyroid tumor. Mutation analysis of the MEN1 gene is a powerful tool for the early diagnosis of MEN1; however, the clinical significance of the identified mutations is not always obvious. In this study, a previously unreported missense MEN1 mutation, c.824G>T was identified in a patient with primary hyperparathyroidism and evaluated for its pathogenicity. This mutation was predicted to generate a putative missense menin protein, R275M. A stability test of the menin protein demonstrated that the stability of R275M mutant was reduced only slightly as compared with wild type menin, and therefore could not preclude the possibility that it was a rare benign polymorphism. However, further analysis of leukocyte mRNA and minigene experiments indicated that the mutant c.824G>T allele gives rise to abnormally spliced menin mRNA, and thereby confirmed that c.824G>T mutation is causative for MEN1. Thus, leukocyte mRNA analysis has been demonstrated useful to identify a splicing mutation of the MEN1 gene. PMID:22447146

Nagamura, Yuko; Yamazaki, Masanori; Shimazu, Satoko; Sano, Kenji; Tsukada, Toshihiko; Sakurai, Akihiro

2012-03-23

68

Novel MEK1 Mutation Identified by Mutational Analysis of Epidermal Growth Factor Receptor Signaling Pathway Genes in Lung Adenocarcinoma  

Microsoft Academic Search

Genetic lesions affecting a number of kinases and other elements within the epidermal growth factor receptor (EGFR) signaling pathway have been implicated in the pathogenesis of human non-small-cell lung cancer (NSCLC). We performed mutational profiling of a large cohort of lung adenocarcino- mas to uncover other potential somatic mutations in genes of this pathway that could contribute to lung tumorigenesis.

Dhananjay Chitale; Ben Golas; Michael D. McLellan; Yumi Kasai; Elaine R. Mardis; Richard K. Wilson; David Solit; Ross Levine; Kathrin Michel; Roman K. Thomas; Valerie W. Rusch; Marc Ladanyi; William Pao

69

NOTCH1 mutations identify a genetic subgroup of chronic lymphocytic leukemia patients with high risk of transformation and poor outcome.  

PubMed

NOTCH1 has been found recurrently mutated in a subset of patients with chronic lymphocytic leukemia (CLL). To analyze biological features and clinical impact of NOTCH1 mutations in CLL, we sequenced this gene in 565 patients. NOTCH1 mutations, found in 63 patients (11%), were associated with unmutated IGHV, high expression of CD38 and ZAP-70, trisomy 12, advanced stage and elevated lactate dehydrogenase. Sequential analysis in 200 patients demonstrated acquisition of mutation in one case (0.5%) and disappearance after treatment in two. Binet A and B patients with NOTCH1-mutated had a shorter time to treatment. NOTCH1-mutated patients were more frequently refractory to therapy and showed shorter progression-free and overall survival after complete remission. Overall survival was shorter in NOTCH1-mutated patients, although not independently from IGHV. NOTCH1 mutation increased the risk of transformation to diffuse large B-cell lymphoma independently from IGHV, with this being validated in resampling tests of replicability. In summary, NOTCH1 mutational status, that was rarely acquired during the course of the disease, identify a genetic subgroup with high risk of transformation and poor outcome. This recently identified genetic subgroup of CLL patients deserves prospective studies to define their best management. PMID:23295735

Villamor, N; Conde, L; Martínez-Trillos, A; Cazorla, M; Navarro, A; Beà, S; López, C; Colomer, D; Pinyol, M; Aymerich, M; Rozman, M; Abrisqueta, P; Baumann, T; Delgado, J; Giné, E; González-Díaz, M; Hernández, J M; Colado, E; Payer, A R; Rayon, C; Navarro, B; José Terol, M; Bosch, F; Quesada, V; Puente, X S; López-Otín, C; Jares, P; Pereira, A; Campo, E; López-Guillermo, A

2012-12-06

70

Three novel mutations in the CFTR gene identified in Galician patients.  

PubMed

We report three novel CFTR missense mutations detected in Spanish patients from Galicia (North West of Spain). In the first case, a patient homozygous for a novel S1045Y mutation died due to pulmonary problems. In the other two cases, both heterozygous for novel mutations combined with the F508del mutation, clinical symptoms were different depending on the mutation, detected as M595I and A107V. PMID:18676185

Rana-Díez, P; Colón, C; Alonso-Fernández, J R; Solar, A; Barros-Tizón, J C; Barros-Casas, D; Sirvent, J; Carracedo, A; Barros, F

2008-08-03

71

Three novel mutations in the CFTR gene identified in Galician patients  

Microsoft Academic Search

We report three novel CFTR missense mutations detected in Spanish patients from Galicia (North West of Spain). In the first case, a patient homozygous for a novel S1045Y mutation died due to pulmonary problems. In the other two cases, both heterozygous for novel mutations combined with the F508del mutation, clinical symptoms were different depending on the mutation, detected as M595I

P. Rana-Díez; C. Colón; J. R. Alonso-Fernández; A. Solar; J. C. Barros-Tizón; D. Barros-Casas; J. Sirvent; A. Carracedo; F. Barros

2008-01-01

72

Functional analysis of human mismatch repair gene mutations identifies weak alleles and polymorphisms capable of polygenic interactions  

PubMed Central

Many of the mutations reported as potentially causing Lynch syndrome are missense mutations in human mismatch repair (MMR) genes. Here, we used a Saccharomyces cerevisiae-based system to study polymorphisms and suspected missense mutations in human MMR genes by modeling them at the appropriate S. cerevisiae chromosomal locus and determining their effect on mutation rates. We identified a number of weak alleles of MMR genes and MMR gene polymorphisms that are capable of interacting with other weak alleles of MMR genes to produce strong polygenic MMR defects. We also identified a number of alleles of MSH2 that act as if they inactivate the Msh2-Msh3 mispair recognition complex thus causing weak MMR defects that interact with an msh6? mutation to result in complete MMR defects. These results indicate that weak MMR gene alleles capable of polygenic interactions with other MMR gene alleles may be relatively common.

Martinez, Sandra L.; Kolodner, Richard D.

2010-01-01

73

Cytotoxic T-lymphocyte escape mutations identified by HLA association favor those which escape and revert rapidly.  

PubMed

Identifying human immunodeficiency virus (HIV) immune escape mutations has implications for understanding the impact of host immunity on pathogen evolution and guiding the choice of vaccine antigens. One means of identifying cytotoxic-T-lymphocyte (CTL) escape mutations is to search for statistical associations between mutations and host human leukocyte antigen (HLA) class I alleles at the population level. The impact of evolutionary rates on the strength of such associations is not well defined. Here, we address this topic using a mathematical model of within-host evolution and between-host transmission of CTL escape mutants that predicts the prevalence of escape mutants at the population level. We ask how the rates at which an escape mutation emerges in a host who bears the restricting HLA and reverts when transmitted to a host who does not bear the HLA affect the strength of an association. We consider the impact of these factors when using a standard statistical method to test for an association and when using an adaptation of that method that corrects for phylogenetic relationships. We show that with both methods, the average sample size required to identify an escape mutation is smaller if the mutation escapes and reverts quickly. Thus, escape mutations identified as HLA associated systematically favor those that escape and revert rapidly. We also present expressions that can be used to infer escape and reversion rates from cross-sectional escape prevalence data. PMID:22674992

Fryer, Helen R; Frater, John; Duda, Anna; Palmer, Duncan; Phillips, Rodney E; McLean, Angela R

2012-06-06

74

Whole-exome sequencing identifies mutated c12orf57 in recessive corpus callosum hypoplasia.  

PubMed

The corpus callosum is the principal cerebral commissure connecting the right and left hemispheres. The development of the corpus callosum is under tight genetic control, as demonstrated by abnormalities in its development in more than 1,000 genetic syndromes. We recruited more than 25 families in which members affected with corpus callosum hypoplasia (CCH) lacked syndromic features and had consanguineous parents, suggesting recessive causes. Exome sequence analysis identified C12orf57 mutations at the initiator methionine codon in four different families. C12orf57 is ubiquitously expressed and encodes a poorly annotated 126 amino acid protein of unknown function. This protein is without significant paralogs but has been tightly conserved across evolution. Our data suggest that this conserved gene is required for development of the human corpus callosum. PMID:23453666

Akizu, Naiara; Shembesh, Nuri M; Ben-Omran, Tawfeg; Bastaki, Laila; Al-Tawari, Asma; Zaki, Maha S; Koul, Roshan; Spencer, Emily; Rosti, Rasim Ozgur; Scott, Eric; Nickerson, Elizabeth; Gabriel, Stacey; da Gente, Gilberto; Li, Jiang; Deardorff, Matthew A; Conlin, Laura K; Horton, Margaret A; Zackai, Elaine H; Sherr, Elliott H; Gleeson, Joseph G

2013-02-28

75

Whole-Exome Sequencing Identifies Mutated C12orf57 in Recessive Corpus Callosum Hypoplasia  

PubMed Central

The corpus callosum is the principal cerebral commissure connecting the right and left hemispheres. The development of the corpus callosum is under tight genetic control, as demonstrated by abnormalities in its development in more than 1,000 genetic syndromes. We recruited more than 25 families in which members affected with corpus callosum hypoplasia (CCH) lacked syndromic features and had consanguineous parents, suggesting recessive causes. Exome sequence analysis identified C12orf57 mutations at the initiator methionine codon in four different families. C12orf57 is ubiquitously expressed and encodes a poorly annotated 126 amino acid protein of unknown function. This protein is without significant paralogs but has been tightly conserved across evolution. Our data suggest that this conserved gene is required for development of the human corpus callosum.

Akizu, Naiara; Shembesh, Nuri M.; Ben-Omran, Tawfeg; Bastaki, Laila; Al-Tawari, Asma; Zaki, Maha S.; Koul, Roshan; Spencer, Emily; Rosti, Rasim Ozgur; Scott, Eric; Nickerson, Elizabeth; Gabriel, Stacey; da Gente, Gilberto; Li, Jiang; Deardorff, Matthew A.; Conlin, Laura K.; Horton, Margaret A.; Zackai, Elaine H.; Sherr, Elliott H.; Gleeson, Joseph G.

2013-01-01

76

A computational-experimental approach identifies mutations that enhance surface expression of an oseltamivir-resistant influenza neuraminidase.  

PubMed

The His274?Tyr (H274Y) oseltamivir (Tamiflu) resistance mutation causes a substantial decrease in the total levels of surface-expressed neuraminidase protein and activity in early isolates of human seasonal H1N1 influenza, and in the swine-origin pandemic H1N1. In seasonal H1N1, H274Y only became widespread after the occurrence of secondary mutations that counteracted this decrease. H274Y is currently rare in pandemic H1N1, and it remains unclear whether secondary mutations exist that might similarly counteract the decreased neuraminidase surface expression associated with this resistance mutation in pandemic H1N1. Here we investigate the possibility of predicting such secondary mutations. We first test the ability of several computational approaches to retrospectively identify the secondary mutations that enhanced levels of surface-expressed neuraminidase protein and activity in seasonal H1N1 shortly before the emergence of oseltamivir resistance. We then use the most successful computational approach to predict a set of candidate secondary mutations to the pandemic H1N1 neuraminidase. We experimentally screen these mutations, and find that several of them do indeed partially counteract the decrease in neuraminidase surface expression caused by H274Y. Two of the secondary mutations together restore surface-expressed neuraminidase activity to wildtype levels, and also eliminate the very slight decrease in viral growth in tissue-culture caused by H274Y. Our work therefore demonstrates a combined computational-experimental approach for identifying mutations that enhance neuraminidase surface expression, and describes several specific mutations with the potential to be of relevance to the spread of oseltamivir resistance in pandemic H1N1. PMID:21799795

Bloom, Jesse D; Nayak, Jagannath S; Baltimore, David

2011-07-20

77

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells.  

PubMed

Substantial regressions of metastatic lesions have been observed in up to 70% of patients with melanoma who received adoptively transferred autologous tumor-infiltrating lymphocytes (TILs) in phase 2 clinical trials. In addition, 40% of patients treated in a recent trial experienced complete regressions of all measurable lesions for at least 5 years following TIL treatment. To evaluate the potential association between the ability of TILs to mediate durable regressions and their ability to recognize potent antigens that presumably include mutated gene products, we developed a new screening approach involving mining whole-exome sequence data to identify mutated proteins expressed in patient tumors. We then synthesized and evaluated candidate mutated T cell epitopes that were identified using a major histocompatibility complex-binding algorithm for recognition by TILs. Using this approach, we identified mutated antigens expressed on autologous tumor cells that were recognized by three bulk TIL lines from three individuals with melanoma that were associated with objective tumor regressions following adoptive transfer. This simplified approach for identifying mutated antigens recognized by T cells avoids the need to generate and laboriously screen cDNA libraries from tumors and may represent a generally applicable method for identifying mutated antigens expressed in a variety of tumor types. PMID:23644516

Robbins, Paul F; Lu, Yong-Chen; El-Gamil, Mona; Li, Yong F; Gross, Colin; Gartner, Jared; Lin, Jimmy C; Teer, Jamie K; Cliften, Paul; Tycksen, Eric; Samuels, Yardena; Rosenberg, Steven A

2013-05-05

78

Functional characterization and pharmacological rescue of melanocortin-4 receptor mutations identified from obese patients.  

PubMed

As the most common monogenic form of human obesity, about 130 naturally occurring melanocortin-4 receptor (MC4R) gene mutations have been identified. In this study, we reported detailed functional characterization of 10 novel human MC4R (hMC4R) mutants including R7C, C84R, S127L, S136F, W174C, A219V, P230L, F261S, I317V and L325F. Flow cytometry experiments showed that six mutants, including R7C, C84R, S127L, W174C, P230L and F261S, have decreased cell surface expression. The other four mutants are expressed at similar levels as the wild-type hMC4R. Binding assays showed that the mutants have similar binding affinities for the agonist and endogenous antagonist agouti-related protein. Signalling assays showed that S136F is defective in signalling. Multiple mutagenesis showed that S136 of hMC4R is required for the normal function of the receptor. To identify potential therapeutic approaches for patients with intracellularly retained MC4R mutants, we tested the effect of an MC4R inverse agonist, ML00253764, on C84R and W174C. We showed that ML00253764 could function as a pharmacological chaperone rescuing the mutant MC4Rs to the cell surface. The rescued mutants are functional with increased cAMP production in response to agonist stimulation. In conclusion, of 10 mutants we studied, 6 had decreased cell surface expression. Pharmacological chaperone is a potential approach for treating obesity caused by MC4R mutations that result in intracellular retention. PMID:19298524

Fan, Zhen-Chuan; Tao, Ya-Xiong

2009-02-27

79

Mapping and exome sequencing identifies a mutation in the IARS gene as the cause of hereditary perinatal weak calf syndrome.  

PubMed

We identified an IARS (isoleucyl-tRNA synthetase) c.235G>C (p.Val79Leu) substitution as the causative mutation for neonatal weakness with intrauterine growth retardation (perinatal weak calf syndrome). In Japanese Black cattle, the syndrome was frequently found in calves sired by Bull A. Hence, we employed homozygosity mapping and linkage analysis. In order to identify the perinatal weak calf syndrome locus in a 4.04-Mb region of BTA 8, we analysed a paternal half-sibling family with a BovineSNP50 BeadChip and microsatellites. In this critical region, we performed exome sequencing to identify a causative mutation. Three variants were detected as possible candidates for causative mutations that were predicted to disrupt the protein function, including a G>C (p.Val79Leu) mutation in IARS c.235. The IARS c.235G>C mutation was not a homozygous risk allele in the 36 healthy offspring of Bull A. Moreover, the IARS Val79 residue and its flanking regions were evolutionarily and highly conserved. The IARS mutant (Leu79) had decreased aminoacylation activity. Additionally, the homozygous mutation was not found in any of 1526 healthy cattle. Therefore, we concluded that the IARS c.235G>C mutation was the cause of hereditary perinatal weak calf syndrome. PMID:23700453

Hirano, Takashi; Kobayashi, Naohiko; Matsuhashi, Tamako; Watanabe, Daisaku; Watanabe, Toshio; Takasuga, Akiko; Sugimoto, Mayumi; Sugimoto, Yoshikazu

2013-05-21

80

Exome Sequencing and Functional Analysis Identifies a Novel Mutation in EXT1 Gene That Causes Multiple Osteochondromas  

PubMed Central

Multiple osteochondromas (MO) is an inherited skeletal disorder, and the molecular mechanism of MO remains elusive. Exome sequencing has high chromosomal coverage and accuracy, and has recently been successfully used to identify pathogenic gene mutations. In this study, exome sequencing followed by Sanger sequencing validation was first used to screen gene mutations in two representative MO patients from a Chinese family. After filtering the data from the 1000 Genome Project and the dbSNP database (build 132), the detected candidate gene mutations were further validated via Sanger sequencing of four other members of the same MO family and 200 unrelated healthy subjects. Immunohistochemisty and multiple sequence alignment were performed to evaluate the importance of the identified causal mutation. A novel frameshift mutation, c.1457insG at codon 486 of exon 6 of EXT1 gene, was identified, which truncated the glycosyltransferase domain of EXT1 gene. Multiple sequence alignment showed that codon 486 of EXT1 gene was highly conserved across various vertebrates. Immunohistochemisty demonstrated that the chondrocytes with functional EXT1 in MO were less than those in extragenetic solitary chondromas. The novel c.1457insG deleterious mutation of EXT1 gene reported in this study expands the causal mutation spectrum of MO, and may be helpful for prenatal genetic screening and early diagnosis of MO.

Guo, Xiong; Zhang, Yingang; Wen, Yan; Li, Qiang; Zhang, Zengtie; Ma, Weijuan; Dai, Lanlan; Liu, Xuanzhu; Yang, Ling; Wang, Jun

2013-01-01

81

Exome sequencing and functional analysis identifies a novel mutation in EXT1 gene that causes multiple osteochondromas.  

PubMed

Multiple osteochondromas (MO) is an inherited skeletal disorder, and the molecular mechanism of MO remains elusive. Exome sequencing has high chromosomal coverage and accuracy, and has recently been successfully used to identify pathogenic gene mutations. In this study, exome sequencing followed by Sanger sequencing validation was first used to screen gene mutations in two representative MO patients from a Chinese family. After filtering the data from the 1000 Genome Project and the dbSNP database (build 132), the detected candidate gene mutations were further validated via Sanger sequencing of four other members of the same MO family and 200 unrelated healthy subjects. Immunohistochemisty and multiple sequence alignment were performed to evaluate the importance of the identified causal mutation. A novel frameshift mutation, c.1457insG at codon 486 of exon 6 of EXT1 gene, was identified, which truncated the glycosyltransferase domain of EXT1 gene. Multiple sequence alignment showed that codon 486 of EXT1 gene was highly conserved across various vertebrates. Immunohistochemisty demonstrated that the chondrocytes with functional EXT1 in MO were less than those in extragenetic solitary chondromas. The novel c.1457insG deleterious mutation of EXT1 gene reported in this study expands the causal mutation spectrum of MO, and may be helpful for prenatal genetic screening and early diagnosis of MO. PMID:24009674

Zhang, Feng; Liang, Jinlong; Guo, Xiong; Zhang, Yingang; Wen, Yan; Li, Qiang; Zhang, Zengtie; Ma, Weijuan; Dai, Lanlan; Liu, Xuanzhu; Yang, Ling; Wang, Jun

2013-08-29

82

Wilson disease: Identifi cation of two novel mutations and clinical correlation in Eastern Chinese patients  

Microsoft Academic Search

AIM: To study mutations in the P-type ATPase (ATP7B) gene responsible for Wilson disease (WD) in the Eastern Chinese population, and the possible correlation of specifi c mutations with clinical characteristics. METHODS: Mutations of the ATP7B gene were sought by means of direct sequencing in 50 Eastern Chinese WD patients of Han ethnic origin. RESULTS: Two novel mutations, Asp96Gly and

Sheng Ye; Liang Gong; Quan-Xiang Shui; Lin-Fu Zhou

2007-01-01

83

Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2  

PubMed Central

We assessed somatic alleles of six receptor tyrosine kinase genes mutated in lung adenocarcinoma for oncogenic activity. Five of these genes failed to score in transformation assays; however, novel recurring extracellular domain mutations of the receptor tyrosine kinase gene ERBB2 were potently oncogenic. These ERBB2 extracellular domain mutants were activated by two distinct mechanisms, characterized by elevated C-terminal tail phosphorylation or by covalent dimerization mediated by intermolecular disulfide bond formation. These distinct mechanisms of receptor activation converged upon tyrosine phosphorylation of cellular proteins, impacting cell motility. Survival of Ba/F3 cells transformed to IL-3 independence by the ERBB2 extracellular domain mutants was abrogated by treatment with small-molecule inhibitors of ERBB2, raising the possibility that patients harboring such mutations could benefit from ERBB2-directed therapy.

Greulich, Heidi; Kaplan, Bethany; Mertins, Philipp; Chen, Tzu-Hsiu; Tanaka, Kumiko E.; Yun, Cai-Hong; Zhang, Xiaohong; Lee, Se-Hoon; Ambrogio, Lauren; Liao, Rachel; Imielinski, Marcin; Banerji, Shantanu; Berger, Alice H.; Lawrence, Michael S.; Zhang, Jinghui; Pho, Nam H.; Walker, Sarah R.; Winckler, Wendy; Getz, Gad; Frank, David; Hahn, William C.; Eck, Michael J.; Mani, D. R.; Jaffe, Jacob D.; Carr, Steven A.; Wong, Kwok-Kin; Meyerson, Matthew

2012-01-01

84

Whole-genome sequencing in autism identifies hot spots for de novo germline mutation.  

PubMed

De novo mutation plays an important role in autism spectrum disorders (ASDs). Notably, pathogenic copy number variants (CNVs) are characterized by high mutation rates. We hypothesize that hypermutability is a property of ASD genes and may also include nucleotide-substitution hot spots. We investigated global patterns of germline mutation by whole-genome sequencing of monozygotic twins concordant for ASD and their parents. Mutation rates varied widely throughout the genome (by 100-fold) and could be explained by intrinsic characteristics of DNA sequence and chromatin structure. Dense clusters of mutations within individual genomes were attributable to compound mutation or gene conversion. Hypermutability was a characteristic of genes involved in ASD and other diseases. In addition, genes impacted by mutations in this study were associated with ASD in independent exome-sequencing data sets. Our findings suggest that regional hypermutation is a significant factor shaping patterns of genetic variation and disease risk in humans. PMID:23260136

Michaelson, Jacob J; Shi, Yujian; Gujral, Madhusudan; Zheng, Hancheng; Malhotra, Dheeraj; Jin, Xin; Jian, Minghan; Liu, Guangming; Greer, Douglas; Bhandari, Abhishek; Wu, Wenting; Corominas, Roser; Peoples, Aine; Koren, Amnon; Gore, Athurva; Kang, Shuli; Lin, Guan Ning; Estabillo, Jasper; Gadomski, Therese; Singh, Balvindar; Zhang, Kun; Akshoomoff, Natacha; Corsello, Christina; McCarroll, Steven; Iakoucheva, Lilia M; Li, Yingrui; Wang, Jun; Sebat, Jonathan

2012-12-21

85

Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors  

PubMed Central

Background Assays of multiple tumor samples frequently reveal recurrent genomic aberrations, including point mutations and copy-number alterations, that affect individual genes. Analyses that extend beyond single genes are often restricted to examining pathways, interactions and functional modules that are already known. Methods We present a method that identifies functional modules without any information other than patterns of recurrent and mutually exclusive aberrations (RME patterns) that arise due to positive selection for key cancer phenotypes. Our algorithm efficiently constructs and searches networks of potential interactions and identifies significant modules (RME modules) by using the algorithmic significance test. Results We apply the method to the TCGA collection of 145 glioblastoma samples, resulting in extension of known pathways and discovery of new functional modules. The method predicts a role for EP300 that was previously unknown in glioblastoma. We demonstrate the clinical relevance of these results by validating that expression of EP300 is prognostic, predicting survival independent of age at diagnosis and tumor grade. Conclusions We have developed a sensitive, simple, and fast method for automatically detecting functional modules in tumors based solely on patterns of recurrent genomic aberration. Due to its ability to analyze very large amounts of diverse data, we expect it to be increasingly useful when applied to the many tumor panels scheduled to be assayed in the near future.

2011-01-01

86

A novel SOD1 mutation p.V31A identified with a slowly progressive form of amyotrophic lateral sclerosis.  

PubMed

The SOD1 gene encoding the superoxide dismutase 1 (SOD1) protein is mutated in approximately 15% of familial amyotrophic lateral sclerosis (ALS) and 3% of sporadic ALS. We identified a novel mutation in SOD1 in a man who presented at age 49 with lower limb stiffness, and at age 53, a spastic paraparesia with distal muscular atrophy in the lower limbs and fasciculations in the quadriceps. A diagnosis of ALS was established. Eleven years after disease onset his condition continues gradually and slowly to deteriorate. The heterozygous mutation observed in exon 2 resulted in a valine to alanine substitution at position 31 in the ?-barrel domain of the SOD1 protein. Functional analysis in NSC34 cells showed that the overexpression of the mutant form of SOD1(V31A) induced aggregates and decreased cell viability. This mutation is located outside of the regions carrying most of the ALS-related mutations (i.e., the catalytic center, the region of dimerization, and the loops between the ?-strands of the ?-barrel). In conclusion, we identified a novel SOD1 mutation in a patient with slow disease progression and supported the idea that different SOD1 mutations can lead to distinct ALS phenotypes. PMID:23954173

Dangoumau, Audrey; Verschueren, Annie; Hammouche, Ellen; Papon, Marie-Amélie; Blasco, Hélène; Cherpi-Antar, Catherine; Pouget, Jean; Corcia, Philippe; Andres, Christian R; Vourc'h, Patrick

2013-08-15

87

Three novel ZBTB24 mutations identified in Japanese and Cape Verdean type 2 ICF syndrome patients.  

PubMed

Immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome is a rare autosomal recessive disorder that shows DNA hypomethylation at pericentromeric satellite-2 and -3 repeats in chromosomes 1, 9 and 16. ICF syndrome is classified into two groups: type 1 (ICF1) patients have mutations in the DNMT3B gene and about half of type 2 (ICF2) patients have mutations in the ZBTB24 gene. Besides satellite-2 and -3 repeats, ?-satellite repeats are also hypomethylated in ICF2. In this study, we report three novel ZBTB24 mutations in ICF2. A Japanese patient was homozygous for a missense mutation (C383Y), and a Cape Verdean patient was compound heterozygous for a nonsense mutation (K263X) and a frame-shift mutation (C327W fsX54). In addition, the second Japanese patient was homozygous for a previously reported nonsense mutation (R320X). The C383Y mutation abolished a C2H2 motif in one of the eight zinc-finger domains, and the other three mutations caused a complete or large loss of the zinc-finger domains. Our immunofluorescence analysis revealed that mouse Zbtb24 proteins possessing a mutation corresponding to either C383Y or R320X are mislocalized from pericentrometic heterochromatin, suggesting the importance of the zinc-finger domains in proper intranuclear localization of this protein. We further revealed that the proper localization of wild-type Zbtb24 protein does not require DNA methylation. PMID:23739126

Nitta, Hirohisa; Unoki, Motoko; Ichiyanagi, Kenji; Kosho, Tomoki; Shigemura, Tomonari; Takahashi, Hiroshi; Velasco, Guillaume; Francastel, Claire; Picard, Capucine; Kubota, Takeo; Sasaki, Hiroyuki

2013-06-06

88

Extragenic suppressors of paralyzed flagellar mutations in Chlamydomonas reinhardtii identify loci that alter the inner dynein arms  

PubMed Central

We have analyzed extragenic suppressors of paralyzed flagella mutations in Chlamydomonas reinhardtii in an effort to identify new dynein mutations. A temperature-sensitive allele of the PF16 locus was mutagenized and then screened for revertants that could swim at the restrictive temperature (Dutcher et al. 1984. J. Cell Biol. 98:229- 236). In backcrosses of one of the revertant strains to wild-type, we recovered both the original pf16 mutation and a second, unlinked suppressor mutation with its own flagellar phenotype. This mutation has been identified by both recombination and complementation tests as a new allele of the previously uncharacterized PF9 locus on linkage group XII/XIII. SDS-PAGE analysis of isolated flagellar axonemes and dynein extracts has demonstrated that the pf9 strains are missing four polypeptides that form the I1 inner arm dynein subunit. The primary effect of the loss of the I1 subunit is a decrease in the forward swimming velocity due to a change in the flagellar waveform. Both the flagellar beat frequency and the axonemal ATPase activity are nearly wild-type. Examination of axonemes by thin section electron microscopy and image averaging methods reveals that a specific domain of the inner arm complex is missing in the pf9 mutant strains (see accompanying paper by Mastronarde et al.). When combined with other flagellar defects, the loss of the I1 subunit has synergistic effects on both flagellar assembly and flagellar motility. These synthetic phenotypes provide a screen for new suppressor mutations in other loci. Using this approach, we have identified the first interactive suppressors of a dynein arm mutation and an unusual bypass suppressor mutation.

1992-01-01

89

Impact of disease-causing mutations on TMEM165 subcellular localization, a recently identified protein involved in CDG-II.  

PubMed

TMEM165 has recently been identified as a novel protein involved in CDG-II. TMEM165 has no biological function described so far. Different mutations were recently found in patients with Golgi glycosylation defects and harboring a peculiar skeletal phenotype. In this study, we examined the effect of naturally occurring mutations on the intracellular localization of TMEM165 and their abilities to complement the TMEM165-deficient yeast, gdt1?. Wild-type TMEM165 was present within Golgi compartment, plasma membrane and late endosomes/lysosomes, whereas mutated TMEM165 were found differentially localized according to the mutations. We demonstrated that, in the yeast functional assay with TMEM165 ortholog Gdt1, the homozygous point mutation correlating with a mild phenotype restores the yeast functional assay, whereas the truncated mutation, associated with severe disease, failed to restore Gdt1 function. These studies highly suggest that these clinically relevant point mutations do not affect the protein function but critically changes the subcellular protein localization. Moreover, the data point to a critical role of the YNRL motif in TMEM165 subcellular localization. PMID:23575229

Rosnoblet, Claire; Legrand, Dominique; Demaegd, Didier; Hacine-Gherbi, Hêla; de Bettignies, Geoffroy; Bammens, Riet; Borrego, Cindy; Duvet, Sandrine; Morsomme, Pierre; Matthijs, Gert; Foulquier, François

2013-04-10

90

Spectrum of mutations in the RPGR gene that are identified in 20% of families with X-linked retinitis pigmentosa.  

PubMed Central

The RPGR (retinitis pigmentosa GTPase regulator) gene for RP3, the most frequent genetic subtype of X-linked retinitis pigmentosa (XLRP), has been shown to be mutated in 10%-15% of European XLRP patients. We have examined the RPGR gene for mutations in a cohort of 80 affected males from apparently unrelated XLRP families, by direct sequencing of the PCR-amplified products from the genomic DNA. Fifteen different putative disease-causing mutations were identified in 17 of the 80 families; these include four nonsense mutations, one missense mutation, six microdeletions, and four intronic-sequence substitutions resulting in splice defects. Most of the mutations were detected in the conserved N-terminal region of the RPGR protein, containing tandem repeats homologous to those present in the RCC-1 protein (a guanine nucleotide-exchange factor for Ran-GTPase). Our results indicate that mutations either in as yet uncharacterized sequences of the RPGR gene or in another gene located in its vicinity may be a more frequent cause of XLRP. The reported studies will be beneficial in establishing genotype-phenotype correlations and should lead to further investigations seeking to understand the mechanism of disease pathogenesis. Images Figure 1

Buraczynska, M; Wu, W; Fujita, R; Buraczynska, K; Phelps, E; Andreasson, S; Bennett, J; Birch, D G; Fishman, G A; Hoffman, D R; Inana, G; Jacobson, S G; Musarella, M A; Sieving, P A; Swaroop, A

1997-01-01

91

Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations.  

PubMed

The recent publication of the draft genome sequences of the Neanderthal and a ?50,000-year-old archaic hominin from Denisova Cave in southern Siberia has ushered in a new age in molecular archaeology. We previously cross-compared the human, chimpanzee and Neanderthal genome sequences with respect to a set of disease-causing/disease-associated missense and regulatory mutations (Human Gene Mutation Database) and succeeded in identifying genetic variants which, although apparently pathogenic in humans, may represent a 'compensated' wild-type state in at least one of the other two species. Here, in an attempt to identify further 'potentially compensated mutations' (PCMs) of interest, we have compared our dataset of disease-causing/disease-associated mutations with their corresponding nucleotide positions in the Denisovan hominin, Neanderthal and chimpanzee genomes. Of the 15 human putatively disease-causing mutations that were found to be compensated in chimpanzee, Denisovan or Neanderthal, only a solitary F5 variant (Val1736Met) was specific to the Denisovan. In humans, this missense mutation is associated with activated protein C resistance and an increased risk of thromboembolism and recurrent miscarriage. It is unclear at this juncture whether this variant was indeed a PCM in the Denisovan or whether it could instead have been associated with disease in this ancient hominin. PMID:21807602

Zhang, Guojie; Pei, Zhang; Ball, Edward V; Mort, Matthew; Kehrer-Sawatzki, Hildegard; Cooper, David N

2011-07-01

92

Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations  

PubMed Central

The recent publication of the draft genome sequences of the Neanderthal and a ~50,000-year-old archaic hominin from Denisova Cave in southern Siberia has ushered in a new age in molecular archaeology. We previously cross-compared the human, chimpanzee and Neanderthal genome sequences with respect to a set of disease-causing/disease-associated missense and regulatory mutations (Human Gene Mutation Database) and succeeded in identifying genetic variants which, although apparently pathogenic in humans, may represent a 'compensated' wild-type state in at least one of the other two species. Here, in an attempt to identify further 'potentially compensated mutations' (PCMs) of interest, we have compared our dataset of disease-causing/disease-associated mutations with their corresponding nucleotide positions in the Denisovan hominin, Neanderthal and chimpanzee genomes. Of the 15 human putatively disease-causing mutations that were found to be compensated in chimpanzee, Denisovan or Neanderthal, only a solitary F5 variant (Val1736Met) was specific to the Denisovan. In humans, this missense mutation is associated with activated protein C resistance and an increased risk of thromboembolism and recurrent miscarriage. It is unclear at this juncture whether this variant was indeed a PCM in the Denisovan or whether it could instead have been associated with disease in this ancient hominin.

2011-01-01

93

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations  

Microsoft Academic Search

Treatment of HIV-infected individuals with antire- troviral agents selects for drug-resistant mutants, resulting in frequent treatment failures. Although the major antiretroviral resistance mutations are routinely characterized by DNA sequencing, treat- ment failures are still common, probably in part because undetected rare resistance mutations facilitate viral escape. Here we combined DNA bar coding and massively parallel pyrosequencing to quantify rare drug

Christian Hoffmann; Nana Minkah; Jeremy Leipzig; Gary Wang; Max Q. Arens; Pablo Tebas; Frederic D. Bushman

2007-01-01

94

The cry b Mutation Identifies Cryptochrome as a Circadian Photoreceptor in Drosophila  

Microsoft Academic Search

A new rhythm mutation was isolated based on its elimination of per-controlled luciferase cycling. Levels of period or timeless clock gene products in the mutant are flat in daily light–dark cycles or constant darkness (although PER and TIM oscillate normally in temperature cycles). Consistent with the fact that light normally suppresses TIM, cryb is an apparent null mutation in a

Ralf Stanewsky; Maki Kaneko; Patrick Emery; Bonnie Beretta; Karen Wager-Smith; Steve A Kay; Michael Rosbash; Jeffrey C Hall

1998-01-01

95

Novel DEPDC5 mutations causing familial focal epilepsy with variable foci identified.  

PubMed

Mutations in DEPDC5 cause familial focal epilepsy with variable foci Dibbens et al. (2013) Nature Genetics 45: 546-551. Mutations of DEPDC5 cause autosomal dominant focal epilepsies Ishida et al. (2013) Nature Genetics 45: 552-555. PMID:23869883

Kaur, A

2013-08-21

96

Suppressors of an Arabidopsis thaliana phyB mutation identify genes that control light signaling and hypocotyl elongation.  

PubMed Central

Ambient light controls the development and physiology of plants. The Arabidopsis thaliana photoreceptor phytochrome B (PHYB) regulates developmental light responses at both seedling and adult stages. To identify genes that mediate control of development by light, we screened for suppressors of the long hypocotyl phenotype caused by a phyB mutation. Genetic analyses show that the shy (short hypocotyl) mutations we have isolated fall in several loci. Phenotypes of the mutants suggest that some of the genes identified have functions in control of light responses. Other loci specifically affect cell elongation or expansion.

Reed, J W; Elumalai, R P; Chory, J

1998-01-01

97

Structural and functional analysis of APOA5 mutations identified in patients with severe hypertriglyceridemia.  

PubMed

During the diagnosis of three unrelated patients with severe hypertriglyceridemia, three APOA5 mutations [p.(Ser232_Leu235)del, p.Leu253Pro, and p.Asp332ValfsX4] were found without evidence of concomitant LPL, APOC2, or GPIHBP1 mutations. The molecular mechanisms by which APOA5 mutations result in severe hypertriglyceridemia remain poorly understood, and the functional impairment/s induced by these specific mutations was not obvious. Therefore, we performed a thorough structural and functional analysis that included follow-up of patients and their closest relatives, measurement of apoA-V serum concentrations, and sequencing of the APOA5 gene in 200 nonhyperlipidemic controls. Further, we cloned, overexpressed, and purified both wild-type and mutant apoA-V variants and characterized their capacity to activate LPL. The interactions of recombinant wild-type and mutated apoA-V variants with liposomes of different composition, heparin, LRP1, sortilin, and SorLA/LR11 were also analyzed. Finally, to explore the possible structural consequences of these mutations, we developed a three-dimensional model of full-length, lipid-free human apoA-V. A complex, wide array of impairments was found in each of the three mutants, suggesting that the specific residues affected are critical structural determinants for apoA-V function in lipoprotein metabolism and, therefore, that these APOA5 mutations are a direct cause of hypertriglyceridemia. PMID:23307945

Mendoza-Barberá, Elena; Julve, Josep; Nilsson, Stefan K; Lookene, Aivar; Martín-Campos, Jesús M; Roig, Rosa; Lechuga-Sancho, Alfonso M; Sloan, John H; Fuentes-Prior, Pablo; Blanco-Vaca, Francisco

2013-01-10

98

Whole exome sequencing identifies a novel mutation in the transglutaminase 6 gene for spinocerebellar ataxia in a Chinese family.  

PubMed

Autosomal dominant spinocerebellar ataxias (SCA) constitute a heterogeneous group of inherited disorders. The transglutaminase 6 (TGM6) gene was recently suggested as a SCA causative gene in Chinese SCA families. In this study, two affected members of a three-generation Chinese family with SCA characterized by progressive cerebellar ataxia and lower limb pyramidal signs were subjected to whole exome sequencing. Through bioinformatics analysis of the sequence variants in these two individuals, we identified a novel mutation in the TGM6 gene (c.1528G>C) which showed perfect co-segregation with disease phenotype in all nine members of this family. This finding confirms that mutations in TGM6 gene represent an important cause of SCA in Chinese. This study also shows that whole exome sequencing of a small number of affected individuals, leveraged on bioinformatics analysis, can be an efficient strategy for identifying causative mutations in rare Mendelian disorders. PMID:22554020

Li, M; Pang, S Y Y; Song, Y; Kung, M H W; Ho, S-L; Sham, P-C

2012-05-29

99

Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia  

Microsoft Academic Search

Abnormal epigenetic regulation has been implicated in oncogenesis. We report here the identification of somatic mutations by exome sequencing in acute monocytic leukemia, the M5 subtype of acute myeloid leukemia (AML-M5). We discovered mutations in DNMT3A (encoding DNA methyltransferase 3A) in 23 of 112 (20.5%) cases. The DNMT3A mutants showed reduced enzymatic activity or aberrant affinity to histone H3 in

Xiao-Jing Yan; Jie Xu; Zhao-Hui Gu; Chun-Ming Pan; Gang Lu; Yang Shen; Jing-Yi Shi; Yong-Mei Zhu; Lin Tang; Xiao-Wei Zhang; Wen-Xue Liang; Jian-Qing Mi; Huai-Dong Song; Ke-Qin Li; Zhu Chen; Sai-Juan Chen

2011-01-01

100

Self-EcoTILLING to identify single-nucleotide mutations in multigene family  

Microsoft Academic Search

TILLING (Targeting Induced Local Lesions IN Genomes) is a low-cost, high-throughput reverse genetic technique that employs a mismatch-specific endonuclease CEL-1 to discover induced point mutations in the genes of interest. The use of the TILLING technique to survey natural variation in genes is called EcoTILLING. Here, we report a modified EcoTILLING method for the discovery of mutations in multigene family,

Guang-Xi Wang; Toshiyuki Imaizumi; Wei Li; Hiromasa Saitoh; Ryohei Terauchi; Takanori Ohsako; Tohru Tominaga

2008-01-01

101

A new point mutation in the ND1 mitochondrial gene identified in a type II diabetic patient  

SciTech Connect

A novel mutation in a mitochondrial gene was identified in a patient with type II diabetes mellitus. G-to-A transition was localized at the nt3316 position of gene ND1 and resulted in alanine threonine replacement at position 4 of mitochondrial NAD-H-dehydrogenase. 6 refs., 2 figs.

Kalinin, V.N. [Research Center of Medical Genetics, Moscow (Russian Federation); Schmidt, W.; Olek, K. [Institut fuer Molekularbiologische Diagnostik, Bonn (Germany)] [and others

1995-08-01

102

Structural interpretation of mutations in phenylalanine hydroxylase protein aids in identifying genotype–phenotype correlations in phenylketonuria  

Microsoft Academic Search

Phenylalanine hydroxylase (PAH) is the enzyme that converts phenylalanine to tyrosine as a rate-limiting step in phenylalanine catabolism and protein and neurotransmitter biosynthesis. Over 300 mutations have been identified in the gene encoding PAH that result in a deficient enzyme activity and lead to the disorders hyperphenylalaninaemia and phenylketonuria. The determination of the crystal structure of PAH now allows the

Ian G Jennings; Richard GH Cotton; Bostjan Kobe

2000-01-01

103

A Novel SRD5A2 Mutation with Loss of Function Identified in Chinese Patients with Hypospadias  

Microsoft Academic Search

Objective: To investigate the functional change of SRD5A2 gene mutations identified in patients with 5?-reductase type 2 deficiency. Patients and Methods: Three unrelated subjects born with ambiguous genitalia were included. All patients were initially reared as girls, but they gradually exhibited variable degrees of virilization at puberty without breast development, followed by a change of gender role. Sequencing analysis of

Manna Zhang; Jun Yang; Huijie Zhang; Guang Ning; Xiaoying Li; Shouyue Sun

2011-01-01

104

Dana-Farber Cancer Institute researchers identify genetic mutation responsible for most cases of a rare lymphoma:  

Cancer.gov

Scientists at Dana-Farber Cancer Institute have identified a gene mutation that underlies the vast majority of cases of Waldenström's macroglobulinemia, a rare form of lymphoma that has eluded all previous efforts to find a genetic cause.

105

Functional Characterization of a CRH Missense Mutation Identified in an ADNFLE Family  

PubMed Central

Nocturnal frontal lobe epilepsy has been historically considered a channelopathy caused by mutations in subunits of the neuronal nicotinic acetylcholine receptor or in a recently reported potassium channel. However, these mutations account for only a minority of patients, and the existence of at least a new locus for the disease has been demonstrated. In 2005, we detected two nucleotide variations in the promoter of the CRH gene coding for the corticotropin releasing hormone in 7 patients. These variations cosegregated with the disease and were demonstrated to alter the cellular levels of this hormone. Here, we report the identification in an Italian affected family of a novel missense mutation (hpreproCRH p.Pro30Arg) located in the region of the CRH coding for the protein pro-sequence. The mutation was detected in heterozygosity in the two affected individuals. In vitro assays demonstrated that this mutation results in reduced levels of protein secretion in the short time thus suggesting that mutated people could present an altered capability to respond immediately to stress agents.

Sansoni, Veronica; Forcella, Matilde; Mozzi, Alessandra; Fusi, Paola; Ambrosini, Roberto; Ferini-Strambi, Luigi; Combi, Romina

2013-01-01

106

Next-generation sequencing identifies the Danforth's short tail mouse mutation as a retrotransposon insertion affecting Ptf1a expression.  

PubMed

The semidominant Danforth's short tail (Sd) mutation arose spontaneously in the 1920s. The homozygous Sd phenotype includes severe malformations of the axial skeleton with an absent tail, kidney agenesis, anal atresia, and persistent cloaca. The Sd mutant phenotype mirrors features seen in human caudal malformation syndromes including urorectal septum malformation, caudal regression, VACTERL association, and persistent cloaca. The Sd mutation was previously mapped to a 0.9 cM region on mouse chromosome 2qA3. We performed Sanger sequencing of exons and intron/exon boundaries mapping to the Sd critical region and did not identify any mutations. We then performed DNA enrichment/capture followed by next-generation sequencing (NGS) of the critical genomic region. Standard bioinformatic analysis of paired-end sequence data did not reveal any causative mutations. Interrogation of reads that had been discarded because only a single end mapped correctly to the Sd locus identified an early transposon (ETn) retroviral insertion at the Sd locus, located 12.5 kb upstream of the Ptf1a gene. We show that Ptf1a expression is significantly upregulated in Sd mutant embryos at E9.5. The identification of the Sd mutation will lead to improved understanding of the developmental pathways that are misregulated in human caudal malformation syndromes. PMID:23437000

Vlangos, Christopher N; Siuniak, Amanda N; Robinson, Dan; Chinnaiyan, Arul M; Lyons, Robert H; Cavalcoli, James D; Keegan, Catherine E

2013-02-21

107

VWF mutations and new sequence variations identified in healthy controls are more frequent in the African-American population  

PubMed Central

Diagnosis and classification of VWD is aided by molecular analysis of the VWF gene. Because VWF polymorphisms have not been fully characterized, we performed VWF laboratory testing and gene sequencing of 184 healthy controls with a negative bleeding history. The controls included 66 (35.9%) African Americans (AAs). We identified 21 new sequence variations, 13 (62%) of which occurred exclusively in AAs and 2 (G967D, T2666M) that were found in 10%-15% of the AA samples, suggesting they are polymorphisms. We identified 14 sequence variations reported previously as VWF mutations, the majority of which were type 1 mutations. These controls had VWF Ag levels within the normal range, suggesting that these sequence variations might not always reduce plasma VWF levels. Eleven mutations were found in AAs, and the frequency of M740I, H817Q, and R2185Q was 15%-18%. Ten AA controls had the 2N mutation H817Q; 1 was homozygous. The average factor VIII level in this group was 99 IU/dL, suggesting that this variation may confer little or no clinical symptoms. This study emphasizes the importance of sequencing healthy controls to understand ethnic-specific sequence variations so that asymptomatic sequence variations are not misidentified as mutations in other ethnic or racial groups.

Christopherson, Pamela A.; Flood, Veronica H.; Gill, Joan Cox; Friedman, Kenneth D.; Haberichter, Sandra L.; Shapiro, Amy D.; Abshire, Thomas C.; Leissinger, Cindy; Hoots, W. Keith; Lusher, Jeanne M.; Ragni, Margaret V.; Montgomery, Robert R.

2012-01-01

108

Mutation analysis of congenital cataract in a Basotho family identified a new missense allele in CRYBB2  

PubMed Central

Purpose To identify the causative genetic mutation among the known cataract candidate genes underlying the observed phenotype in a Basotho family, with congenital nuclear cataracts. Methods Because of the small family size, we used the functional candidate gene analysis approach. We screened a Basotho family, clinically documented to have congenital nuclear cataracts, for mutation in the candidate genes CRYG (C & D; Crystallin, gamma C and Crystallin, gamma D), GJA8 (Gap junction protein, alpha 8), CRY (AA & AB; Crystallin, alpha A and Crystallin, alpha B), CRYBA (Crystallin, beta A) and CRY (BB1 & BB2; Crystallin, beta B1 and Crystallin, beta B2) through polymerase chain reaction analyses and sequencing. Results Mutation screening identified only one significant alteration in exon 6 (607G>A) of CRYBB2, with a substitution of Valine to Methionine at position 187. This mutation segregated in all five affected family members but it was not observed in any of the unaffected persons of the family. The putative mutation led also to the appearance of a new NIaIII restriction site in the samples of the affected family members that was not present in 100 randomly selected DNA samples from ophthalmologically normal individuals and in 40 unrelated senile cataract patients of the same ethnic background as the family members. Conclusions This study identified a missense mutation in CRYBB2 in a family of Basotho with autosomal dominant congenital cataract (ADCC). In summary, we believe this new missense allele is the probable causative molecular lesion for the observed phenotype in this family.

Mothobi, Maneo Emily; Guo, Shuren; Liu, Yuanyuan; Chen, Qiang; Yussuf, Ali Said; Zhu, Xinli

2009-01-01

109

Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia.  

PubMed

The identification of new genetic lesions in chronic lymphocytic leukemia (CLL) prompts a comprehensive and dynamic prognostic algorithm including gene mutations and chromosomal abnormalities and their changes during clonal evolution. By integrating mutational and cytogenetic analysis in 1274 CLL samples and using both a training-validation and a time-dependent design, 4 CLL subgroups were hierarchically classified: (1) high-risk, harboring TP53 and/or BIRC3 abnormalities (10-year survival: 29%); (2) intermediate-risk, harboring NOTCH1 and/or SF3B1 mutations and/or del11q22-q23 (10-year survival: 37%); (3) low-risk, harboring +12 or a normal genetics (10-year survival: 57%); and (4) very low-risk, harboring del13q14 only, whose 10-year survival (69.3%) did not significantly differ from a matched general population. This integrated mutational and cytogenetic model independently predicted survival, improved CLL prognostication accuracy compared with FISH karyotype (P < .0001), and was externally validated in an independent CLL cohort. Clonal evolution from lower to higher risk implicated the emergence of NOTCH1, SF3B1, and BIRC3 abnormalities in addition to TP53 and 11q22-q23 lesions. By taking into account clonal evolution through time-dependent analysis, the genetic model maintained its prognostic relevance at any time from diagnosis. These findings may have relevant implications for the design of clinical trials aimed at assessing the use of mutational profiling to inform therapeutic decisions. PMID:23243274

Rossi, Davide; Rasi, Silvia; Spina, Valeria; Bruscaggin, Alessio; Monti, Sara; Ciardullo, Carmela; Deambrogi, Clara; Khiabanian, Hossein; Serra, Roberto; Bertoni, Francesco; Forconi, Francesco; Laurenti, Luca; Marasca, Roberto; Dal-Bo, Michele; Rossi, Francesca Maria; Bulian, Pietro; Nomdedeu, Josep; Del Poeta, Giovanni; Gattei, Valter; Pasqualucci, Laura; Rabadan, Raul; Foà, Robin; Dalla-Favera, Riccardo; Gaidano, Gianluca

2012-12-13

110

Founder Mutation in RSPH4A Identified in Patients of Hispanic Descent with Primary Ciliary Dyskinesia.  

PubMed

Primary ciliary dyskinesia (PCD) is a rare, autosomal recessive, genetically heterogeneous disorder characterized by ciliary dysfunction resulting in chronic oto-sino-pulmonary disease, respiratory distress in term neonates, laterality (situs) defects, and bronchiectasis. Diagnosis has traditionally relied on ciliary ultrastructural abnormalities seen by electron microscopy. Mutations in radial spoke head proteins occur in PCD patients with central apparatus defects. Advances in genetic testing have been crucial in addressing the diagnostic challenge. Here, we describe a novel splice-site mutation (c.921+3_6delAAGT) in RSPH4A, which leads to a premature translation termination signal in nine subjects with PCD (seven families). Loss-of-function was confirmed with quantitative ciliary ultrastructural analysis, measurement of ciliary beat frequency and waveform, and transcript analysis. All nine individuals carrying c.921+3_6delAAGT splice-site mutation in RSPH4A were Hispanic with ancestry tracing to Puerto Rico. This mutation is a founder mutation and a common cause of PCD without situs abnormalities in patients of Puerto Rican descent. PMID:23798057

Daniels, M Leigh Anne; Leigh, Margaret W; Davis, Stephanie D; Armstrong, Michael C; Carson, Johnny L; Hazucha, Milan; Dell, Sharon D; Eriksson, Maria; Collins, Francis S; Knowles, Michael R; Zariwala, Maimoona A

2013-08-06

111

Mutations in the ?-subunit of rod phosphodiesterase identified in consanguineous Pakistani families with autosomal recessive retinitis pigmentosa  

PubMed Central

Purpose This study was designed to identify pathogenic mutations causing autosomal recessive retinitis pigmentosa (RP) in consanguineous Pakistani families. Methods Two consanguineous families affected with autosomal recessive RP were identified from the Punjab Province of Pakistan. All affected individuals underwent a thorough ophthalmologic examination. Blood samples were collected, and genomic DNAs were extracted. Exclusion analysis was completed, and two-point LOD scores were calculated. Bidirectional sequencing of the ? subunit of phosphodiesterase 6 (PDE6?) was completed. Results During exclusion analyses both families localized to chromosome 4p, harboring PDE6?, a gene previously associated with autosomal recessive RP. Sequencing of PDE6? identified missense mutations: c.1655G>A (p.R552Q) and c.1160C>T (p.P387L) in families PKRP161 and PKRP183, respectively. Bioinformatic analyses suggested that both mutations are deleterious for the native three-dimensional structure of the PDE6? protein. Conclusions These results strongly suggest that mutations in PDE6? are responsible for the disease phenotype in the consanguineous Pakistani families.

Ali, Shahbaz; Riazuddin, S. Amer; Shahzadi, Amber; Nasir, Idrees A.; Khan, Shaheen N.; Husnain, Tayyab; Akram, Javed; Sieving, Paul A.; Hejtmancik, J. Fielding

2011-01-01

112

Fabry_CEP: a tool to identify Fabry mutations responsive to pharmacological chaperones.  

PubMed

Fabry_CEP is a user-friendly web-application designed to help clinicians Choose Eligible Patients for the therapy with pharmacological chaperones. It provides a database and a predictive tool to evaluate the responsiveness of lysosomal alpha-galactosidase mutants to a small molecule drug, namely 1-Deoxy-galactonojirimycin. The user can introduce any missense/nonsense mutation in the coding sequence, learn whether it is has been tested and gain access to appropriate reference literature. In the absence of experimental data structural, functional and evolutionary analysis provides a prediction and the probability that a given mutation is responsive to the drug. PMID:23883437

Cammisa, Marco; Correra, Antonella; Andreotti, Giuseppina; Cubellis, Maria Vittoria

2013-07-24

113

A Novel Nonsense Mutation of the GPR143 Gene Identified in a Chinese Pedigree with Ocular Albinism  

PubMed Central

Background The purpose of this study was to elucidate the molecular basis of ocular albinism type I in a Chinese pedigree. Methodology/Principal Findings Complete ophthalmologic examinations were performed on 4 patients, 7 carriers and 17 unaffected individuals in this five-generation family. All coding exons of four-point-one (4.1), ezrin, radixin, moesin (FERM) domain-containing 7 (FRMD7) and G protein-coupled receptor 143 (GPR143) genes were amplified by polymerase chain reaction (PCR), sequenced and compared with a reference database. Ocular albinism and nystagmus were found in all patients of this family. Macular hypoplasia was present in the patients including the proband. A novel nonsense hemizygous mutation c.807T>A in the GPR143 gene was identified in four patients and the heterozygous mutation was found in seven asymptomatic individuals. This mutation is a substitution of tyrosine for adenine which leads to a premature stop codon at position 269 (p.Y269X) of GPR143. Conclusions/Significance This is the first report that p.Y269X mutation of GPR143 gene is responsible for the pathogenesis of familial ocular albinism. These results expand the mutation spectrum of GPR143, and demonstrate the clinical characteristics of ocular albinism type I in Chinese population.

Lan, Changjun; Wang, Yun; Zhou, Xiaomin; Yin, Yan; Yu, Wenhan; Liu, Xuyang

2012-01-01

114

Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer  

PubMed Central

While genomically targeted therapies have improved outcomes for patients with lung adenocarcinoma, little is known about the genomic alterations which drive squamous cell lung cancer. Sanger sequencing of the tyrosine kinome identified mutations in the DDR2 kinase gene in 3.8% of squamous cell lung cancers and cell lines. Squamous lung cancer cell lines harboring DDR2 mutations were selectively killed by knock-down of DDR2 by RNAi or by treatment with the multi-targeted kinase inhibitor dasatinib. Tumors established from a DDR2 mutant cell line were sensitive to dasatinib in xenograft models. Expression of mutated DDR2 led to cellular transformation which was blocked by dasatinib. A squamous cell lung cancer patient with a response to dasatinib and erlotinib treatment harbored a DDR2 kinase domain mutation. These data suggest that gain-of-function mutations in DDR2 are important oncogenic events and are amenable to therapy with dasatinib. As dasatinib is already approved for use, these findings could be rapidly translated into clinical trials.

Hammerman, Peter S; Sos, Martin L; Ramos, Alex H; Xu, Chunxiao; Dutt, Amit; Zhou, Wenjun; Brace, Lear E; Woods, Brittany A; Lin, Wenchu; Zhang, Jianming; Deng, Xianming; Lim, Sang Min; Heynck, Stefanie; Peifer, Martin; Simard, Jeffrey R; Lawrence, Michael S; Onofrio, Robert C; Salvesen, Helga B; Seidel, Danila; Zander, Thomas; Heuckmann, Johannes M; Soltermann, Alex; Moch, Holger; Koker, Mirjam; Leenders, Frauke; Gabler, Franziska; Querings, Silvia; Ansen, Sascha; Brambilla, Elisabeth; Brambilla, Christian; Lorimier, Philippe; Brustugun, Odd Terje; Helland, Aslaug; Petersen, Iver; Clement, Joachim H; Groen, Harry; Timens, Wim; Sietsma, Hannie; Stoelben, Erich; Wolf, Jurgen; Beer, David G; Tsao, Ming Sound; Hanna, Megan; Hatton, Charles; Eck, Michael J; Janne, Pasi A; Johnson, Bruce E; Winckler, Wendy; Greulich, Heidi; Bass, Adam J; Cho, Jeonghee; Rauh, Daniel; Gray, Nathanael S; Wong, Kwok-Kin; Haura, Eric B; Thomas, Roman K; Meyerson, Matthew

2011-01-01

115

One novel and two recurrent mutations in the keratin 5 gene identified in Chinese patients with epidermolysis bullosa simplex.  

PubMed

Epidermolysis bullosa simplex (EBS) is a group of inherited skin diseases, characterized by the formation of intraepidermal blisters. We performed genetic analysis of the keratin 5 (KRT5) gene in two Chinese pedigrees. One novel missense mutation was identified in a patient with sporadic EBS (general, non-Dowling-Meara). Sequence analysis showed a heterozygous T > A transition at nucleotide 1730 of KRT5, changing phenylalanine (Phe) to tyrosine (Tyr) at position 577 of the keratin 5 (K5). In addition, two recurrent mutations c.1649delG (p.Gly550AlafsX77) and c.508G > (p.Glu170Lys) in KRT5 were identified in Chinese patients with mottled pigmentation EBS and localized EBS, respectively. None of the mutations were found in any unaffected family members or in an additional 100 unrelated control samples. These results suggest that these mutations are pathogenic and might be one of the potential causes of EBS in these Chinese patients. PMID:20055872

Tang, H Y; Du, W D; Cui, Y; Fan, X; Quan, C; Fang, Q Y; Zhou, F S; Yao, F M; Wang, J F; Yang, S; Zhang, X

2009-12-01

116

Exome Sequencing and Functional Analysis Identifies BANF1 Mutation as the Cause of a Hereditary Progeroid Syndrome  

PubMed Central

Accelerated aging syndromes represent a valuable source of information about the molecular mechanisms involved in normal aging. Here, we describe a progeroid syndrome that partially phenocopies Hutchinson-Gilford progeria syndrome (HGPS) but also exhibits distinctive features, including the absence of cardiovascular deficiencies characteristic of HGPS, the lack of mutations in LMNA and ZMPSTE24, and a relatively long lifespan of affected individuals. Exome sequencing and molecular analysis in two unrelated families allowed us to identify a homozygous mutation in BANF1 (c.34G>A [p.Ala12Thr]), encoding barrier-to-autointegration factor 1 (BAF), as the molecular abnormality responsible for this Mendelian disorder. Functional analysis showed that fibroblasts from both patients have a dramatic reduction in BAF protein levels, indicating that the p.Ala12Thr mutation impairs protein stability. Furthermore, progeroid fibroblasts display profound abnormalities in the nuclear lamina, including blebs and abnormal distribution of emerin, an interaction partner of BAF. These nuclear abnormalities are rescued by ectopic expression of wild-type BANF1, providing evidence for the causal role of this mutation. These data demonstrate the utility of exome sequencing for identifying the cause of rare Mendelian disorders and underscore the importance of nuclear envelope alterations in human aging.

Puente, Xose S.; Quesada, Victor; Osorio, Fernando G.; Cabanillas, Ruben; Cadinanos, Juan; Fraile, Julia M.; Ordonez, Gonzalo R.; Puente, Diana A.; Gutierrez-Fernandez, Ana; Fanjul-Fernandez, Miriam; Levy, Nicolas; Freije, Jose M.P.; Lopez-Otin, Carlos

2011-01-01

117

Convenient, nonradioactive, heteroduplex-based methods for identifying recurrent mutations in the BRCA1 and BRCA2 genes.  

PubMed

The ability to identify individuals who are predisposed to specific malignant tumors is a promising molecular diagnostic by-product of over two decades of intensive research into the genetic pathogenesis of human cancer. Approximately 2% of Ashkenazi Jews carry recurrent germline mutations in either the BRCA1 or BRCA2 genes that may predispose these individuals to the development of breast and ovarian cancer. We have developed a nonisotopic method, based on the formation of heteroduplexes between polymerase chain reaction (PCR) amplified wild-type and mutant alleles, which can be used to identify the BRCA1 185delAG and the BRCA2 6174delT mutations. The same assay can also be used to verify the loss of heterozygosity in a tumor sample arising in an individual with a germline mutation. The four steps described in this report (PCR amplification, heteroduplex formation, acrylamide gel electrophoresis, and ethidium bromide staining/UV-fluorescence photography) can be readily and reproducibly performed in the course of a single day, making this a useful method for the routine identification of these mutations. PMID:9360844

Mansukhani, M M; Nastiuk, K L; Hibshoosh, H; Kularatne, P; Russo, D; Krolewski, J J

1997-08-01

118

Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation  

PubMed Central

While there have been significant advances in understanding the genetic etiology of human hair loss over the previous decade, there remain a number of hereditary disorders for which a causative gene has yet to be identified. We studied a large, consanguineous Brazilian family that presented with sparse woolly hair at birth that progressed to severe hypotrichosis by the age of 5, in which 6 of the 14 offspring were affected. After exclusion of known candidate genes, a genome-wide scan was performed to identify the disease locus. Autozygosity mapping revealed a highly significant region of extended homozygosity (LOD score of 10.41) that contained a haplotype with a linkage LOD score of 3.28. Results of these two methods defined a 9 Mb region on chromosome 13q14.11-q14.2. The interval contains the P2RY5 gene, in which we recently identified pathogenic mutations in several families of Pakistani origin affected with autosomal recessive woolly and sparse hair. After the exclusion of several other candidate genes, we sequenced the P2RY5 gene and identified a homozygous mutation (C278Y) in all affected individuals in this family. Our findings show that mutations in P2RY5 display variable expressivity, underlying both hypotrichosis and woolly hair, and underscore the essential role of P2RY5 in the tissue integrity and the maintenance of the hair follicle.

Petukhova, Lynn; Sousa, Edilson C.; Martinez-Mir, Amalia; Vitebsky, Anna; dos Santos, Lina G; Shapiro, Lawrence; Haynes, Chad; Gordon, Derek; Shimomura, Yutaka; Christiano, Angela M.

2012-01-01

119

Novel Ribosomal Mutations in Staphylococcus aureus Strains Identified through Selection with the Oxazolidinones Linezolid and Torezolid (TR-700)?  

PubMed Central

TR-700 (torezolid), the active moiety of the novel oxazolidinone phosphate prodrug TR-701, is highly potent against gram-positive pathogens, including strains resistant to linezolid (LZD). Here we investigated the potential of Staphylococcus aureus strains ATCC 29213 (methicillin-susceptible S. aureus [MSSA]) and ATCC 33591 (methicillin-resistant S. aureus [MRSA]) to develop resistance to TR-700. The spontaneous frequencies of mutation of MSSA 29213 and MRSA 33591 resulting in reduced susceptibility to TR-700 at 2× the MIC were 1.1 × 10?10 and 1.9 × 10?10, respectively. These values are ?16-fold lower than the corresponding LZD spontaneous mutation frequencies of both strains. Following 30 serial passages in the presence of TR-700, the MIC for MSSA 29213 remained constant (0.5 ?g/ml) while increasing eightfold (0.25 to 2.0 ?g/ml) for MRSA 33591. Serial passage of MSSA 29213 and MRSA 33591 in LZD resulted in 64- and 32-fold increases in LZD resistance (2 to 128 ?g/ml and 1 to 32 ?g/ml, respectively). Domain V 23S rRNA gene mutations (Escherichia coli numbering) found in TR-700-selected mutants included T2500A and a novel coupled T2571C/G2576T mutation, while LZD-selected mutants included G2447T, T2500A, and G2576T. We also identified mutations correlating with decreased susceptibility to TR-700 and LZD in the rplC and rplD genes, encoding the 50S ribosomal proteins L3 and L4, respectively. L3 mutations included Gly152Asp, Gly155Arg, Gly155Arg/Met169Leu, and ?Phe127-His146. The only L4 mutation detected was Lys68Gln. TR-700 maintained a fourfold or greater potency advantage over LZD against all strains with ribosomal mutations. These data bring to light a variety of novel and less-characterized mutations associated with S. aureus resistance to oxazolidinones and demonstrate the low resistance potential of torezolid.

Locke, Jeffrey B.; Hilgers, Mark; Shaw, Karen Joy

2009-01-01

120

Structure-based Protocol for Identifying Mutations that Enhance Protein–Protein Binding Affinities  

Microsoft Academic Search

The ability to manipulate protein binding affinities is important for the development of proteins as biosensors, industrial reagents, and therapeutics. We have developed a structure-based method to rationally predict single mutations at protein–protein interfaces that enhance binding affinities. The protocol is based on the premise that increasing buried hydrophobic surface area and\\/or reducing buried hydrophilic surface area will generally lead

Deanne W. Sammond; Ziad M. Eletr; Carrie Purbeck; Randall J. Kimple; David P. Siderovski; Brian Kuhlman

2007-01-01

121

Convergent Evolutionary Analysis Identifies Significant Mutations in Drug Resistance Targets of Mycobacterium tuberculosis  

Microsoft Academic Search

Mycobacterium tuberculosis adapts to the environment by selecting for advantageous single-nucleotide poly- morphisms (SNPs). We studied whether advantageous SNPs could be distinguished from neutral mutations within genes associated with drug resistance. A total of 1,003 clinical isolates of M. tuberculosis were related phylogenetically and tested for the distribution of SNPs in putative drug resistance genes. Drug resistance- associated versus non-drug-resistance-associated

Manzour Hernando Hazbon; Alifiya S. Motiwala; Magali Cavatore; Michael Brimacombe; Thomas S. Whittam; David Alland

2008-01-01

122

Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy  

Microsoft Academic Search

Nephronophthisis-related ciliopathies (NPHP-RC) are recessive disorders that feature dysplasia or degeneration occurring preferentially in the kidney, retina and cerebellum. Here we combined homozygosity mapping with candidate gene analysis by performing 'ciliopathy candidate exome capture' followed by massively parallel sequencing. We identified 12 different truncating mutations of SDCCAG8 (serologically defined colon cancer antigen 8, also known as CCCAP) in 10 families

Edgar A Otto; Toby W Hurd; Rannar Airik; Moumita Chaki; Weibin Zhou; Corinne Stoetzel; Suresh B Patil; Shawn Levy; Amiya K Ghosh; Carlos A Murga-Zamalloa; Jeroen van Reeuwijk; Stef J F Letteboer; Liyun Sang; Rachel H Giles; Qin Liu; Karlien L M Coene; Alejandro Estrada-Cuzcano; Rob W J Collin; Heather M McLaughlin; Susanne Held; Jennifer M Kasanuki; Gokul Ramaswami; Jinny Conte; Irma Lopez; Joseph Washburn; James MacDonald; Jinghua Hu; Yukiko Yamashita; Eamonn R Maher; Lisa M Guay-Woodford; Hartmut P H Neumann; Nicholas Obermüller; Robert K Koenekoop; Carsten Bergmann; Xiaoshu Bei; Richard A Lewis; Nicholas Katsanis; Vanda Lopes; David S Williams; Robert H Lyons; Chi V Dang; Daniela A Brito; Mónica Bettencourt Dias; Xinmin Zhang; James D Cavalcoli; Gudrun Nürnberg; Peter Nürnberg; Eric A Pierce; Peter K Jackson; Corinne Antignac; Sophie Saunier; Ronald Roepman; Helene Dollfus; Hemant Khanna; Friedhelm Hildebrandt

2010-01-01

123

AIP mutation identified in a patient with acromegaly caused by pituitary somatotroph adenoma with neuronal choristoma.  

PubMed

Pituitary adenoma with neuronal choristoma (PANCH) is a rare condition that includes ganglion cells and GH-producing tumor that is characterized by sparsely granulated somatotroph cell type. However, the pathophysiology of this condition remains to be elucidated. We report a case of 46-year-old woman with acromegaly caused by PANCH. The patient had a large and invasive macroadenoma that was resistant to preoperative therapy with somatostatin analogue (SSA) and dopamine agonist. Histological examination showed typical diffuse, chromophobe-type adenoma containing ganglion cells, and sparsely granulated somatotroph cell type, which were consistent with PANCH. Genetic analysis showed heterozygous germline missense mutation in the AIP gene that results in Y261X amino acid substitution. The clinical characteristics of acromegaly associated with AIP mutations are reportedly macroadenomas with tumor extension and invasion, lower decreases in GH and IGF-I and less tumor shrinkage with SSA treatment, and sparsely granulated somatotroph cell type, which are comparable with those observed in PANCH. Taken together, the mutation in AIP gene may explain the clinical characteristics and pathogenesis of PANCH. PMID:23674160

Nishizawa, H; Fukuoka, H; Iguchi, G; Inoshita, N; Yamada, S; Takahashi, Y

2013-05-14

124

Novel dedicator of cytokinesis 8 mutations identified by multiplex ligation-dependent probe amplification.  

PubMed

Dedicator of cytokinesis 8 (DOCK8) deficiency is an innate error of adaptive immunity characterized by recurrent infections with viruses, bacteria and fungi, very high serum IgE concentrations, and a progressive deterioration of T- and B-cell-mediated immunity. We studied the genetic and immunological features of two sisters (aged 11 and 6 yr). Mutational analysis of genomic DNA and cDNA from the patients and their parents, by a combination of PCR and bidirectional targeted sequencing, failed to localize the mutation site. However, a multiplex ligation-dependent probe amplification (MLPA) assay revealed two novel large deletions, del1-14 exons and del8-18 exons, of DOCK8 in both patients. Immunoblot analysis demonstrated that DOCK8 protein was absent from the peripheral blood lymphocytes of both patients. These data suggest that compound heterozygous del1-14 exons and del8-18 exons mutations result in a loss of function of DOCK8 protein and a typical DOCK8 deficiency phenotype. PMID:23859592

Tóth, Beáta; Pistár, Zsuzsanna; Csorba, Gabriella; Balogh, István; Kovács, Tímea; Erd?s, Melinda; Maródi, László

2013-08-20

125

Massively Parallel DNA Sequencing Successfully Identifies New Causative Mutations in Deafness Genes in Patients with Cochlear Implantation and EAS.  

PubMed

Genetic factors, the most common etiology in severe to profound hearing loss, are one of the key determinants of Cochlear Implantation (CI) and Electric Acoustic Stimulation (EAS) outcomes. Satisfactory auditory performance after receiving a CI/EAS in patients with certain deafness gene mutations indicates that genetic testing would be helpful in predicting CI/EAS outcomes and deciding treatment choices. However, because of the extreme genetic heterogeneity of deafness, clinical application of genetic information still entails difficulties. Target exon sequencing using massively parallel DNA sequencing is a new powerful strategy to discover rare causative genes in Mendelian disorders such as deafness. We used massive sequencing of the exons of 58 target candidate genes to analyze 8 (4 early-onset, 4 late-onset) Japanese CI/EAS patients, who did not have mutations in commonly found genes including GJB2, SLC26A4, or mitochondrial 1555A>G or 3243A>G mutations. We successfully identified four rare causative mutations in the MYO15A, TECTA, TMPRSS3, and ACTG1 genes in four patients who showed relatively good auditory performance with CI including EAS, suggesting that genetic testing may be able to predict the performance after implantation. PMID:24130743

Miyagawa, Maiko; Nishio, Shin-Ya; Ikeda, Takuo; Fukushima, Kunihiro; Usami, Shin-Ichi

2013-10-09

126

Massively Parallel DNA Sequencing Successfully Identifies New Causative Mutations in Deafness Genes in Patients with Cochlear Implantation and EAS  

PubMed Central

Genetic factors, the most common etiology in severe to profound hearing loss, are one of the key determinants of Cochlear Implantation (CI) and Electric Acoustic Stimulation (EAS) outcomes. Satisfactory auditory performance after receiving a CI/EAS in patients with certain deafness gene mutations indicates that genetic testing would be helpful in predicting CI/EAS outcomes and deciding treatment choices. However, because of the extreme genetic heterogeneity of deafness, clinical application of genetic information still entails difficulties. Target exon sequencing using massively parallel DNA sequencing is a new powerful strategy to discover rare causative genes in Mendelian disorders such as deafness. We used massive sequencing of the exons of 58 target candidate genes to analyze 8 (4 early-onset, 4 late-onset) Japanese CI/EAS patients, who did not have mutations in commonly found genes including GJB2, SLC26A4, or mitochondrial 1555A>G or 3243A>G mutations. We successfully identified four rare causative mutations in the MYO15A, TECTA, TMPRSS3, and ACTG1 genes in four patients who showed relatively good auditory performance with CI including EAS, suggesting that genetic testing may be able to predict the performance after implantation.

Miyagawa, Maiko; Nishio, Shin-ya; Ikeda, Takuo; Fukushima, Kunihiro; Usami, Shin-ichi

2013-01-01

127

Identifying mutation regions for closely related individuals without a known pedigree  

PubMed Central

Background Linkage analysis is the first step in the search for a disease gene. Linkage studies have facilitated the identification of several hundred human genes that can harbor mutations leading to a disease phenotype. In this paper, we study a very important case, where the sampled individuals are closely related, but the pedigree is not given. This situation happens very often when the individuals share a common ancestor 6 or more generations ago. To our knowledge, no algorithm can give good results for this case. Results To solve this problem, we first developed some heuristic algorithms for haplotype inference without any given pedigree. We propose a model using the parsimony principle that can be viewed as an extension of the model first proposed by Dan Gusfield. Our heuristic algorithm uses Clark’s inference rule to infer haplotype segments. Conclusions We ran our program both on the simulated data and a set of real data from the phase II HapMap database. Experiments show that our program performs well. The recall value is from 90% to 99% in various cases. This implies that the program can report more than 90% of the true mutation regions. The value of precision varies from 29% to 90%. When the precision is 29%, the size of the reported regions is three times that of the true mutation region. This is still very useful for narrowing down the range of the disease gene location. Our program can complete the computation for all the tested cases, where there are about 110,000 SNPs on a chromosome, within 20 seconds.

2012-01-01

128

Mutations in PRDM5 in Brittle Cornea Syndrome Identify a Pathway Regulating Extracellular Matrix Development and Maintenance  

PubMed Central

Extreme corneal fragility and thinning, which have a high risk of catastrophic spontaneous rupture, are the cardinal features of brittle cornea syndrome (BCS), an autosomal-recessive generalized connective tissue disorder. Enucleation is frequently the only management option for this condition, resulting in blindness and psychosocial distress. Even when the cornea remains grossly intact, visual function could also be impaired by a high degree of myopia and keratoconus. Deafness is another common feature and results in combined sensory deprivation. Using autozygosity mapping, we identified mutations in PRDM5 in families with BCS. We demonstrate that regulation of expression of extracellular matrix components, particularly fibrillar collagens, by PRDM5 is a key molecular mechanism that underlies corneal fragility in BCS and controls normal corneal development and maintenance. ZNF469, encoding a zinc finger protein of hitherto undefined function, has been identified as a quantitative trait locus for central corneal thickness, and mutations in this gene have been demonstrated in Tunisian Jewish and Palestinian kindreds with BCS. We show that ZNF469 and PRDM5, two genes that when mutated cause BCS, participate in the same regulatory pathway.

Burkitt Wright, Emma M.M.; Spencer, Helen L.; Daly, Sarah B.; Manson, Forbes D.C.; Zeef, Leo A.H.; Urquhart, Jill; Zoppi, Nicoletta; Bonshek, Richard; Tosounidis, Ioannis; Mohan, Meyyammai; Madden, Colm; Dodds, Annabel; Chandler, Kate E.; Banka, Siddharth; Au, Leon; Clayton-Smith, Jill; Khan, Naz; Biesecker, Leslie G.; Wilson, Meredith; Rohrbach, Marianne; Colombi, Marina; Giunta, Cecilia; Black, Graeme C.M.

2011-01-01

129

Novel Mutations in the ZEB1 Gene Identified in Czech and British Patients With Posterior Polymorphous Corneal Dystrophy  

PubMed Central

We describe the search for mutations in six unrelated Czech and four unrelated British families with posterior polymorphous corneal dystrophy (PPCD); a relatively rare eye disorder. Coding exons and intron/exon boundaries of all three genes (VSX1, COL8A2, and ZEB1/TCF8) previously reported to be implicated in the pathogenesis of this disorder were screened by DNA sequencing. Four novel pathogenic mutations were identified in four families; two deletions, one nonsense, and one duplication within exon 7 in the ZEB1 gene located at 10p11.2. We also genotyped the Czech patients to test for a founder haplotype and lack of disease segregation with the 20p11.2 locus we previously described. Although a systematic clinical examination was not performed, our investigation does not support an association between ZEB1 changes and self reported non-ocular anomalies. In the remaining six families no disease causing mutations were identified thereby indicating that as yet unidentified gene(s) are likely to be responsible for PPCD.

Liskova, Petra; Tuft, Stephen J.; Gwilliam, Rhian; Ebenezer, Neil D.; Jirsova, Katerina; Prescott, Quincy; Martincova, Radka; Pretorius, Marike; Sinclair, Neil; Boase, David L.; Jeffrey, Margaret J.; Deloukas, Panos; Hardcastle, Alison J.; Filipec, Martin; Bhattacharya, Shomi S.

2009-01-01

130

Whole-Exome sequencing identifies FAM20A mutations as a cause of amelogenesis imperfecta and gingival hyperplasia syndrome.  

PubMed

Amelogenesis imperfecta (AI) describes a clinically and genetically heterogeneous group of disorders of biomineralization resulting from failure of normal enamel formation. AI is found as an isolated entity or as part of a syndrome, and an autosomal-recessive syndrome associating AI and gingival hyperplasia was recently reported. Using whole-exome sequencing, we identified a homozygous nonsense mutation in exon 2 of FAM20A that was not present in the Single Nucleotide Polymorphism database (dbSNP), the 1000 Genomes database, or the Centre d'Etude du Polymorphisme Humain (CEPH) Diversity Panel. Expression analyses indicated that Fam20a is expressed in ameloblasts and gingivae, providing biological plausibility for mutations in FAM20A underlying the pathogenesis of this syndrome. PMID:21549343

O'Sullivan, James; Bitu, Carolina C; Daly, Sarah B; Urquhart, Jill E; Barron, Martin J; Bhaskar, Sanjeev S; Martelli-Júnior, Hercilio; dos Santos Neto, Pedro Eleuterio; Mansilla, Maria A; Murray, Jeffrey C; Coletta, Ricardo D; Black, Graeme C M; Dixon, Michael J

2011-05-05

131

Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice  

PubMed Central

Background Inflammation of the middle ear (otitis media) is very common and can lead to serious complications if not resolved. Genetic studies suggest an inherited component, but few of the genes that contribute to this condition are known. Mouse mutants have contributed significantly to the identification of genes predisposing to otitis media Results The dearisch mouse mutant is an ENU-induced mutant detected by its impaired Preyer reflex (ear flick in response to sound). Auditory brainstem responses revealed raised thresholds from as early as three weeks old. Pedigree analysis suggested a dominant but partially penetrant mode of inheritance. The middle ear of dearisch mutants shows a thickened mucosa and cellular effusion suggesting chronic otitis media with effusion with superimposed acute infection. The inner ear, including the sensory hair cells, appears normal. Due to the low penetrance of the phenotype, normal backcross mapping of the mutation was not possible. Exome sequencing was therefore employed to identify a non-conservative tyrosine to cysteine (Y71C) missense mutation in the Islet1 gene, Isl1Drsh. Isl1 is expressed in the normal middle ear mucosa. The findings suggest the Isl1Drshmutation is likely to predispose carriers to otitis media. Conclusions Dearisch, Isl1Drsh, represents the first point mutation in the mouse Isl1 gene and suggests a previously unrecognized role for this gene. It is also the first recorded exome sequencing of the C3HeB/FeJ background relevant to many ENU-induced mutants. Most importantly, the power of exome resequencing to identify ENU-induced mutations without a mapped gene locus is illustrated.

2011-01-01

132

Assessment of canine BEST1 variations identifies new mutations and establishes an independent bestrophinopathy model (cmr3)  

PubMed Central

Purpose Mutations in bestrophin 1 (BEST1) are associated with a group of retinal disorders known as bestrophinopathies in man and canine multifocal retinopathies (cmr) in the dog. To date, the dog is the only large animal model suitable for the complex characterization and in-depth studies of Best-related disorders. In the first report of cmr, the disease was described in a group of mastiff-related breeds (cmr1) and the Coton de Tulear (cmr2). Additional breeds, e.g., the Lapponian herder (LH) and others, subsequently were recognized with similar phenotypes, but linked loci are unknown. Analysis of the BEST1 gene aimed to identify mutations in these additional populations and extend our understanding of genotype–phenotype associations. Methods Animals were subjected to routine eye exams, phenotypically characterized, and samples were collected for molecular studies. Known BEST1 mutations were assessed, and the canine BEST1 coding exons were amplified and sequenced in selected individuals that exhibited a cmr compatible phenotype but that did not carry known mutations. Resulting sequence changes were genotyped in several different breeds and evaluated in the context of the phenotype. Results Seven novel coding variants were identified in exon 10 of cBEST1. Two linked mutations were associated with cmr exclusive to the LH breed (cmr3). Two individuals of Jämthund and Norfolk terrier breeds were heterozygous for two conservative changes, but these were unlikely to have disease-causing potential. Another three substitutions were found in the Bernese mountain dog that were predicted to have a deleterious effect on protein function. Previously reported mutations were excluded from segregation in these populations, but cmr1 was confirmed in another mastiff-related breed, the Italian cane corso. Conclusions A third independent canine model for human bestrophinopathies has been established in the LH breed. While exhibiting a phenotype comparable to cmr1 and cmr2, the novel cmr3 mutation is predicted to be based on a distinctly different molecular mechanism. So far cmr2 and cmr3 are exclusive to a single dog breed each. In contrast, cmr1 is found in multiple related breeds. Additional sequence alterations identified in exon 10 of cBEST1 in other breeds exhibit potential disease-causing features. The inherent genetic and phenotypic variation observed with retinal disorders in canines is complicated further by cmr3 being one of four distinct genetic retinal traits found to segregate in LH. Thus, a combination of phenotypic, molecular, and population analysis is required to establish a strong phenotype–genotype association. These results indicate that cmr has a larger impact on the general dog population than was initially suspected. The complexity of these models further confirms the similarity to human bestrophinopathies. Moreover, analyses of multiple canine models will provide additional insight into the molecular basis underlying diseases caused by mutations in BEST1.

Wickstrom, Kaisa; Slavik, Julianna; Lindauer, Sarah J.; Ahonen, Saija; Schelling, Claude; Lohi, Hannes; Guziewicz, Karina E.; Aguirre, Gustavo D.

2010-01-01

133

Analysis of 30 putative BRCA1 splicing mutations in hereditary breast and ovarian cancer families identifies exonic splice site mutations that escape in silico prediction.  

PubMed

Screening for pathogenic mutations in breast and ovarian cancer genes such as BRCA1/2, CHEK2 and RAD51C is common practice for individuals from high-risk families. However, test results may be ambiguous due to the presence of unclassified variants (UCV) in the concurrent absence of clearly cancer-predisposing mutations. Especially the presence of intronic or exonic variants within these genes that possibly affect proper pre-mRNA processing poses a challenge as their functional implications are not immediately apparent. Therefore, it appears necessary to characterize potential splicing UCV and to develop appropriate classification tools. We investigated 30 distinct BRCA1 variants, both intronic and exonic, regarding their spliceogenic potential by commonly used in silico prediction algorithms (HSF, MaxEntScan) along with in vitro transcript analyses. A total of 25 variants were identified spliceogenic, either causing/enhancing exon skipping or activation of cryptic splice sites, or both. Except from a single intronic variant causing minor effects on BRCA1 pre-mRNA processing in our analyses, 23 out of 24 intronic variants were correctly predicted by MaxEntScan, while HSF was less accurate in this cohort. Among the 6 exonic variants analyzed, 4 severely impair correct pre-mRNA processing, while the remaining two have partial effects. In contrast to the intronic alterations investigated, only half of the spliceogenic exonic variants were correctly predicted by HSF and/or MaxEntScan. These data support the idea that exonic splicing mutations are commonly disease-causing and concurrently prone to escape in silico prediction, hence necessitating experimental in vitro splicing analysis. PMID:23239986

Wappenschmidt, Barbara; Becker, Alexandra A; Hauke, Jan; Weber, Ute; Engert, Stefanie; Köhler, Juliane; Kast, Karin; Arnold, Norbert; Rhiem, Kerstin; Hahnen, Eric; Meindl, Alfons; Schmutzler, Rita K

2012-12-11

134

Analysis of 30 Putative BRCA1 Splicing Mutations in Hereditary Breast and Ovarian Cancer Families Identifies Exonic Splice Site Mutations That Escape In Silico Prediction  

PubMed Central

Screening for pathogenic mutations in breast and ovarian cancer genes such as BRCA1/2, CHEK2 and RAD51C is common practice for individuals from high-risk families. However, test results may be ambiguous due to the presence of unclassified variants (UCV) in the concurrent absence of clearly cancer-predisposing mutations. Especially the presence of intronic or exonic variants within these genes that possibly affect proper pre-mRNA processing poses a challenge as their functional implications are not immediately apparent. Therefore, it appears necessary to characterize potential splicing UCV and to develop appropriate classification tools. We investigated 30 distinct BRCA1 variants, both intronic and exonic, regarding their spliceogenic potential by commonly used in silico prediction algorithms (HSF, MaxEntScan) along with in vitro transcript analyses. A total of 25 variants were identified spliceogenic, either causing/enhancing exon skipping or activation of cryptic splice sites, or both. Except from a single intronic variant causing minor effects on BRCA1 pre-mRNA processing in our analyses, 23 out of 24 intronic variants were correctly predicted by MaxEntScan, while HSF was less accurate in this cohort. Among the 6 exonic variants analyzed, 4 severely impair correct pre-mRNA processing, while the remaining two have partial effects. In contrast to the intronic alterations investigated, only half of the spliceogenic exonic variants were correctly predicted by HSF and/or MaxEntScan. These data support the idea that exonic splicing mutations are commonly disease-causing and concurrently prone to escape in silico prediction, hence necessitating experimental in vitro splicing analysis.

Hauke, Jan; Weber, Ute; Engert, Stefanie; Kohler, Juliane; Kast, Karin; Arnold, Norbert; Rhiem, Kerstin; Hahnen, Eric; Meindl, Alfons; Schmutzler, Rita K.

2012-01-01

135

Whole-exome capture and sequencing identifies HEATR2 mutation as a cause of primary ciliary dyskinesia.  

PubMed

Motile cilia are essential components of the mucociliary escalator and are central to respiratory-tract host defenses. Abnormalities in these evolutionarily conserved organelles cause primary ciliary dyskinesia (PCD). Despite recent strides characterizing the ciliome and sensory ciliopathies through exploration of the phenotype-genotype associations in model organisms, the genetic bases of most cases of PCD remain elusive. We identified nine related subjects with PCD from geographically dispersed Amish communities and performed exome sequencing of two affected individuals and their unaffected parents. A single autosomal-recessive nonsynonymous missense mutation was identified in HEATR2, an uncharacterized gene that belongs to a family not previously associated with ciliary assembly or function. Airway epithelial cells isolated from PCD-affected individuals had markedly reduced HEATR2 levels, absent dynein arms, and loss of ciliary beating. MicroRNA-mediated silencing of the orthologous gene in Chlamydomonas reinhardtii resulted in absent outer dynein arms, reduced flagellar beat frequency, and decreased cell velocity. These findings were recapitulated by small hairpin RNA-mediated knockdown of HEATR2 in airway epithelial cells from unaffected donors. Moreover, immunohistochemistry studies in human airway epithelial cells showed that HEATR2 was localized to the cytoplasm and not in cilia, which suggests a role in either dynein arm transport or assembly. The identification of HEATR2 contributes to the growing number of genes associated with PCD identified in both individuals and model organisms and shows that exome sequencing in family studies facilitates the discovery of novel disease-causing gene mutations. PMID:23040496

Horani, Amjad; Druley, Todd E; Zariwala, Maimoona A; Patel, Anand C; Levinson, Benjamin T; Van Arendonk, Laura G; Thornton, Katherine C; Giacalone, Joe C; Albee, Alison J; Wilson, Kate S; Turner, Emily H; Nickerson, Deborah A; Shendure, Jay; Bayly, Philip V; Leigh, Margaret W; Knowles, Michael R; Brody, Steven L; Dutcher, Susan K; Ferkol, Thomas W

2012-10-01

136

Whole-Exome Capture and Sequencing Identifies HEATR2 Mutation as a Cause of Primary Ciliary Dyskinesia  

PubMed Central

Motile cilia are essential components of the mucociliary escalator and are central to respiratory-tract host defenses. Abnormalities in these evolutionarily conserved organelles cause primary ciliary dyskinesia (PCD). Despite recent strides characterizing the ciliome and sensory ciliopathies through exploration of the phenotype-genotype associations in model organisms, the genetic bases of most cases of PCD remain elusive. We identified nine related subjects with PCD from geographically dispersed Amish communities and performed exome sequencing of two affected individuals and their unaffected parents. A single autosomal-recessive nonsynonymous missense mutation was identified in HEATR2, an uncharacterized gene that belongs to a family not previously associated with ciliary assembly or function. Airway epithelial cells isolated from PCD-affected individuals had markedly reduced HEATR2 levels, absent dynein arms, and loss of ciliary beating. MicroRNA-mediated silencing of the orthologous gene in Chlamydomonas reinhardtii resulted in absent outer dynein arms, reduced flagellar beat frequency, and decreased cell velocity. These findings were recapitulated by small hairpin RNA-mediated knockdown of HEATR2 in airway epithelial cells from unaffected donors. Moreover, immunohistochemistry studies in human airway epithelial cells showed that HEATR2 was localized to the cytoplasm and not in cilia, which suggests a role in either dynein arm transport or assembly. The identification of HEATR2 contributes to the growing number of genes associated with PCD identified in both individuals and model organisms and shows that exome sequencing in family studies facilitates the discovery of novel disease-causing gene mutations.

Horani, Amjad; Druley, Todd E.; Zariwala, Maimoona A.; Patel, Anand C.; Levinson, Benjamin T.; Van Arendonk, Laura G.; Thornton, Katherine C.; Giacalone, Joe C.; Albee, Alison J.; Wilson, Kate S.; Turner, Emily H.; Nickerson, Deborah A.; Shendure, Jay; Bayly, Philip V.; Leigh, Margaret W.; Knowles, Michael R.; Brody, Steven L.; Dutcher, Susan K.; Ferkol, Thomas W.

2012-01-01

137

Splicing analysis of unclassified variants in COL2A1 and COL11A1 identifies deep intronic pathogenic mutations.  

PubMed

UK NHS diagnostic service sequence analysis of genes generally examines and reports on variations within a designated region 5' and 3' of each exon, typically 30 bp up and downstream. However, because of the degenerate nature of the splice sites, intronic variants outside the AG and GT dinucleotides of the acceptor and donor splice sites (ASS and DSS) are most often classified as being of unknown clinical significance, unless there is some functional evidence of their pathogenicity. It is now becoming clear that mutations deep within introns can also interfere with normal processing of pre-mRNA and result in pathogenic effects on the mature transcript. In diagnostic laboratories, these deep intronic variants most often fall outside of the regions analysed and so are rarely reported. With the likelihood that next generation sequencing will identify more of these unclassified variants, it will become important to perform additional studies to determine the pathogenicity of such sequence anomalies. Here, we analyse variants detected in either COL2A1 or COL11A1 in patients with Stickler syndrome. These have been analysed both in silico and functionally using either RNA isolated from the patient's cells or, more commonly, minigenes as splicing reporters. We show that deep intronic mutations are not a rare occurrence, including one variant that results in multiple transcripts, where both de novo donor and ASS are created by the mutation. Another variant produces transcripts that result in either haploinsufficiency or a dominant negative effect, potentially modifying the disease phenotype. PMID:22189268

Richards, Allan J; McNinch, Annie; Whittaker, Joanne; Treacy, Becky; Oakhill, Kim; Poulson, Arabella; Snead, Martin P

2011-12-21

138

Splicing analysis of unclassified variants in COL2A1 and COL11A1 identifies deep intronic pathogenic mutations  

PubMed Central

UK NHS diagnostic service sequence analysis of genes generally examines and reports on variations within a designated region 5? and 3? of each exon, typically 30?bp up and downstream. However, because of the degenerate nature of the splice sites, intronic variants outside the AG and GT dinucleotides of the acceptor and donor splice sites (ASS and DSS) are most often classified as being of unknown clinical significance, unless there is some functional evidence of their pathogenicity. It is now becoming clear that mutations deep within introns can also interfere with normal processing of pre-mRNA and result in pathogenic effects on the mature transcript. In diagnostic laboratories, these deep intronic variants most often fall outside of the regions analysed and so are rarely reported. With the likelihood that next generation sequencing will identify more of these unclassified variants, it will become important to perform additional studies to determine the pathogenicity of such sequence anomalies. Here, we analyse variants detected in either COL2A1 or COL11A1 in patients with Stickler syndrome. These have been analysed both in silico and functionally using either RNA isolated from the patient's cells or, more commonly, minigenes as splicing reporters. We show that deep intronic mutations are not a rare occurrence, including one variant that results in multiple transcripts, where both de novo donor and ASS are created by the mutation. Another variant produces transcripts that result in either haploinsufficiency or a dominant negative effect, potentially modifying the disease phenotype.

Richards, Allan J; McNinch, Annie; Whittaker, Joanne; Treacy, Becky; Oakhill, Kim; Poulson, Arabella; Snead, Martin P

2012-01-01

139

Gene expression profiling and candidate gene resequencing identifies pathways and mutations important for malignant transformation caused by leukemogenic fusion genes.  

PubMed

NUP98-HOXD13 (NHD13) and CALM-AF10 (CA10) are oncogenic fusion proteins produced by recurrent chromosomal translocations in patients with acute myeloid leukemia (AML). Transgenic mice that express these fusions develop AML with a long latency and incomplete penetrance, suggesting that collaborating genetic events are required for leukemic transformation. We employed genetic techniques to identify both preleukemic abnormalities in healthy transgenic mice as well as collaborating events leading to leukemic transformation. Candidate gene resequencing revealed that 6 of 27 (22%) CA10 AMLs spontaneously acquired a Ras pathway mutation and 8 of 27 (30%) acquired an Flt3 mutation. Two CA10 AMLs acquired an Flt3 internal-tandem duplication, demonstrating that these mutations can be acquired in murine as well as human AML. Gene expression profiles revealed a marked upregulation of Hox genes, particularly Hoxa5, Hoxa9, and Hoxa10 in both NHD13 and CA10 mice. Furthermore, mir196b, which is embedded within the Hoxa locus, was overexpressed in both CA10 and NHD13 samples. In contrast, the Hox cofactors Meis1 and Pbx3 were differentially expressed; Meis1 was increased in CA10 AMLs but not NHD13 AMLs, whereas Pbx3 was consistently increased in NHD13 but not CA10 AMLs. Silencing of Pbx3 in NHD13 cells led to decreased proliferation, increased apoptosis, and decreased colony formation in vitro, suggesting a previously unexpected role for Pbx3 in leukemic transformation. PMID:22885519

Novak, Rachel L; Harper, David P; Caudell, David; Slape, Christopher; Beachy, Sarah H; Aplan, Peter D

2012-08-08

140

Genetic Analysis of Saccharomyces Cerevisiae Chromosome I: On the Role of Mutagen Specificity in Delimiting the Set of Genes Identifiable Using Temperature-Sensitive-Lethal Mutations  

PubMed Central

In a previous attempt to identify as many as possible of the essential genes on Saccharomyces cerevisiae chromosome I, temperature-sensitive (Ts(-)) lethal mutations that had been induced by ethyl methanesulfonate or nitrosoguanidine were analyzed. Thirty-two independently isolated mutations that mapped to chromosome I identified only three complementation groups, all of which had been known previously. In contrast, molecular analyses of segments of the chromosome have suggested the presence of numerous additional essential genes. In order to assess the degree to which problems of mutagen specificity had limited the set of genes detected using Ts(-) lethal mutations, we isolated a new set of such mutations after mutagenesis with UV or nitrogen mustard. Surprisingly, of 21 independently isolated mutations that mapped to chromosome I, 17 were again in the same three complementation groups as identified previously, and two of the remaining four mutations were apparently in a known gene involved in cysteine biosynthesis. Of the remaining two mutations, one was in one of the essential genes identified in the molecular analyses, and the other was too leaky to be mapped. These results suggest that only a minority of the essential genes in yeast can be identified using Ts(-) lethal mutations, regardless of the mutagen used, and thus emphasize the need to use multiple genetic strategies in the investigation of cellular processes.

Harris, S. D.; Pringle, J. R.

1991-01-01

141

Genetic analysis of Saccharomyces cerevisiae chromosome I: On the role of mutagen specificity in delimiting the set of genes identifiable using temperature-sensitive-lethal mutations  

SciTech Connect

In a previous attempt to identify as many as possible of the essential genes on Saccharomyces cerevisiae chromosome I, temperature-sensitive (Ts-) lethal mutations that had been induced by ethyl methane-sulfonate or nitrosoguanidine were analyzed. Thirty-two independently isolated mutations that mapped to chromosome I identified only three complementation groups, all of which had been known previously. In contrast, molecular analyses of segments of the chromosome have suggested the presence of numerous additional essential genes. In order to assess the degree to which problems of mutagen specificity had limited the set of genes detected using Ts- lethal mutations, we isolated a new set of such mutations after mutagenesis with UV or nitrogen mustard. Surprisingly, of 21 independently isolated mutations that mapped to chromosome I, 17 were again in the same three complementation groups as identified previously, and two of the remaining four mutations were apparently in a known gene involved in cysteine biosynthesis. Of the remaining two mutations, one was in one of the essential genes identified in the molecular analyses, and the other was too leaky to be mapped. These results suggest that only a minority of the essential genes in yeast can be identified using Ts- lethal mutations, regardless of the mutagen used, and thus emphasize the need to use multiple genetic strategies in the investigation of cellular processes.

Harris, S.D.; Pringle, J.R. (Univ. of Michigan, Ann Arbor (USA))

1991-02-01

142

Identifying potential pitfalls in interpreting mitochondrial DNA mutations of male infertility cases  

PubMed Central

Background & objectives: Recently, a significantly higher ratio of nucleotide changes in the mtDNA genes: COII, ATPase 6, ATPase 8, ND2, ND3, ND4, and ND5 was reported in spermatozoa from populations of infertile Indian men, compared suggesting that screening for mtDNA mutations could provide insight into the aetiology of male infertility. In this study, we examined the published data and found serious errors in the original acquisition and analysis of the data. Methods: The mtDNA data associated with male infertility in Indian populations were retrieved from the published sources. The mtDNA substitution values of infertile and control groups were evaluated using phylogenetic methods and previously published mtDNA phylogenies. Results: Most of the mtDNA polymorphisms reported as significantly correlated with infertility were more commonly found in general populations. Further, our analysis showed that some of the mtDNA substitutions were erroneously overestimated in the infertile groups and underestimated in the control groups, and vice-versa. Interpretation & conclusions: Contrary to earlier claims, our analysis demonstrated no significant association between the mtDNA polymorphisms and male infertility in these studies. Further, these errors in the published data impune the usefulness of mitochondrial molecular analyses in male infertility diagnosis.

Palanichamy, Malliya Gounder; Zhang, Ya-Ping

2011-01-01

143

New Mutations in Chronic Lymphocytic Leukemia Identified by Target Enrichment and Deep Sequencing  

Microsoft Academic Search

Chronic lymphocytic leukemia (CLL) is a heterogeneous disease without a well-defined genetic alteration responsible for the onset of the disease. Several lines of evidence coincide in identifying stimulatory and growth signals delivered by B-cell receptor (BCR), and co-receptors together with NFkB pathway, as being the driving force in B-cell survival in CLL. However, the molecular mechanism responsible for this activation

Elena Doménech; Gonzalo Gómez-López; Daniel Gzlez-Peña; Mar López; Beatriz Herreros; Juliane Menezes; Natalia Gómez-Lozano; Angel Carro; Osvaldo Graña; David G. Pisano; Orlando Domínguez; José A. García-Marco; Miguel A. Piris; Margarita Sánchez-Beato

2012-01-01

144

Transcriptional Profile Analysis of RPGRORF15 Frameshift Mutation Identifies Novel Genes Associated with Retinal Degeneration  

PubMed Central

Purpose. To identify genes and molecular mechanisms associated with photoreceptor degeneration in a canine model of XLRP caused by an RPGR exon ORF15 microdeletion. Methods. Expression profiles of mutant and normal retinas were compared by using canine retinal custom cDNA microarrays. qRT-PCR, Western blot analysis, and immunohistochemistry (IHC) were applied to selected genes, to confirm and expand the microarray results. Results. At 7 and 16 weeks, respectively, 56 and 18 transcripts were downregulated in the mutant retinas, but none were differentially expressed (DE) at both ages, suggesting the involvement of temporally distinct pathways. Downregulated genes included the known retina-relevant genes PAX6, CHML, and RDH11 at 7 weeks and CRX and SAG at 16 weeks. Genes directly or indirectly active in apoptotic processes were altered at 7 weeks (CAMK2G, NTRK2, PRKCB, RALA, RBBP6, RNF41, SMYD3, SPP1, and TUBB2C) and 16 weeks (SLC25A5 and NKAP). Furthermore, the DE genes at 7 weeks (ELOVL6, GLOD4, NDUFS4, and REEP1) and 16 weeks (SLC25A5 and TARS2) are related to mitochondrial functions. qRT-PCR of 18 genes confirmed the microarray results and showed DE of additional genes not on the array. Only GFAP was DE at 3 weeks of age. Western blot and IHC analyses also confirmed the high reliability of the transcriptomic data. Conclusions. Several DE genes were identified in mutant retinas. At 7 weeks, a combination of nonclassic anti- and proapoptosis genes appear to be involved in photoreceptor degeneration, whereas at both 7 and 16 weeks, the expression of mitochondria-related genes indicates that they may play a relevant role in the disease process.

Genini, Sem; Zangerl, Barbara; Slavik, Julianna; Acland, Gregory M.; Beltran, William A.

2010-01-01

145

A novel high-throughput in vivo molecular screen for shade avoidance mutants identifies a novel phyA mutation  

PubMed Central

The shade avoidance syndrome (SAS) allows plants to anticipate and avoid shading by neighbouring plants by initiating an elongation growth response. The phytochrome photoreceptors are able to detect a reduction in the red:far red ratio in incident light, the result of selective absorption of red and blue wavelengths by proximal vegetation. A shade-responsive luciferase reporter line (PHYB::LUC) was used to carry out a high-throughput screen to identify novel SAS mutants. The dracula 1 (dra1) mutant, that showed no avoidance of shade for the PHYB::LUC response, was the result of a mutation in the PHYA gene. Like previously characterized phyA mutants, dra1 showed a long hypocotyl in far red light and an enhanced hypocotyl elongation response to shade. However, dra1 additionally showed a long hypocotyl in red light. Since phyB levels are relatively unaffected in dra1, this gain-of-function red light phenotype strongly suggests a disruption of phyB signalling. The dra1 mutation, G773E within the phyA PAS2 domain, occurs at a residue absolutely conserved among phyA sequences. The equivalent residue in phyB is absolutely conserved as a threonine. PAS domains are structurally conserved domains involved in molecular interaction. Structural modelling of the dra1 mutation within the phyA PAS2 domain shows some similarity with the structure of the phyB PAS2 domain, suggesting that the interference with phyB signalling may be the result of non-functional mimicry. Hence, it was hypothesized that this PAS2 residue forms a key distinction between the phyA and phyB phytochrome species.

Roig-Villanova, Irma; Khan, Safina; Shanahan, Hugh; Quail, Peter H.; Martinez-Garcia, Jaime F.; Devlin, Paul F.

2011-01-01

146

Mutations Affecting Internal TEA Blockade Identify the Probable Pore-Forming Region of a K^+ Channel  

NASA Astrophysics Data System (ADS)

The active site of voltage-activated potassium channels is a transmembrane aqueous pore that permits ions to permeate the cell membrane in a rapid yet highly selective manner. A useful probe for the pore of potassium-selective channels is the organic ion tetraethylammonium (TEA), which binds with millimolar affinity to the intracellular opening of the pore and blocks potassium current. In the potassium channel encoded by the Drosophila Shaker gene, an amino acid residue that specifically affects the affinity for intracellular TEA has now been identified by site-directed mutagenesis. This residue is in the middle of a conserved stretch of 18 amino acids that separates two locations that are both near the external opening of the pore. These findings suggest that this conserved region is intimately involved in the formation of the ion conduction pore of voltage-activated potassium channels. Further, a stretch of only eight amino acid residues must traverse 80 percent of the transmembrane electric potential difference.

Yellen, Gary; Jurman, Mark E.; Abramson, Tatiana; MacKinnon, Roderick

1991-02-01

147

TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation  

PubMed Central

Background The TM4SF10 gene encodes a putative four-transmembrane domains protein of unknown function termed Brain Cell Membrane Protein 1 (BCMP1), and is abundantly expressed in the brain. This gene is located on the short arm of human chromosome X at p21.1. The hypothesis that mutations in the TM4SF10 gene are associated with impaired brain function was investigated by sequencing the gene in individuals with hereditary X-linked mental retardation (XLMR). Methods The coding region (543 bp) of TM4SF10, including intronic junctions, and the long 3' untranslated region (3 233 bp), that has been conserved during evolution, were sequenced in 16 male XLMR patients from 14 unrelated families with definite, or suggestive, linkage to the TM4SF10 gene locus, and in 5 normal males. Results Five sequence changes were identified but none was found to be associated with the disease. Two of these changes correspond to previously known SNPs, while three other were novel SNPs in the TM4SF10 gene. Conclusion We have investigated the majority of the known MRX families linked to the TM4SF10 gene region. In the absence of mutations detected, our study indicates that alterations of TM4SF10 are not a frequent cause of XLMR.

Christophe-Hobertus, Christiane; Kooy, Frank; Gecz, Jozef; Abramowicz, Marc J; Holinski-Feder, Elke; Schwartz, Charles; Christophe, Daniel

2004-01-01

148

Genes that control the fidelity of endoplasmic reticulum to Golgi transport identified as suppressors of vesicle budding mutations.  

PubMed Central

Although convergent evidence suggests that proteins destined for export from the endoplasmic reticulum (ER) are separated from resident ER proteins and are concentrated into transport vesicles, the proteins that regulate this process have remained largely unknown. In a screen for suppressors of mutations in the essential COPII gene SEC13, we identified three genes (BST1, BST2/EMP24, and BST3) that negatively regulate COPII vesicle formation, preventing the production of vesicles with defective or missing subunits. Mutations in these genes slow the secretion of some secretory proteins and cause the resident ER proteins Kar2p and Pdi1p to leak more rapidly from the ER, indicating that these genes are also required for proper discrimination between resident ER proteins and Golgi-bound cargo molecules. The BST1 and BST2/EMP24 genes code for integral membrane proteins that reside predominantly in the ER. Our data suggest that the BST gene products represent a novel class of ER proteins that link the regulation of vesicle coat assembly to cargo sorting. Images

Elrod-Erickson, M J; Kaiser, C A

1996-01-01

149

Mutational analysis of Polycomb genes in solid tumours identifies PHC3 amplification as a possible cancer-driving genetic alteration.  

PubMed

Background:Polycomb group genes (PcGs) are epigenetic effectors implicated in most cancer hallmarks. The mutational status of all PcGs has never been systematically assessed in solid tumours.Methods:We conducted a multi-step analysis on publically available databases and patient samples to identify somatic aberrations of PcGs.Results:Data from more than 1000 cancer patients show for the first time that the PcG member PHC3 is amplified in three epithelial neoplasms (rate: 8-35%). This aberration predicts poorer prognosis in lung and uterine carcinomas (P<0.01). Gene amplification correlates with mRNA overexpression (P<0.01), suggesting a functional role of this aberration.Conclusion:PHC3 amplification may emerge as a biomarker and potential therapeutic target in a relevant fraction of epithelial tumours. PMID:23942079

Crea, F; Sun, L; Pikor, L; Frumento, P; Lam, W L; Helgason, C D

2013-08-13

150

Currarino syndrome with pelvic neuroendocrine tumor diagnosed by post-mortem genetic analysis of tissue specimens.  

PubMed

Currarino syndrome (CS) is an autosomal dominant disorder of embryonic development characterized by the triad of anorectal abnormalities, partial sacral agenesis, and presacral mass. Mutations of the HLXB9 gene have been identified in most CS cases, but a precise genotype-phenotype correlation has not been described so far. We report the clinical case of a 44-year-old Caucasian woman with malignant neuroendocrine transformation of a pre-sacrococcygeal mass combined with bicornuate uterus, dermoid cyst of the ovaries, and chronic constipation. After the patient died, a sacrococcygeal malformation and anterior meningocele were diagnosed in her 22-year-old son. CS diagnosis was then retrospectively confirmed by molecular analysis of normal and pathological tissue specimens of the mother, with identification of a HLXB9 mutation (c.727C>T; p.R243W). CS should be considered, and genetic counseling recommended, to all patients with presacral masses. Since malignant neuroendocrine transformation of presacral mass in CS is a possible complication, even thought rare, close follow up in these patients is advisable. PMID:21915987

Ciotti, Paola; Mandich, Paola; Bellone, Emilia; Ceppa, Paola; Bovio, Marta; Ameri, Pietro; Torre, Giancarlo; Fiocca, Roberto; Murialdo, Giovanni

2011-09-13

151

Autosomal Dominant Familial Dyskinesia and Facial Myokymia: Single Exome Sequencing Identifies a Mutation in Adenylate Cyclase 5  

PubMed Central

Background Familial dyskinesia with facial myokymia (FDFM) is an autosomal dominant disorder that is exacerbated by anxiety. In a five-generation family of German ancestry we previously mapped FDFM to chromosome 3p21-3q21. The 72.5 Mbp linkage region was too large for traditional positional mutation identification. Objective To identify the gene responsible for FDFM by exome resequencing of a single affected individual. Design, Setting and Participants We performed whole exome sequencing in one affected individual and used a series of bioinformatic filters, including functional significance and presence in dbSNP or 1000 Genomes project, to reduce the number of candidate variants. Co-segregation analysis was performed in 15 additional individuals in three generations. Results The exome contained 23428 single nucleotide variants, of which 9391 were missense, nonsense or splice site alterations. The critical region contained 323 variants, five of which were not present in one of the sequence-databases. Adenylate cyclase 5 (ADCY5) was the only gene in which the variant (c.2176G>A) was co-transmitted perfectly with disease status and was not present in 3510 control Caucasian exomes. This residue is highly conserved and the change is nonconservative and predicted to be damaging. Conclusions ADCY5 is highly expressed in striatum. Mice deficient in Adcy5 develop a movement disorder that is worsened by stress. We conclude that FDFM likely results from a missense mutation in ADCY5. This study demonstrates the power of a single exome sequence in combination with linkage information to identify causative genes for rare autosomal dominant Mendelian diseases.

Chen, Ying-Zhang; Matsushita, Mark M.; Robertson, Peggy; Rieder, Mark; Girirajan, Santhosh; Antonacci, Francesca; Lipe, Hillary; Eichler, Evan E.; Nickerson, Deborah A.; Bird, Thomas D.; Raskind, Wendy H.

2012-01-01

152

Whole Exome Sequencing Identifies a Causal RBM20 Mutation in a Large Pedigree With Familial Dilated Cardiomyopathy.  

PubMed

Background- Whole exome sequencing is a powerful technique for Mendelian disease gene discovery. However, variant prioritization remains a challenge. We applied whole exome sequencing to identify the causal variant in a large family with familial dilated cardiomyopathy of unknown pathogenesis. Methods and Results- A large family with autosomal dominant, familial dilated cardiomyopathy was identified. Exome capture and sequencing were performed in 3 remotely related, affected subjects predicted to share <0.1% of their genomes by descent. Shared variants were filtered for rarity, evolutionary conservation, and predicted functional significance, and remaining variants were filtered against 71 locally generated exomes. Variants were also prioritized using the Variant Annotation Analysis and Search Tool. Final candidates were validated by Sanger sequencing and tested for segregation. There were 664 shared heterozygous nonsense, missense, or splice site variants, of which 26 were rare (minor allele frequency ?0.001 or not reported) in 2 public databases. Filtering against internal exomes reduced the number of candidates to 2, and of these, a single variant (c.1907 G>A) in RBM20, segregated with disease status and was absent in unaffected internal reference exomes. Bioinformatic prioritization with Variant Annotation Analysis and Search Tool supported this result. Conclusions- Whole exome sequencing of remotely related dilated cardiomyopathy subjects from a large, multiplex family, followed by systematic filtering, identified a causal RBM20 mutation without the need for linkage analysis. PMID:23861363

Wells, Quinn S; Becker, Jason R; Su, Yan R; Mosley, Jonathan D; Weeke, Peter; D'Aoust, Laura; Ausborn, Natalie L; Ramirez, Andrea H; Pfotenhauer, Jean P; Naftilan, Allen J; Markham, Larry; Exil, Vernat; Roden, Dan M; Hong, Charles C

2013-07-16

153

Driver mutations among never smoking female lung cancer tissues in China identify unique EGFR and KRAS mutation pattern associated with household coal burning.  

PubMed

Lung cancer in never smokers, which has been partially attributed to household solid fuel use (i.e., coal), is etiologically and clinically different from lung cancer attributed to tobacco smoking. To explore the spectrum of driver mutations among lung cancer tissues from never smokers, specifically in a population where high lung cancer rates have been attributed to indoor air pollution from domestic coal use, multiplexed assays were used to detect >40 point mutations, insertions, and deletions (EGFR, KRAS, BRAF, HER2, NRAS, PIK3CA, MEK1, AKT1, and PTEN) among the lung tumors of confirmed never smoking females from Xuanwei, China [32 adenocarcinomas (ADCs), 7 squamous cell carcinomas (SCCs), 1 adenosquamous carcinoma (ADSC)]. EGFR mutations were detected in 35% of tumors. 46% of these involved EGFR exon 18 G719X, while 14% were exon 21 L858R mutations. KRAS mutations, all of which were G12C_34G>T, were observed in 15% of tumors. EGFR and KRAS mutations were mutually exclusive, and no mutations were observed in the other tested genes. Most point mutations were transversions and were also found in tumors from patients who used coal in their homes. Our high mutation frequencies in EGFR exon 18 and KRAS and low mutation frequency in EGFR exon 21 are strikingly divergent from those in other smoking and never smoking populations from Asia. Given that our subjects live in a region where coal is typically burned indoors, our findings provide new insights into the pathogenesis of lung cancer among never smoking females exposed to indoor air pollution from coal. PMID:24055406

Hosgood, H Dean; Pao, William; Rothman, Nathaniel; Hu, Wei; Pan, Yumei Helen; Kuchinsky, Kyle; Jones, Kirk D; Xu, Jun; Vermeulen, Roel; Simko, Jeff; Lan, Qing

2013-09-03

154

ASXL1 mutations identify a high-risk subgroup of older patients with primary cytogenetically normal AML within the ELN Favorable genetic category  

PubMed Central

The associations of mutations in the enhancer of trithorax and polycomb family gene ASXL1 with pretreatment patient characteristics, outcomes, and gene-/microRNA-expression profiles in primary cytogenetically normal acute myeloid leukemia (CN-AML) are unknown. We analyzed 423 adult patients for ASXL1 mutations, other prognostic gene mutations, and gene-/microRNA-expression profiles. ASXL1 mutations were 5 times more common in older (? 60 years) patients (16.2%) than those younger than 60 years (3.2%; P < .001). Among older patients, ASXL1 mutations associated with wild-type NPM1 (P < .001), absence of FLT3-internal tandem duplications (P = .002), mutated CEBPA (P = .01), and with inferior complete remission (CR) rate (P = .04), disease-free survival (DFS; P = .03), overall survival (OS; P = .006), and event-free survival (EFS; P = .002). Within the European LeukemiaNet (ELN) genetic categories of older CN-AML, ASXL1 mutations associated with inferior CR rate (P = .02), OS (P < .001), and EFS (P < .001) among ELN Favorable, but not among ELN Intermediate-I patients. Multivariable analyses confirmed associations of ASXL1 mutations with unfavorable CR rate (P = .03), DFS (P < .001), OS (P < .001), and EFS (P < .001) among ELN Favorable patients. We identified an ASXL1 mutation-associated gene-expression signature, but no microRNA-expression signature. This first study of ASXL1 mutations in primary CN-AML demonstrates that ASXL1mutated older patients, particularly within the ELN Favorable group, have unfavorable outcomes and may be candidates for experimental treatment approaches.

Metzeler, Klaus H.; Becker, Heiko; Maharry, Kati; Radmacher, Michael D.; Kohlschmidt, Jessica; Mrozek, Krzysztof; Nicolet, Deedra; Whitman, Susan P.; Wu, Yue-Zhong; Schwind, Sebastian; Powell, Bayard L.; Carter, Thomas H.; Wetzler, Meir; Moore, Joseph O.; Kolitz, Jonathan E.; Baer, Maria R.; Carroll, Andrew J.; Larson, Richard A.; Caligiuri, Michael A.; Marcucci, Guido

2011-01-01

155

Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum  

PubMed Central

Background The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistance can also assist in identifying the mode of action of uncharacterized but potent antimalarial compounds identified in high-throughput chemical screening campaigns against Plasmodium falciparum. Results Here we show that tiling microarrays can detect de novo a large proportion of the genetic changes that differentiate one genome from another. We show that we detect most single nucleotide polymorphisms or small insertion deletion events and all known copy number variations that distinguish three laboratory isolates using readily accessible methods. We used the approach to discover mutations that occur during the selection process after transfection. We also elucidated a mechanism by which parasites acquire resistance to the antimalarial fosmidomycin, which targets the parasite isoprenoid synthesis pathway. Our microarray-based approach allowed us to attribute in vitro derived fosmidomycin resistance to a copy number variation event in the pfdxr gene, which enables the parasite to overcome fosmidomycin-mediated inhibition of isoprenoid biosynthesis. Conclusions We show that newly emerged single nucleotide polymorphisms can readily be detected and that malaria parasites can rapidly acquire gene amplifications in response to in vitro drug pressure. The ability to define comprehensively genetic variability in P. falciparum with a single overnight hybridization creates new opportunities to study parasite evolution and improve the treatment and control of malaria.

Dharia, Neekesh V; Sidhu, Amar Bir Singh; Cassera, Maria Belen; Westenberger, Scott J; Bopp, Selina ER; Eastman, Rich T; Plouffe, David; Batalov, Serge; Park, Daniel J; Volkman, Sarah K; Wirth, Dyann F; Zhou, Yingyao; Fidock, David A; Winzeler, Elizabeth A

2009-01-01

156

Whole-exome sequencing identifies MYO15A mutations as a cause of autosomal recessive nonsyndromic hearing loss in Korean families  

PubMed Central

Background The genetic heterogeneity of hearing loss makes genetic diagnosis expensive and time consuming using available methods. Whole-exome sequencing has recently been introduced as an alternative approach to identifying causative mutations in Mendelian disorders. Methods To identify the hidden mutations that cause autosomal recessive nonsyndromic hearing loss (ARNSHL), we performed whole-exome sequencing of 13 unrelated Korean small families with ARNSHL who were negative for GJB2 or SLC26A4 mutations. Results We found two novel compound heterozygous mutations, IVS11?+?1 and p.R2146Q, of MYO15A in one (SR903 family) of the 13 families with ARNSHL. In addition to these causative mutations, 13 nonsynonymous variants, including variants with uncertain pathogenicity (SR285 family), were identified in the coding exons of MYO15A from Korean exomes. Conclusion This is the first report of MYO15A mutations in an East Asian population. We suggest that close attention should be paid to this gene when performing genetic testing of patients with hearing loss in East Asia. The present results also indicate that whole-exome sequencing is a valuable method for comprehensive medical diagnosis of a genetically heterogeneous recessive disease, especially in small-sized families.

2013-01-01

157

Population-based risk estimates of Wilms tumor in sporadic aniridia. A comprehensive mutation screening procedure of PAX6 identifies 80% of mutations in aniridia.  

PubMed

Aniridia is a severe eye disease characterized by iris hypoplasia; both sporadic cases and familial cases with an autosomal dominant inheritance exist. Mutations in the PAX6 gene have been shown to be the genetic cause of the disease. Some of the sporadic cases are caused by large chromosomal deletions, some of which also include the Wilms tumor gene (WAGR syndrome), resulting in an increased risk of developing Wilms tumor. Based on the unique registration of both cancer and aniridia cases in Denmark, we have made the most accurate risk estimate to date for Wilms tumor in sporadic aniridia. We have found that patients with sporadic aniridia have a relative risk of 67 (confidence interval: 8.1-241) of developing Wilms tumor. Among patients investigated for mutations, Wilms tumor developed in only two patients out of 5 with the Wilms tumor gene (WT1) deleted. None of the patients with smaller chromosomal deletions or intragenic mutations were found to develop Wilms tumor. Our observations suggest a smaller risk for Wilms tumor than previous estimates, and that tumor development requires deletion of WT1. We report a strategy for the mutational analysis of aniridia cases resulting in the detection of mutations in 68% of sporadic cases and 89% of familial cases. We also report four novel mutations in PAX6, and furthermore, we have discovered a new alternatively spliced form of PAX6. PMID:11479730

Grønskov, K; Olsen, J H; Sand, A; Pedersen, W; Carlsen, N; Bak Jylling, A M; Lyngbye, T; Brøndum-Nielsen, K; Rosenberg, T

2001-07-01

158

DFNA8/12 Caused by TECTA Mutations is the Most Identified Subtype of Non-syndromic Autosomal Dominant Hearing Loss  

PubMed Central

The prevalence of DFNA8/DFNA12 (DFNA8/12), a type of autosomal dominant non-syndromic hearing loss (ADNSHL), is unknown as comprehensive population-based genetic screening has not been conducted. We therefore completed unbiased screening for TECTA mutations in a Spanish cohort of 372 probands from ADNSHL families. Three additional families (Spanish, Belgian and English) known to be linked to DFNA8/12 were also included in the screening. In an additional cohort of 835 American ADNSHL families, we preselected 73 probands for TECTA screening based on audiometric data. In aggregate, we identified 23 TECTA mutations in this process. Remarkably 20 of these mutations are novel, more than doubling the number of reported TECTA ADNSHL mutations from 13 to 33. Mutations lie in all domains of the ?-tectorin protein, including those for the first time identified in the entactin domain, the vWFD1, vWFD2 and vWFD3 repeats, and the D1-D2 and TIL2 connectors. While the majority are private mutations, four of them – p.Cys1036Tyr, p.Cys1837Gly, p.Thr1866Met and p.Arg1890Cys – were observed in more than one unrelated family. For two of these mutations founder effects were also confirmed. Our data validate previously observed genotype-phenotype correlations in DFNA8/12 and introduce new correlations. Specifically, mutations in the N-terminal region of ?-tectorin (entactin domain, vWFD1 and vWFD2) lead to mid frequency NSHL, a phenotype previously associated only with mutations in the ZP domain. Collectively, our results indicate that DFNA8/12 hearing loss is a frequent type of ADNSHL.

Hildebrand, Michael S.; Morin, Matias; Meyer, Nicole C.; Mayo, Fernando; Modamio-Hoybjor, Silvia; Mencia, Angeles; Olavarrieta, Leticia; Morales-Angulo, Carmelo; Nishimura, Carla J.; Workman, Heather; DeLuca, Adam P.; del Castillo, Ignacio; Taylor, Kyle R.; Tompkins, Bruce; Goodman, Corey W.; Schrauwen, Isabelle; Van Wesemael, Maarten; Lachlan, K.; Shearer, A. Eliot; Braun, Terry A.; Huygen, Patrick L.M.; Kremer, Hannie; Van Camp, Guy; Moreno, Felipe; Casavant, Thomas L.; Smith, Richard J.H.; Moreno-Pelayo, Miguel A.

2012-01-01

159

A Genetic Screen for Suppressors of a Mutated 5' Splice Site Identifies Factors Associated With Later Steps of Spliceosome Assembly  

Microsoft Academic Search

Many alleles of human disease genes have mutations within splicing consensus sequences that activate cryptic splice sites. In Caenorhabditis elegans, the unc-73(e936) allele has a G-to-U mutation at the first base of the intron downstream of exon 15, which results in an uncoordinated phenotype. This mutation triggers cryptic splicing at the ? 1 and 123 positions and retains some residual

MaryAnn Dassah; Sophie Patzek; Valerie M. Hunt; Pedro E. Medina; Alan M. Zahler

2009-01-01

160

An ENU Mutagenesis Screen in Zebrafish for Visual System Mutants Identifies a Novel Splice-Acceptor Site Mutation in patched2 that Results in Colobomas  

PubMed Central

Purpose. To identify recessive mutations affecting development and/or maintenance of the zebrafish visual system. Methods. A three-generation ENU (N-Nitroso-N-ethylurea)-based forward genetic screen was performed. F3 embryos were screened visually from 1 to 5 days postfertilization (dpf) for ocular abnormalities, and 5 dpf embryos were fixed and processed for cryosectioning, after which eye sections were screened for defects in cellular organization within the retina, lens, and cornea. A combination of PCR and DNA sequencing, in situ hybridization, and pharmacological treatments were used to clone and characterize a coloboma mutant. Results. A total of 126 F2 families were screened, and, from these, 18 recessive mutations were identified that affected eye development. Phenotypes included lens malformations and cataracts, photoreceptor defects, oculocutaneous albinism, microphthalmia, and colobomas. Analysis of one such coloboma mutant, uta1, identified a splice-acceptor mutation in the patched2 gene that resulted in an in-frame deletion of 19 amino acids that are predicted to contribute to the first extracellular loop of Patched2. ptch2uta1 mutants possessed elevated Hedgehog (Hh) pathway activity, and blocking the Hh pathway with cyclopamine prevented colobomas in ptch2uta1 mutant embryos. Conclusions. We have identified 18 recessive mutations affecting development of the zebrafish visual system and we have characterized a novel splice-acceptor site mutation in patched2 that results in enhanced Hh pathway activity and colobomas.

Lee, Jiwoon; Cox, Ben D.; Daly, Christina M. S.; Lee, Chanjae; Nuckels, Richard J.; Tittle, Rachel K.; Uribe, Rosa A.; Gross, Jeffrey M.

2012-01-01

161

Genetic analysis of wild-isolated Neurospora crassa strains identified as dominant suppressors of repeat-induced point mutation.  

PubMed Central

Repeat-induced point mutation (RIP) in Neurospora results in inactivation of duplicated DNA sequences. RIP is thought to provide protection against foreign elements such as retrotransposons, only one of which has been found in N. crassa. To examine the role of RIP in nature, we have examined seven N. crassa strains, identified among 446 wild isolates scored for dominant suppression of RIP. The test system involved a small duplication that targets RIP to the easily scorable gene erg-3. We previously showed that RIP in a small duplication is suppressed if another, larger duplication is present in the cross, as expected if the large duplication competes for the RIP machinery. In two of the strains, RIP suppression was associated with a barren phenotype--a characteristic of Neurospora duplications that is thought to result in part from a gene-silencing process called meiotic silencing by unpaired DNA (MSUD). A suppressor of MSUD (Sad-1) was shown not to prevent known large duplications from impairing RIP. Single-gene duplications also can be barren but are too short to suppress RIP. RIP suppression in strains that were not barren showed inheritance that was either simple Mendelian or complex. Adding copies of the LINE-like retrotransposon Tad did not affect RIP efficiency.

Bhat, Ashwin; Noubissi, Felicite K; Vyas, Meenal; Kasbekar, Durgadas P

2003-01-01

162

Functional analysis of non-hotspot AKT1 mutants found in human breast cancers identifies novel driver mutations: implications for personalized medicine  

PubMed Central

The phosphatidylinositol 3-kinase (PI3-kinase)-Akt-mTOR pathway is mutated at high frequency in human breast cancer, and this pathway is the focus of active drug discovery and clinical investigation. Trials of personalized cancer therapy seek to leverage knowledge of cancer gene mutations by using mutations to guide the choice of targeted therapies. At the same time, cancer genome sequencing studies are identifying low frequency variants of unknown significance in known cancer genes, as well as genes of unknown function. We have performed functional analysis of six non-hotspot AKT1 pleckstrin homology domain mutants identified in recent large-scale breast cancer sequencing studies. Three of these mutants cause constitutive activation of Akt1 in the absence of growth factors, leading to phosphorylation of downstream target proteins. Like the hotspot E17K mutation, these mutants confer constitutive membrane localization of Akt1. Finally, the same three mutants showed oncogenic activity in a cellular transformation assay. The other three mutants were inactive in all assays. These findings validate novel driver mutations in AKT1, and extend the number and type of mutations that activate the PI3-kinase pathway in human breast cancers.

Yi, Kyung H.; Axtmayer, Jossette; Gustin, John P.; Rajpurohit, Anandita; Lauring, Josh

2013-01-01

163

Functional analysis of non-hotspot AKT1 mutants found in human breast cancers identifies novel driver mutations: implications for personalized medicine.  

PubMed

The phosphatidylinositol 3-kinase (PI3-kinase)-Akt-mTOR pathway is mutated at high frequency in human breast cancer, and this pathway is the focus of active drug discovery and clinical investigation. Trials of personalized cancer therapy seek to leverage knowledge of cancer gene mutations by using mutations to guide the choice of targeted therapies. At the same time, cancer genome sequencing studies are identifying low frequency variants of unknown significance in known cancer genes, as well as genes of unknown function. We have performed functional analysis of six non-hotspot AKT1 pleckstrin homology domain mutants identified in recent large-scale breast cancer sequencing studies. Three of these mutants cause constitutive activation of Akt1 in the absence of growth factors, leading to phosphorylation of downstream target proteins. Like the hotspot E17K mutation, these mutants confer constitutive membrane localization of Akt1. Finally, the same three mutants showed oncogenic activity in a cellular transformation assay. The other three mutants were inactive in all assays. These findings validate novel driver mutations in AKT1, and extend the number and type of mutations that activate the PI3-kinase pathway in human breast cancers. PMID:23237847

Yi, Kyung H; Axtmayer, Jossette; Gustin, John P; Rajpurohit, Anandita; Lauring, Josh

2013-01-01

164

Whole genome re-sequencing identifies a mutation in an ABC transporter (mdr2) in a Plasmodium chabaudi clone with altered susceptibility to antifolate drugs?  

PubMed Central

In malaria parasites, mutations in two genes of folate biosynthesis encoding dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps) modify responses to antifolate therapies which target these enzymes. However, the involvement of other genes which modify the availability of exogenous folate, for example, has been proposed. Here, we used short-read whole-genome re-sequencing to determine the mutations in a clone of the rodent malaria parasite, Plasmodium chabaudi, which has altered susceptibility to both sulphadoxine and pyrimethamine. This clone bears a previously identified S106N mutation in dhfr and no mutation in dhps. Instead, three additional point mutations in genes on chromosomes 2, 13 and 14 were identified. The mutated gene on chromosome 13 (mdr2 K392Q) encodes an ABC transporter. Because Quantitative Trait Locus analysis previously indicated an association of genetic markers on chromosome 13 with responses to individual and combined antifolates, MDR2 is proposed to modulate antifolate responses, possibly mediated by the transport of folate intermediates.

Martinelli, Axel; Henriques, Gisela; Cravo, Pedro; Hunt, Paul

2011-01-01

165

SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry  

Microsoft Academic Search

Some mutations resulting in protein sequence change might be tightly related to certain human diseases by affecting its roles, such as sickle cell anemia. Until now several databases, such as PMD, OMIM and HGMD, have been developed, pro- viding useful information about human disease- related mutation. Tandem mass spectrometry (MS) has been used for characterizing proteins in various conditions; however,

Hong Xi; Jongsun Park; Yong-hwan Lee; Yixue Li

2009-01-01

166

Mutations in the SUP-PF-1 Locus of Chlamydomonas reinhardtii Identify a Regulatory Domain in the Dynein Heavy Chain  

Microsoft Academic Search

We have characterized a group of regula- tory mutations that alter the activity of the outer dynein arms. Three mutations were obtained as sup- pressors of the paralyzed central pair mutant pf6 (Luck, D. J. L., and G. Piperno. 1989. Cell Move- ment. pp. 49-60), whereas two others were obtained as suppressors of the central pair mutant pfl6. Recom- bination

Mary E. Porter; Julie A. Knott; Lynne C. Gardner; David R. Mitchell; Susan K. Dutcher

1994-01-01

167

The imprinted oedematous-small mutation on mouse chromosome 2 identifies new roles for Gnas and Gnasxl in development.  

PubMed

The Gnas locus is highly complex and encodes several oppositely imprinted and alternatively spliced transcripts. Gnas itself encodes Gsalpha, which is involved in endocrine function and bone development, but the roles for the other transcripts have not been established. Here we describe a mouse mutation that provides further biological functions for the Gnas locus. The mutation Oed-Sml, induced by ethylnitrosourea (ENU), has been mapped to the distal chromosome 2 imprinting region that includes Gnas. The mutation displays two distinct phenotypes dependent on parental origin. When the mutation is maternally transmitted, a microcardia with gross edema (Oed) results. By contrast, when the mutation is paternally transmitted, a growth retardation (Sml) is seen that becomes evident within 5 days of birth. Here we show Oed-Sml to be a point mutation in Gnas exon 6, resulting in a valine to glutamate substitution at residue 159 (V159E). Both maternal- and paternal-specific transcripts derive from this missense mutation. The maternally expressed mutant Gnas transcript is the candidate for Oed and the paternally expressed mutant Gnasxl transcript is the candidate for Sml. We propose a new role for Gnas in heart growth and a role for Gnasxl in postnatal growth. These findings potentially have implications for human Albright hereditary osteodystrophy, a condition caused by mutations in GNAS. PMID:12376090

Skinner, Judith A; Cattanach, Bruce M; Peters, Jo

2002-10-01

168

Mutations in PDGFRB and NOTCH3 are the first genetic causes identified for autosomal dominant infantile myofibromatosis.  

PubMed

A recurrent PDGFRB mutation causes familial infantile myofibromatosis Cheung et al. (2013) The American Journal of Human Genetics 92: 996-1000. Mutations in PDGFRB cause autosomal-dominant infantile myofibromatosis Martignetti et al. (2013) The American Journal of Human Genetics 92: 1001-1007. PMID:23865785

Lee, Jw

2013-07-31

169

[Genotyping of Vaginal Candida glabrata Isolates Using Microsatellite Marker Analysis and DNA Sequencing to Identify Mutations Associated with Antifungal Resistance].  

PubMed

Vulvovaginal candidosis is the second most common cause of vaginitis (17-39%) after bacterial vaginosis (22-50%). Since the diagnosis of vulvovaginal candidosis mainly depends on clinical findings without mycologic confirmatory tests and treated empirically, the actual incidence rate of vulvovaginal candidosis is unknown. Approximately 70-90% of vulvovaginal candidosis cases are caused by Candida albicans, however the increasing incidence of C.glabrata infections and its reduced susceptibility to azole drug therapy have generated increasing attention. The epidemiology and population structure of vulvovaginal candidosis due to C.glabrata are poorly characterized. This study was aimed to genotype the C.glabrata strains isolated from vaginal samples in Cukurova region, Turkey by microsatellite markers, to investigate the antifungal susceptibility profiles of the strains and to determine the molecular mechanisms leading to phenotypical azole resistance. A total of 34 unrelated vaginal C.glabrata strains isolated from patients with acute (n= 11) and recurrent (n= 14) vulvovaginal candidosis, control group (n= 9) without vaginitis symptoms, and a reference strain of C.glabrata CBS 138 (ATCC 2001) were included in the study. These isolates were genotyped using multiple-locus variable number tandem repeat analysis of three microsatellite markers (RPM2, MTI, and Cg6). Analysis of microsatellite markers was performed by fragment size determination of RPM2, MTI, and Cg6 PCR products through capillary electrophoresis. For each of the evaluated strains, DNA sequence analysis was performed for one gene (CgERG11) and four loci (CgPDR1, NTM1, TRP1, and URA3) to detect mutations possibly associated with antifungal resistance in each strain. In vitro susceptibility profiles of the strains to 13 antifungals and boric acid were determined according to CLSI document M27-A3 to investigate possible relationships between detected mutations and phenotypic resistance. C.glabrata CBS 138 strain was found to be susceptible to all the antifungals tested, while one of (%2.9) 34 vaginal C.glabrata isolates was found to be dose-dependent susceptible to fluconazole, 13 (38.2%) to itraconazole and 3 (8.8%) to voriconazole. No resistant strain were detected in the study population. Only three isolates were found to be resistant to clotrimazole (8.8%), however no relationship was identified between the genotypes and phenotypic resistance (p> 0.05). Thirteen genotypes were detected by microsatellite marker analysis, with high discrimination power (DP= 0.877). As a result, microsatellite marker analysis was validated as a rapid, reliable method for genotyping C.glabrata strains with good, but not optimal discriminatory power. Further studies examining larger numbers of isolates are needed to verify possible relationships between mutations and phenotypic resistance. PMID:23390908

Dö?en, Aylin; Durukan, Hüseyin; Güzel, Ahmet Bar??; Oksüz, Zehra; Kaplan, Engin; Serin, Mehmet Sami; Serin, Ay?e; Emekda?, Gürol; Aslan, Gönül; Tezcan, Seda; Kalkanc?, Ay?e; Ilkit, Macit

2013-01-01

170

A new human p34 protein kinase, CDK2, identified by complementation of a cdc28 mutation in Saccharomyces cerevisiae, is a homolog of Xenopus Eg1.  

PubMed Central

The onset of S-phase and M-phase in both Schizosaccharomyces pombe and Saccharomyces cerevisiae requires the function of the cdc2/CDC28 gene product, p34, a serine-threonine protein kinase. A human homolog, p34cdc2, was identified by functional complementation of the S.pombe cdc2 mutation (Lee and Nurse, 1987). Using a human cDNA expression library to search for suppressors of cdc28 mutations in S. cerevisiae, we have identified a second functional p34 homolog, CDK2 cell division kinase). This gene is expressed as a 2.1 kb transcript encoding a polypeptide of 298 amino acids. This protein retains nearly all of the amino acids highly conserved among previously identified p34 homologs from other species, but is considerably divergent from all previous p34cdc2 homologs, approximately 65% identity. This gene encodes the human homolog of the Xenopus Eg1 gene, sharing 89% amino acid identity, and defines a second sub-family of CDC2 homologs. A second chromosomal mutation which arose spontaneously was required to allow complementation of the cdc28-4 mutation by CDK2. This mutation blocked the ability of this strain to mate. These results suggest that the machinery controlling the human cell cycle is more complex than that for fission and budding yeast. Images

Elledge, S J; Spottswood, M R

1991-01-01

171

The Evolutionary History of Amino Acid Variations Mediating Increased Resistance of S. aureus Identifies Reversion Mutations in Metabolic Regulators  

PubMed Central

The evolution of resistance in Staphylococcus aureus occurs rapidly, and in response to all known antimicrobial treatments. Numerous studies of model species describe compensatory roles of mutations in mediating competitive fitness, and there is growing evidence that these mutation types also drive adaptation of S. aureus strains. However, few studies have tracked amino acid changes during the complete evolutionary trajectory of antibiotic adaptation or been able to predict their functional relevance. Here, we have assessed the efficacy of computational methods to predict biological resistance of a collection of clinically known Resistance Associated Mutations (RAMs). We have found that >90% of known RAMs are incorrectly predicted to be functionally neutral by at least one of the prediction methods used. By tracing the evolutionary histories of all of the false negative RAMs, we have discovered that a significant number are reversion mutations to ancestral alleles also carried in the MSSA476 methicillin-sensitive isolate. These genetic reversions are most prevalent in strains following daptomycin treatment and show a tendency to accumulate in biological pathway reactions that are distinct from those accumulating non-reversion mutations. Our studies therefore show that in addition to non-reversion mutations, reversion mutations arise in isolates exposed to new antibiotic treatments. It is possible that acquisition of reversion mutations in the genome may prevent substantial fitness costs during the progression of resistance. Our findings pose an interesting question to be addressed by further clinical studies regarding whether or not these reversion mutations lead to a renewed vulnerability of a vancomycin or daptomycin resistant strain to antibiotics administered at an earlier stage of infection.

Champion, Mia D.; Kumar, Sudhir

2013-01-01

172

Screening of a Large Cohort of Leber Congenital Amaurosis and Retinitis Pigmentosa Patients Identifies Novel LCA5 Mutations and New Genotype-Phenotype Correlations.  

PubMed

This study was undertaken to investigate the prevalence of sequence variants in LCA5 in patients with Leber congenital amaurosis (LCA), early-onset retinal dystrophy (EORD), and autosomal recessive retinitis pigmentosa (arRP); to delineate the ocular phenotypes; and to provide an overview of all published LCA5 variants in an online database. Patients underwent standard ophthalmic evaluations after providing informed consent. In selected patients, optical coherence tomography (OCT) and fundus autofluorescence imaging were possible. DNA samples from 797 unrelated patients with LCA and 211 with the various types of retinitis pigmentosa (RP) were screened by Sanger sequence analysis of all LCA5 exons and intron/exon junctions. Some LCA patients were prescreened by APEX technology or selected based on homozygosity mapping. In silico analyses were performed to assess the pathogenicity of the variants. Segregation analysis was performed where possible. Published and novel LCA5 variants were collected, amended for their correct nomenclature, and listed in a Leiden Open Variation Database (LOVD). Sequence analysis identified 18 new probands with 19 different LCA5 variants. Seventeen of the 19 LCA5 variants were novel. Except for two missense variants and one splice site variant, all variants were protein-truncating mutations. Most patients expressed a severe phenotype, typical of LCA. However, some LCA subjects had better vision and intact inner segment/outer segment (IS/OS) junctions on OCT imaging. In two families with LCA5 variants, the phenotype was more compatible with EORD with affected individuals displaying preserved islands of retinal pigment epithelium. One of the families with a milder phenotype harbored a homozygous splice site mutation; a second family was found to have a combination of a stop mutation and a missense mutation. This is the largest LCA5 study to date. We sequenced 1,008 patients (797 with LCA, 211 with arRP) and identified 18 probands with LCA5 mutations. Mutations in LCA5 are a rare cause of childhood retinal dystrophy accounting for ?2% of disease in this cohort, and the majority of LCA5 mutations are likely null. The LCA5 protein truncating mutations are predominantly associated with LCA. However, in two families with the milder EORD, the LCA5 gene analysis revealed a homozygous splice site mutation in one and a stop mutation in combination with a missense mutation in a second family, suggesting that this milder phenotype is due to residual function of lebercilin and expanding the currently known phenotypic spectrum to include the milder early onset RP. Some patients have remaining foveal cone structures (intact IS/OS junctions on OCT imaging) and remaining visual acuities, which may bode well for upcoming treatment trials. PMID:23946133

Mackay, Donna S; Borman, Arundhati Dev; Sui, Ruifang; van den Born, L Ingeborgh; Berson, Eliot L; Ocaka, Louise A; Davidson, Alice E; Heckenlively, John R; Branham, Kari; Ren, Huanan; Lopez, Irma; Maria, Maleeha; Azam, Maleeha; Henkes, Arjen; Blokland, Ellen; Andreasson, Sten; de Baere, Elfride; Bennett, Jean; Chader, Gerald J; Berger, Wolfgang; Golovleva, Irina; Greenberg, Jacquie; den Hollander, Anneke I; Klaver, Caroline C W; Klevering, B Jeroen; Lorenz, Birgit; Preising, Markus N; Ramsear, Raj; Roberts, Lisa; Roepman, Ronald; Rohrschneider, Klaus; Wissinger, Bernd; Qamar, Raheel; Webster, Andrew R; Cremers, Frans P M; Moore, Anthony T; Koenekoop, Robert K

2013-09-17

173

Zebrafish mutations in gart and paics identify crucial roles for de novo purine synthesis in vertebrate pigmentation and ocular development  

PubMed Central

Summary Although purines and purinergic signaling are crucial for numerous biochemical and cellular processes, their functions during vertebrate embryonic development have not been well characterized. We analyze two recessive zebrafish mutations that affect de novo purine synthesis, gart and paics. gart encodes phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase, a trifunctional enzyme that catalyzes steps 2, 3 and 5 of inosine monophosphate (IMP) synthesis. paics encodes phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase, a bifunctional enzyme that catalyzes steps 6 and 7 of this process. Zygotic gart and paics mutants have pigmentation defects in which xanthophore and iridophore pigmentation is almost completely absent, and melanin-derived pigmentation is significantly decreased, even though pigment cells are present in normal amounts and distributions. Zygotic gart and paics mutants are also microphthalmic, resulting from defects in cell cycle exit of proliferative retinoblasts within the developing eye. Maternal-zygotic and maternal-effect mutants demonstrate a crucial requirement for maternally derived gart and paics; these mutants show more severe developmental defects than their zygotic counterparts. Pigmentation and eye growth phenotypes in zygotic gart and paics mutants can be ascribed to separable biosynthetic pathways: pigmentation defects and microphthalmia result from deficiencies in a GTP synthesis pathway and an ATP synthesis pathway, respectively. In the absence of ATP pathway activity, S phase of proliferative retinoblasts is prolonged and cell cycle exit is compromised, which results in microphthalmia. These results demonstrate crucial maternal and zygotic requirements for de novo purine synthesis during vertebrate embryonic development, and identify independent functions for ATP and GTP pathways in mediating eye growth and pigmentation, respectively.

Ng, Anthony; Uribe, Rosa A.; Yieh, Leah; Nuckels, Richard; Gross, Jeffrey M.

2009-01-01

174

Alteration of DNA binding, dimerization, and nuclear translocation of SHOX homeodomain mutations identified in idiopathic short stature and Leri-Weill dyschondrosteosis.  

PubMed

Haploinsufficiency of the short stature homeobox gene SHOX has been found in patients with idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). In addition to complete gene deletions and nonsense mutations, several missense mutations have been identified in both patient groups, leading to amino acid substitutions in the SHOX protein. The majority of missense mutations were found to accumulate in the region encoding the highly conserved homeodomain of the paired-like type. In this report, we investigated nine different amino acid exchanges in the homeodomain of SHOX patients with ISS and LWD. We were able show that these mutations cause an alteration of the biological function of SHOX by loss of DNA binding, reduced dimerization ability, and/or impaired nuclear translocation. Additionally, one of the mutations (c.458G>T, p.R153L) is defective in transcriptional activation even though it is still able to bind to DNA, dimerize, and translocate to the nucleus. Thus, we demonstrate that single missense mutations in the homeodomain fundamentally impair SHOX key functions, thereby leading to the phenotype observed in patients with LWD and ISS. PMID:15931687

Schneider, Katja U; Marchini, Antonio; Sabherwal, Nitin; Röth, Ralph; Niesler, Beate; Marttila, Tiina; Blaschke, Rüdiger J; Lawson, Margaret; Dumic, Miroslav; Rappold, Gudrun

2005-07-01

175

Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing.  

PubMed

Inherited loss-of-function mutations in BRCA1 and BRCA2 and other tumor suppressor genes predispose to ovarian carcinomas, but the overall burden of disease due to inherited mutations is not known. Using targeted capture and massively parallel genomic sequencing, we screened for germ-line mutations in 21 tumor suppressor genes in genomic DNA from women with primary ovarian, peritoneal, or fallopian tube carcinoma. Subjects were consecutively enrolled at diagnosis and not selected for age or family history. All classes of mutations, including point mutations and large genomic deletions and insertions, were detected. Of 360 subjects, 24% carried germ-line loss-of-function mutations: 18% in BRCA1 or BRCA2 and 6% in BARD1, BRIP1, CHEK2, MRE11A, MSH6, NBN, PALB2, RAD50, RAD51C, or TP53. Six of these genes were not previously implicated in inherited ovarian carcinoma. Primary carcinomas were generally characterized by genomic loss of normal alleles of the mutant genes. Of women with inherited mutations, >30% had no family history of breast or ovarian carcinoma, and >35% were 60 y or older at diagnosis. More patients with ovarian carcinoma carry cancer-predisposing mutations and in more genes than previously appreciated. Comprehensive genetic testing for inherited carcinoma is warranted for all women with ovarian, peritoneal, or fallopian tube carcinoma, regardless of age or family history. Clinical genetic testing is currently done gene by gene, with each test costing thousands of dollars. In contrast, massively parallel sequencing allows such testing for many genes simultaneously at low cost. PMID:22006311

Walsh, Tom; Casadei, Silvia; Lee, Ming K; Pennil, Christopher C; Nord, Alex S; Thornton, Anne M; Roeb, Wendy; Agnew, Kathy J; Stray, Sunday M; Wickramanayake, Anneka; Norquist, Barbara; Pennington, Kathryn P; Garcia, Rochelle L; King, Mary-Claire; Swisher, Elizabeth M

2011-10-17

176

A Genetic Screen for Modifiers of Drosophila Src42A Identifies Mutations in Egfr, rolled and a Novel Signaling Gene  

Microsoft Academic Search

Drosophila Src42A, a close relative of the vertebrate c-Src, has been implicated in the Ras-Mapk signaling cascade. An allele of Src42A, Su(Raf )1, dominantly suppresses the lethality of partial loss-of-function Raf mutations. To isolate genes involved in the same pathway where Src42A functions, we carried out genetic screens for dominant suppressor mutations that prevented Su(Raf )1 from suppressing Raf. Thirty-six

Qian Zhang; Qingxia Zheng; Xiangyi Lu

1999-01-01

177

SHANK3 mutations identified in autism lead to modification of dendritic spine morphology via an actin-dependent mechanism  

Microsoft Academic Search

Genetic mutations of SHANK3 have been reported in patients with intellectual disability, autism spectrum disorder (ASD) and schizophrenia. At the synapse, Shank3\\/ProSAP2 is a scaffolding protein that connects glutamate receptors to the actin cytoskeleton via a chain of intermediary elements. Although genetic studies have repeatedly confirmed the association of SHANK3 mutations with susceptibility to psychiatric disorders, very little is known

C M Durand; J Perroy; F Loll; D Perrais; L Fagni; T Bourgeron; M Montcouquiol; N Sans

2012-01-01

178

A Newly Identified Insertion Mutation in the Thyroid Hormone Receptor-? Gene in a Korean Family with Generalized Thyroid Hormone Resistance  

PubMed Central

Thyroid hormone resistance syndrome (RTH) is a rare disorder and is characterized by elevated levels of circulating free thyroid hormones, inappropriate secretion of thyroid stimulating hormone (TSH), and reduced peripheral tissue response to thyroid hormone. 90% of RTH subjects, when studied at the level of the gene, have been found to harbor mutations in the thyroid hormone receptor-? (THRB) gene. These affected individuals have been shown to possess a variety of missense mutations, resulting from changes in a single nucleotide in the THRB gene that corresponds to amino acid alternation. However, insertion or deletion mutations in the THRB gene sequence are quite rare, and have been observed in only a very few cases. In this study, we describe two such cases, in which two members of the same family were determined to harbor an insertion mutation in exon 10, and had also been diagnosed with generalized RTH. This insertion mutation, specifically the insertion of a cytosine at nucleotide 1358 of the THRB gene, is, to the best of our knowledge, the first such mutation reported among RTH patients in Korea.

Kim, Ji Hye; Park, Tae Sun; Baek, Hong Sun; Kim, Gu Hwan; Yoo, Han Wook

2007-01-01

179

A mutation unique in serine protease inhibitors (serpins) identified in a family with type II hereditary angioneurotic edema.  

PubMed Central

BACKGROUND: Hereditary angioneurotic edema (HANE) is an autosomal dominant disease due to genetic alterations at the C1 inhibitor gene. Mutations within the C1 inhibitor gene are responsible for the molecular defect in type II HANE. Most of the dysfunctional proteins result from mutations involving the Arg-444 (the P-1 site of the reactive center) or amino acids NH2-terminal to the reactive center. MATERIALS AND METHODS: We have studied a Spanish family with type II HANE by using polymerase chain reaction (PCR) to amplify the exon eight of the C1 inhibitor gene. The purified 338-bp PCR product was subcloned and transformed into competent cells. After overnight cultures, we extracted the cloning vector from the positive colonies and sequenced both strands of the PCR product from each patient and healthy members of the family. RESULTS: We show that affected individuals in this family have a missense mutation, changing an adenine to cytosine in the codon 445. This substitution changes threonine at the P-1' site of the reactive center to a proline. This mutation generates a new restriction site, recognized by Bsi YI. CONCLUSIONS: To our knowledge, this is the first molecular defect characterized in a Spanish family with type II HANE, and to date, this is the first reported mutation at the P-1' site of the reactive center in individuals with type II HANE. This new mutation located at the reactive center emphasizes once more time the enormous heterogeneity of this gene. Images FIG. 1 FIG. 2 FIG. 3

Ocejo-Vinyals, J. G.; Leyva-CobiA?n, F.; FernA?ndez-Luna, J. L.

1995-01-01

180

Functional characterization of mutations in the promoter proximal region of the telomerase hTERC gene identified in patients with hematological disorders  

PubMed Central

Telomerase RNA gene (hTERC) mutations have been identified in a subset of patients with bone-marrow failure syndromes (BMFS). While most of the mutations were found in the coding region of hTERC, some rare disease-associated mutations as well as polymorphic sequence changes were found in the promoter proximal region of the gene, including the -99C/G sequence change that was thought to modulate hTERC gene expression by disrupting Sp1 transcriptional factor binding [1]. We and other researchers recently identified, in addition to the -99C/G mutation, several other sequence variations (-240delCT, -714+C insertion, and -771A/G) in the hTERC promoter in other cohorts of patients with blood disorders. Using a convenient telomerase reconstitution assay coupled with the hTERC-promoter driven luciferase reporter assay, we characterized each of the hTERC's promoter sequence variants and found that these rare sequence changes did not negatively affect telomerase gene expression or function. We therefore conclude that all known mutations in the promoter proximal region of the hTERC gene to date do not necessarily contribute to the pathogenesis of hematological disorders by directly affecting telomerase transcriptional activity and/or its enzymatic function.

Carroll, Kathryn A; Ly, Hinh

2011-01-01

181

A novel frame shift mutation in the PQBP1 gene identified in a Tunisian family with X-linked mental retardation.  

PubMed

Mental retardation (MR) is the most frequent cause of serious handicap in children and young adults. Despite recent progress, in most cases the molecular defects underlying this disorder remain unknown. Linkage studies followed by mutational analysis of known X-chromosomal genes related to mental retardation (MRX genes) localized within defined genetic intervals represent a rational strategy to identify a genetic cause of the disorder. Here, we report a Tunisian family including 3 males with severe to mild mental retardation, short stature, lean body and microcephaly; we mapped the disease to a unique interval encompassing Xp21.1-Xq21.33 (with a maximum LOD score of 0.90). Subsequent mutation analysis of genes located in this interval allowed us to identify a truncating mutation in the PQBP1 gene. This mutation is an insertion of an adenosine residue in exon 5 (c.631insA). This frameshift insertion causes premature stop codon at amino acid position 226. The observed mutation was found in all males with MR in this family. Together with previously reported observations, our data further confirm that PQBP1 gene should be tested for males showing mental retardation, short stature, lean body and microcephaly. PMID:21315190

Rejeb, Imen; Ben Jemaa, Lamia; Abaied, Leila; Kraoua, Lilia; Saillour, Yoann; Maazoul, Faouzi; Chelly, Jamel; Chaabouni, Habiba

2011-02-26

182

Zebrafish Ciliopathy Screen Plus Human Mutational Analysis Identifies C21orf59 and CCDC65 Defects as Causing Primary Ciliary Dyskinesia.  

PubMed

Primary ciliary dyskinesia (PCD) is caused when defects of motile cilia lead to chronic airway infections, male infertility, and situs abnormalities. Multiple causative PCD mutations account for only 65% of cases, suggesting that many genes essential for cilia function remain to be discovered. By using zebrafish morpholino knockdown of PCD candidate genes as an in vivo screening platform, we identified c21orf59, ccdc65, and c15orf26 as critical for cilia motility. c21orf59 and c15orf26 knockdown in zebrafish and planaria blocked outer dynein arm assembly, and ccdc65 knockdown altered cilia beat pattern. Biochemical analysis in Chlamydomonas revealed that the C21orf59 ortholog FBB18 is a flagellar matrix protein that accumulates specifically when cilia motility is impaired. The Chlamydomonas ida6 mutant identifies CCDC65/FAP250 as an essential component of the nexin-dynein regulatory complex. Analysis of 295 individuals with PCD identified recessive truncating mutations of C21orf59 in four families and CCDC65 in two families. Similar to findings in zebrafish and planaria, mutations in C21orf59 caused loss of both outer and inner dynein arm components. Our results characterize two genes associated with PCD-causing mutations and elucidate two distinct mechanisms critical for motile cilia function: dynein arm assembly for C21orf59 and assembly of the nexin-dynein regulatory complex for CCDC65. PMID:24094744

Austin-Tse, Christina; Halbritter, Jan; Zariwala, Maimoona A; Gilberti, Renée M; Gee, Heon Yung; Hellman, Nathan; Pathak, Narendra; Liu, Yan; Panizzi, Jennifer R; Patel-King, Ramila S; Tritschler, Douglas; Bower, Raqual; O'Toole, Eileen; Porath, Jonathan D; Hurd, Toby W; Chaki, Moumita; Diaz, Katrina A; Kohl, Stefan; Lovric, Svjetlana; Hwang, Daw-Yang; Braun, Daniela A; Schueler, Markus; Airik, Rannar; Otto, Edgar A; Leigh, Margaret W; Noone, Peadar G; Carson, Johnny L; Davis, Stephanie D; Pittman, Jessica E; Ferkol, Thomas W; Atkinson, Jeffry J; Olivier, Kenneth N; Sagel, Scott D; Dell, Sharon D; Rosenfeld, Margaret; Milla, Carlos E; Loges, Niki T; Omran, Heymut; Porter, Mary E; King, Stephen M; Knowles, Michael R; Drummond, Iain A; Hildebrandt, Friedhelm

2013-10-01

183

A comprehensive screen for TWIST mutations in patients with craniosynostosis identifies a new microdeletion syndrome of chromosome band 7p21.1.  

PubMed Central

Mutations in the coding region of the TWIST gene (encoding a basic helix-loop-helix transcription factor) have been identified in some cases of Saethre-Chotzen syndrome. Haploinsufficiency appears to be the pathogenic mechanism involved. To investigate the possibility that complete deletions of the TWIST gene also contribute to this disorder, we have developed a comprehensive strategy to screen for coding-region mutations and for complete gene deletions. Heterozygous TWIST mutations were identified in 8 of 10 patients with Saethre-Chotzen syndrome and in 2 of 43 craniosynostosis patients with no clear diagnosis. In addition to six coding-region mutations, our strategy revealed four complete TWIST deletions, only one of which associated with a translocation was suspected on the basis of conventional cytogenetic analysis. This case and two interstitial deletions were detectable by analysis of polymorphic microsatellite loci, including a novel (CA)n locus 7.9 kb away from TWIST, combined with FISH; these deletions ranged in size from 3.5 Mb to >11.6 Mb. The remaining, much smaller deletion was detected by Southern blot analysis and removed 2,924 bp, with a 2-bp orphan sequence at the breakpoint. Significant learning difficulties were present in the three patients with megabase-sized deletions, which suggests that haploinsufficiency of genes neighboring TWIST contributes to developmental delay. Our results identify a new microdeletion disorder that maps to chromosome band 7p21.1 and that causes a significant proportion of Saethre-Chotzen syndrome.

Johnson, D; Horsley, S W; Moloney, D M; Oldridge, M; Twigg, S R; Walsh, S; Barrow, M; Nj?lstad, P R; Kunz, J; Ashworth, G J; Wall, S A; Kearney, L; Wilkie, A O

1998-01-01

184

GLYCOSYLATION OF THE OCTN2 CARNITINE TRANSPORTER: STUDY OF NATURAL MUTATIONS IDENTIFIED IN PATIENTS WITH PRIMARY CARNITINE DEFICIENCY  

PubMed Central

Primary carnitine deficiency is caused by impaired activity of the Na+-dependent OCTN2 carnitine/organic cation transporter. Carnitine is essential for entry of long-chain fatty acids into mitochondria and its deficiency impairs fatty acid oxidation. Most missense mutations identified in patients with primary carnitine deficiency affect putative transmembrane or intracellular domains of the transporter. Exceptions are the substitutions P46S and R83L located in an extracellular loop close to putative glycosylation sites (N57, N64, and N91) of OCTN2. P46S and R83L impaired glycosylation and maturation of OCTN2 transporters to the plasma membrane. We tested whether glycosylation was essential for the maturation of OCTN2 transporters to the plasma membrane. Substitution of each of the 3 asparagine (N) glycosylation sites with glutamine (Q) decreased carnitine transport. Substitution of two sites at a time caused a further decline in carnitine transport that was fully abolished when all three glycosylation sites were substituted by glutamine (N57Q/N64Q/N91Q). Kinetic analysis of carnitine and sodium-stimulated carnitine transport indicated that all substitutions decreased the Vmax for carnitine transport, but N64Q/N91Q also significantly increased the Km toward carnitine, indicating that these two substitutions affected regions of the transporter important for substrate recognition. Western blot analysis confirmed increased mobility of OCTN2 transporters with progressive substitutions of asparagines 57, 64 and/or 91 with glutamine. Confocal microscopy indicated that glutamine substitutions caused progressive retention of OCTN2 transporters in the cytoplasm, up to full retention (such as that observed with R83L) when all 3 glycosylation sites were substituted. Tunicamycin prevented OCTN2 glycosylation, but it did not impair maturation to the plasma membrane. These results indicate that OCTN2 is physiologically glycosylated and that the P46S and R83L substitutions impair this process. Glycosylation does not affect maturation of OCTN2 transporters to the plasma membrane, but the 3 asparagines that are normally glycosylated are located in a region important for substrate recognition and turnover rate.

di San Filippo, Cristina Amat; Ardon, Orly; Longo, Nicola

2010-01-01

185

Clinical and molecular analysis in families with autosomal recessive osteogenesis imperfecta identifies mutations in five genes and suggests genotype-phenotype correlations.  

PubMed

Autosomal recessive osteogenesis imperfecta (AR-OI) is an inherited condition which in recent years has been shown with increasing genetic and clinical heterogeneity. In this article, we performed clinical assessment and sought mutations in patients from 10 unrelated families with AR-OI, one of whom was presented with the additional features of Bruck syndrome (BS). Pathogenic changes were identified in five different genes: three families had mutations in FKBP10, three in SERPINF1, two in LEPRE1, one in CRTAP, and one in PPIB. With the exception of a FKBP10 mutation in the BS case, all changes are novel. Of note, insertion of an AluYb8 repetitive element was detected in exon 6 of SERPINF1. Since the studied patients had variable manifestations and some distinctive features, genotype/phenotype correlations are suggested. PMID:23613367

Caparrós-Martin, José A; Valencia, María; Pulido, Veronica; Martínez-Glez, Victor; Rueda-Arenas, Inmaculada; Amr, Khalda; Farra, Chantal; Lapunzina, Pablo; Ruiz-Perez, Victor L; Temtamy, Samia; Aglan, Mona

2013-04-23

186

A mutation in the ?-subunit of ENaC identified in a patient with cystic fibrosis-like symptoms has a gain-of-function effect.  

PubMed

In some patients with atypical cystic fibrosis (CF), only one allele of the CF transmembrane conductance regulator (CFTR) gene is affected. Mutations of the epithelial sodium channel (ENaC) may contribute to the pathophysiology of the disease in these patients. To functionally characterize a mutation in the ?-subunit of ENaC (?V348M) recently identified in a patient with severe CF-like symptoms (Mutesa et al. 2009), we expressed wild-type (wt) ???ENaC or mutant ??V348M?ENaC in Xenopus laevis oocytes. The ?V348M mutation stimulated amiloride-sensitive whole-cell current (?I(ami)) by ?40% but had no effect on surface expression or single-channel conductance of ENaC. Instead the mutation increased channel open probability (P(o)). Proteolytic activation of mutant ENaC by chymotrypsin was reduced compared with that of wt ENaC (?3.0-fold vs. ?4.2-fold), which is consistent with the increased baseline P(o) of mutant ENaC. Similarly, the ENaC activator S3969 stimulated mutant ENaC currents to a lesser degree (by ?2.6-fold) than wt ENaC currents (by ?3.5-fold). The gain-of-function effect of the ?V348M mutation was confirmed by whole-cell current measurements in HEK293 cells transiently transfected with wt or mutant ENaC. Computational channel modeling in combination with functional expression of different ?V348 mutants in oocytes suggests that the ?V348M mutation increases channel P(o) by destabilizing the closed channel state. Our findings indicate that the gain-of-function effect of the ?V348M mutation may contribute to CF pathophysiology by inappropriately increasing sodium and fluid absorption in the respiratory tract. PMID:23087020

Rauh, Robert; Soell, Daniel; Haerteis, Silke; Diakov, Alexei; Nesterov, Viatcheslav; Krueger, Bettina; Sticht, Heinrich; Korbmacher, Christoph

2012-10-19

187

Secondary Variants in Individuals Undergoing Exome Sequencing: Screening of 572 Individuals Identifies High-Penetrance Mutations in Cancer-Susceptibility Genes  

PubMed Central

Genome- and exome-sequencing costs are continuing to fall, and many individuals are undergoing these assessments as research participants and patients. The issue of secondary (so-called incidental) findings in exome analysis is controversial, and data are needed on methods of detection and their frequency. We piloted secondary variant detection by analyzing exomes for mutations in cancer-susceptibility syndromes in subjects ascertained for atherosclerosis phenotypes. We performed exome sequencing on 572 ClinSeq participants, and in 37 genes, we interpreted variants that cause high-penetrance cancer syndromes by using an algorithm that filtered results on the basis of mutation type, quality, and frequency and that filtered mutation-database entries on the basis of defined categories of causation. We identified 454 sequence variants that differed from the human reference. Exclusions were made on the basis of sequence quality (26 variants) and high frequency in the cohort (77 variants) or dbSNP (17 variants), leaving 334 variants of potential clinical importance. These were further filtered on the basis of curation of literature reports. Seven participants, four of whom were of Ashkenazi Jewish descent and three of whom did not meet family-history-based referral criteria, had deleterious BRCA1 or BRCA2 mutations. One participant had a deleterious SDHC mutation, which causes paragangliomas. Exome sequencing, coupled with multidisciplinary interpretation, detected clinically important mutations in cancer-susceptibility genes; four of such mutations were in individuals without a significant family history of disease. We conclude that secondary variants of high clinical importance will be detected at an appreciable frequency in exomes, and we suggest that priority be given to the development of more efficient modes of interpretation with trials in larger patient groups.

Johnston, Jennifer J.; Rubinstein, Wendy S.; Facio, Flavia M.; Ng, David; Singh, Larry N.; Teer, Jamie K.; Mullikin, James C.; Biesecker, Leslie G.

2012-01-01

188

Homozygosity for a newly identified missense mutation in a patient with very severe combined immunodeficiency due to adenosine deaminase deficiency (ADA-SCID).  

PubMed Central

We have identified a previously unrecognized missense mutation in a patient with severe combined immunodeficiency due to adenosine deaminase deficiency (ADA-SCID). The mutation is a G646-to-A transition at a CG dinucleotide and predicts a glycine-to-arginine substitution at codon 216. Computer analysis of secondary structure predicts a major alteration with loss of a beta-pleated sheet in a highly conserved region of the protein. The basepair substitution also generates a new site for the restriction enzyme BstXI in exon 7 of the genomic DNA. Digestion of genomic DNA from the patient and from his parents revealed that he was homozygous for the mutation and that his mother and father were carriers. This mutation in homozygous form appears to be associated with very severe disease, since the patient had perinatal onset of clinical manifestations of SCID, the highest concentration of the toxic metabolite deoxyATP in nine patients studied, and a relatively poor immunologic response during the initial 2 years of therapy with polyethylene glycol-adenosine deaminase. Analysis of DNA from 21 additional patients with ADA-SCID and from 19 unrelated normals revealed that, while none of the normal individuals showed the abnormal restriction fragment, two of the 21 patients studied were heterozygous for the G646-to-A mutation. Images Figure 2

Hirschhorn, R; Chakravarti, V; Puck, J; Douglas, S D

1991-01-01

189

Severely Incapacitating Mutations in Patients with Extreme Short Stature Identify RNA-Processing Endoribonuclease RMRP as an Essential Cell Growth Regulator  

PubMed Central

The growth of an individual is deeply influenced by the regulation of cell growth and division, both of which also contribute to a wide variety of pathological conditions, including cancer, diabetes, and inflammation. To identify a major regulator of human growth, we performed positional cloning in an autosomal recessive type of profound short stature, anauxetic dysplasia. Homozygosity mapping led to the identification of novel mutations in the RMRP gene, which was previously known to cause two milder types of short stature with susceptibility to cancer, cartilage hair hypoplasia, and metaphyseal dysplasia without hypotrichosis. We show that different RMRP gene mutations lead to decreased cell growth by impairing ribosomal assembly and by altering cyclin-dependent cell cycle regulation. Clinical heterogeneity is explained by a correlation between the level and type of functional impairment in vitro and the severity of short stature or predisposition to cancer. Whereas the cartilage hair hypoplasia founder mutation affects both pathways intermediately, anauxetic dysplasia mutations do not affect B-cyclin messenger RNA (mRNA) levels but do severely incapacitate ribosomal assembly via defective endonucleolytic cleavage. Anauxetic dysplasia mutations thus lead to poor processing of ribosomal RNA while allowing normal mRNA processing and, therefore, genetically separate the different functions of RNase MRP.

Thiel, Christian T.; Horn, Denise; Zabel, Bernhard; Ekici, Arif B.; Salinas, Kelly; Gebhart, Erich; Ruschendorf, Franz; Sticht, Heinrich; Spranger, Jurgen; Muller, Dietmar; Zweier, Christiane; Schmitt, Mark E.; Reis, Andre; Rauch, Anita

2005-01-01

190

Exome capture and massively parallel sequencing identifies a novel HPSE2 mutation in a Saudi Arabian child with Ochoa (urofacial) syndrome.  

PubMed

We describe a child of Middle Eastern descent by first-cousin coupling with idiopathic neurogenic bladder and high-grade vesicoureteral reflux at 1 year of age, whose characteristic facial grimace led to the diagnosis of Ochoa (urofacial) syndrome at age 5 years. We used homozygosity mapping, exome capture and paired-end sequencing to identify the disease causing mutation in the proband. We reviewed the literature with respect to the urologic manifestations of Ochoa syndrome. A large region of marker homozygosity was observed at 10q24, consistent with known autosomal recessive inheritance, family consanguinity and previous genetic mapping in other families with Ochoa syndrome. A homozygous mutation was identified in the proband in HPSE2: c.1374_1378delTGTGC, a deletion of 5 nucleotides in exon 10 that is predicted to lead to a frameshift followed by replacement of 132 C-terminal amino acids with 153 novel amino acids (p.Ala458Alafsdel132ins153). This mutation is novel relative to very recently published mutations in HPSE2 in other families. Early intervention and recognition of Ochoa syndrome with control of risk factors and close surveillance will decrease complications and renal failure. PMID:21450525

Al Badr, Wisam; Al Bader, Suha; Otto, Edgar; Hildebrandt, Friedhelm; Ackley, Todd; Peng, Weiping; Xu, Jishu; Li, Jun; Owens, Kailey M; Bloom, David; Innis, Jeffrey W

2011-03-29

191

Genomic Strategy Identifies a Missense Mutation in WD-Repeat Domain 65 (WDR65) in an Individual with Van der Woude Syndrome  

PubMed Central

Genetic variation in the transcription factor Interferon Regulatory Factor 6 (IRF6) causes and contributes risk for oral clefting disorders. We hypothesized that genes regulated by IRF6 are also involved in oral clefting disorders. We used five criteria to identify potential IRF6 target genes; differential gene expression in skin taken from wild type and Irf6-deficient murine embryos, localization to the Van der Woude syndrome 2 (VWS2) locus at 1p36–1p32, overlapping expression with Irf6, presence of a conserved predicted binding site in the promoter region, and a mutant murine phenotype that was similar to the Irf6 mutant mouse. Previously, we observed altered expression for 573 genes; 13 were located in the murine region syntenic to the VWS2 locus. Two of these genes, Wdr65 and Stratifin, met four of five criteria. Wdr65 was a novel gene that encoded a predicted protein of 1250 amino acids with two WD domains. As potential targets for Irf6 regulation, we hypothesized that disease-causing mutations will be found in WDR65 and Stratifin in individuals with VWS or VWS-like syndromes. We identified a potentially etiologic missense mutation in WDR65 in a person with VWS who does not have an exonic mutation in IRF6. The expression and mutation data were consistent with the hypothesis that WDR65 was a novel gene involved in oral clefting.

Rorick, Nicholas K.; Kinoshita, Akira; Weirather, Jason; Peyrard-Janvid, Myriam; Ferreira de Lima, Renata L. L.; Dunnwald, Martine; Shanske, Alan L.; Moretti-Ferreira, Danilo; Koillinen, Hannele; Kere, Juha; Mansilla, Maria A.; Murray, Jeffrey C.; Goudy, Steve L.; Schutte, Brian C.

2013-01-01

192

Genomic strategy identifies a missense mutation in WD-repeat domain 65 (WDR65) in an individual with Van der Woude syndrome.  

PubMed

Genetic variation in the transcription factor interferon regulatory factor 6 (IRF6) causes and contributes risk for oral clefting disorders. We hypothesized that genes regulated by IRF6 are also involved in oral clefting disorders. We used five criteria to identify potential IRF6 target genes; differential gene expression in skin taken from wild-type and Irf6-deficient murine embryos, localization to the Van der Woude syndrome 2 (VWS2) locus at 1p36-1p32, overlapping expression with Irf6, presence of a conserved predicted-binding site in the promoter region, and a mutant murine phenotype that was similar to the Irf6 mutant mouse. Previously, we observed altered expression for 573 genes; 13 were located in the murine region syntenic to the VWS2 locus. Two of these genes, Wdr65 and Stratifin, met 4 of 5 criteria. Wdr65 was a novel gene that encoded a predicted protein of 1,250 amino acids with two WD domains. As potential targets for Irf6 regulation, we hypothesized that disease-causing mutations will be found in WDR65 and Stratifin in individuals with VWS or VWS-like syndromes. We identified a potentially etiologic missense mutation in WDR65 in a person with VWS who does not have an exonic mutation in IRF6. The expression and mutation data were consistent with the hypothesis that WDR65 was a novel gene involved in oral clefting. PMID:21574244

Rorick, Nicholas K; Kinoshita, Akira; Weirather, Jason L; Peyrard-Janvid, Myriam; de Lima, Renata L L Ferreira; Dunnwald, Martine; Shanske, Alan L; Moretti-Ferreira, Danilo; Koillinen, Hannele; Kere, Juha; Mansilla, Maria A; Murray, Jeffrey C; Goudy, Steve L; Schutte, Brian C

2011-05-13

193

Whole-exome sequencing identified a homozygous FNBP4 mutation in a family with a condition similar to microphthalmia with limb anomalies.  

PubMed

Microphthalmia with limb anomalies (MLA), also known as Waardenburg anophthalmia syndrome or ophthalmoacromelic syndrome, is a rare autosomal recessive disorder. Recently, we and others successfully identified SMOC1 as the causative gene for MLA. However, there are several MLA families without SMOC1 abnormality, suggesting locus heterogeneity in MLA. We aimed to identify a pathogenic mutation in one Lebanese family having an MLA-like condition without SMOC1 mutation by whole-exome sequencing (WES) combined with homozygosity mapping. A c.683C>T (p.Thr228Met) in FNBP4 was found as a primary candidate, drawing the attention that FNBP4 and SMOC1 may potentially modulate BMP signaling. PMID:23703728

Kondo, Yukiko; Koshimizu, Eriko; Megarbane, Andre; Hamanoue, Haruka; Okada, Ippei; Nishiyama, Kiyomi; Kodera, Hirofumi; Miyatake, Satoko; Tsurusaki, Yoshinori; Nakashima, Mitsuko; Doi, Hiroshi; Miyake, Noriko; Saitsu, Hirotomo; Matsumoto, Naomichi

2013-05-23

194

Diagnostic screening identifies a wide range of mutations involving the SHOX gene, including a common 47.5?kb deletion 160?kb downstream with a variable phenotypic effect.  

PubMed

Léri-Weill dyschondrosteosis (LWD) results from heterozygous mutations of the SHOX gene, with homozygosity or compound heterozygosity resulting in the more severe form, Langer mesomelic dysplasia (LMD). These mutations typically take the form of whole or partial gene deletions, point mutations within the coding sequence, or large (>100?kb) 3' deletions of downstream regulatory elements. We have analyzed the coding sequence of the SHOX gene and its downstream regulatory regions in a cohort of 377 individuals referred with symptoms of LWD, LMD or short stature. A causative mutation was identified in 68% of the probands with LWD or LMD (91/134). In addition, a 47.5?kb deletion was found 160?kb downstream of the SHOX gene in 17 of the 377 patients (12% of the LWD referrals, 4.5% of all referrals). In 14 of these 17 patients, this was the only potentially causative abnormality detected (13 had symptoms consistent with LWD and one had short stature only), but the other three 47.5?kb deletions were found in patients with an additional causative SHOX mutation (with symptoms of LWD rather than LMD). Parental samples were available on 14/17 of these families, and analysis of these showed a more variable phenotype ranging from apparently unaffected to LWD. Breakpoint sequence analysis has shown that the 47.5?kb deletion is identical in all 17 patients, most likely due to an ancient founder mutation rather than recurrence. This deletion was not seen in 471 normal controls (P<0.0001), providing further evidence for a phenotypic effect, albeit one with variable penetration. PMID:23636926

Bunyan, David J; Baker, Kevin R; Harvey, John F; Thomas, N Simon

2013-05-01

195

Two novel exonic point mutations in HEXA identified in a juvenile Tay-Sachs patient: role of alternative splicing and nonsense-mediated mRNA decay.  

PubMed

We have identified three mutations in the beta-hexoseaminidase A (HEXA) gene in a juvenile Tay-Sachs disease (TSD) patient, which exhibited a reduced level of HEXA mRNA. Two mutations are novel, c.814G>A (p.Gly272Arg) and c.1305C>T (p.=), located in exon 8 and in exon 11, respectively. The third mutation, c.1195A>G (p.Asn399Asp) in exon 11, has been previously characterized as a common polymorphism in African-Americans. Hex A activity measured in TSD Glial cells, transfected with HEXA cDNA constructs bearing these mutations, was unaltered from the activity level measured in normal HEXA cDNA. Analysis of RT-PCR products revealed three aberrant transcripts in the patient, one where exon 8 was absent, one where exon 11 was absent and a third lacking both exons 10 and 11. All three novel transcripts contain frameshifts resulting in premature termination codons (PTCs). Transfection of mini-gene constructs carrying the c.814G>A and c.1305C>T mutations proved that the two mutations result in exon skipping. mRNAs that harbor a PTC are detected and degraded by the nonsense-mediated mRNA decay (NMD) pathway to prevent synthesis of abnormal proteins. However, although NMD is functional in the patient's fibroblasts, aberrant transcripts are still present. We suggest that the level of correctly spliced transcripts as well as the efficiency in which NMD degrade the PTC-containing transcripts, apparently plays an important role in the phenotype severity of the unique patient and thus should be considered as a potential target for drug therapy. PMID:20363167

Levit, A; Nutman, D; Osher, E; Kamhi, E; Navon, R

2010-03-19

196

APOA5 Q97X Mutation Identified through homozygosity mapping causes severe hypertriglyceridemia in a Chilean consanguineous family  

PubMed Central

Background Severe hypertriglyceridemia (HTG) has been linked to defects in LPL, APOC2, APOA5, LMF1 and GBIHBP1 genes. However, a number of severe HTG cases are probably caused by as yet unidentified mutations. Very high triglyceride plasma levels (>112 mmol/L at diagnosis) were found in two sisters of a Chilean consanguineous family, which is strongly suggestive of a recessive highly penetrant mutation. The aim of this study was to determine the genetic locus responsible for the severe HTG in this family. Methods We carried out a genome-wide linkage study with nearly 300,000 biallelic markers (Illumina Human CytoSNP-12 panel). Using the homozygosity mapping strategy, we searched for chromosome regions with excess of homozygous genotypes in the affected cases compared to non-affected relatives. Results A large homozygous segment was found in the long arm of chromosome 11, with more than 2,500 consecutive homozygous SNP shared by the proband with her affected sister, and containing the APOA5/A4/C3/A1 cluster. Direct sequencing of the APOA5 gene revealed a known homozygous nonsense Q97X mutation (p.Gln97Ter) found in both affected sisters but not in non-affected relatives nor in a sample of unrelated controls. Conclusion The Q97X mutation of the APOA5 gene in homozygous status is responsible for the severe hypertriglyceridemia in this family. We have shown that homozygosity mapping correctly pinpointed the genomic region containing the gene responsible for severe hypertriglyceridemia in this consanguineous Chilean family.

2012-01-01

197

DFNA8\\/12 caused by TECTA mutations is the most identified subtype of nonsyndromic autosomal dominant hearing loss  

Microsoft Academic Search

The prevalence of DFNA8\\/DFNA12 (DFNA8\\/12), a type of autosomal dominant nonsyndromic hearing loss (ADNSHL), is unknown as comprehensive population-based genetic screening has not been conducted. We therefore completed unbiased screening for TECTA mutations in a Spanish cohort of 372 probands from ADNSHL families. Three additional families (Spanish, Belgian, and English) known to be linked to DFNA8\\/12 were also included in

M. S. Hildebrand; M. Morin; N. C. Meyer; F. Mayo; S. Modamio-Hoybjor; A. Mencia; L. Olavarrieta; C. Morales-Angulo; C. J. Nishimura; H. Workman; A. P. DeLuca; I. del Castillo; K. R. Taylor; B. Tompkins; C. W. Goodman; I. Schrauwen; M. V. Wesemael; K. Lachlan; A. E. Shearer; T. A. Braun; P. L. M. Huygen; J. M. J. Kremer; G. van Camp; F. Moreno; T. L. Casavant; R. J. Smith; M. A. Moreno-Pelayo

2011-01-01

198

Mutational analysis of the discs large tumour suppressor identifies domains responsible for human papillomavirus type 18 E6-mediated degradation  

Microsoft Academic Search

The discs large (Dlg) tumour suppressor protein is targeted for ubiquitin-mediated degradation by the high-risk human papillomavirus E6 proteins. To understand further the mechanisms behind this, a mutational analysis of Dlg was undertaken. This study demonstrates that an intact PDZ domain 2 (PDZ2) on Dlg is necessary for the ability of E6 to bind and degrade Dlg. However, additional residues

Daniela Gardiol; Silvina Galizzi; Lawrence Banks

199

Eight Novel Mutations of ATP2C1 Identified in 17 Chinese Families with Hailey-Hailey Disease  

Microsoft Academic Search

Background: Hailey-Hailey disease (HHD) is a rare autosomal dominantly inherited dermatosis, characterized by persistent blisters and erosions of the skin. It was recently discovered that HHD was caused by mutations in the ATP2C1 gene, a Ca2+ pump located in the Golgi apparatus. Observation: In this study, we sequenced the ATP2C1 gene from blood samples of 31 patients in 17 unrelated

Furen Zhang; Xiaoxiao Yan; Deke Jiang; Hongqing Tian; Changyuan Wang; Long Yu

2007-01-01

200

Exome capture and massively parallel sequencing identifies a novel HPSE2 mutation in a Saudi Arabian child with Ochoa (urofacial) syndrome  

Microsoft Academic Search

We describe a child of Middle Eastern descent by first-cousin coupling with idiopathic neurogenic bladder and high-grade vesicoureteral reflux at 1 year of age, whose characteristic facial grimace led to the diagnosis of Ochoa (urofacial) syndrome at age 5 years. We used homozygosity mapping, exome capture and paired-end sequencing to identify the disease causing mutation in the proband. We reviewed

Wisam Al Badr; Suha Al Bader; Edgar Otto; Friedhelm Hildebrandt; Todd Ackley; Weiping Peng; Jishu Xu; Jun Li; Kailey M. Owens; David Bloom; Jeffrey W. Innis

2011-01-01

201

Genomic Profiling Identifies Novel Mutations and SNPs in ABCD1 Gene: A Molecular, Biochemical and Clinical Analysis of X-ALD Cases in India  

Microsoft Academic Search

X-linked adrenoleukodystrophy (X-ALD) affects the nervous system white matter and adrenal cortex secondary to mutations in the ABCD1 gene that encode the peroxisomal membrane protein. We conducted a genomic and protein expression study of susceptibility gene with its clinical and biochemical analysis. To the best of our knowledge this is the first preliminary comprehensive study in Indian population that identified

Neeraj Kumar; Krishna Kant Taneja; Veena Kalra; Madhuri Behari; Satinder Aneja; Surendra Kumar Bansal; Mark R. Cookson

2011-01-01

202

A Screen for Modifiers of Cyclin E Function in Drosophila melanogaster Identifies Cdk2 Mutations, Revealing the Insignificance of Putative Phosphorylation Sites in Cdk2  

Microsoft Academic Search

In higher eukaryotes, cyclin E is thought to control the progression from G1 into S phase of the cell cycle by associating as a regulatory subunit with cdk2. To identify genes interacting with cyclin E, we have screened in Drosophila melanogaster for mutations that act as dominant modifiers of an eye phenotype caused by a Sevenless-CycE transgene that directs ectopic

Marion Elend; Doris Heidmann; Anabel Herr; Sandra Marzodko; Alf Herzig; Christian F. Lehner

2000-01-01

203

Genomic Analysis of hESC Pedigrees Identifies De Novo Mutations and Enables Determination of the Timing and Origin of Mutational Events.  

PubMed

Given the association between mutational load and cancer, the observation that genetic aberrations are frequently found in human pluripotent stem cells (hPSCs) is of concern. Prior studies in human induced pluripotent stem cells (hiPSCs) have shown that deletions and regions of loss of heterozygosity (LOH) tend to arise during reprogramming and early culture, whereas duplications more frequently occur during long-term culture. For the corresponding experiments in human embryonic stem cells (hESCs), we studied two sets of hESC lines: one including the corresponding parental DNA and the other generated from single blastomeres from four sibling embryos. Here, we show that genetic aberrations observed in hESCs can originate during preimplantation embryo development and/or early derivation. These early aberrations are mainly deletions and LOH, whereas aberrations arising during long-term culture of hESCs are more frequently duplications. Our results highlight the importance of close monitoring of genomic integrity and the development of improved methods for derivation and culture of hPSCs. PMID:24035391

Ben-Yosef, Dalit; Boscolo, Francesca S; Amir, Hadar; Malcov, Mira; Amit, Ami; Laurent, Louise C

2013-09-12

204

Deep intronic mutation in OFD1, identified by targeted genomic next-generation sequencing, causes a severe form of X-linked retinitis pigmentosa (RP23).  

PubMed

X-linked retinitis pigmentosa (XLRP) is genetically heterogeneous with two causative genes identified, RPGR and RP2. We previously mapped a locus for a severe form of XLRP, RP23, to a 10.71 Mb interval on Xp22.31-22.13 containing 62 genes. Candidate gene screening failed to identify a causative mutation, so we adopted targeted genomic next-generation sequencing of the disease interval to determine the molecular cause of RP23. No coding variants or variants within or near splice sites were identified. In contrast, a variant deep within intron 9 of OFD1 increased the splice site prediction score 4 bp upstream of the variant. Mutations in OFD1 cause the syndromic ciliopathies orofaciodigital syndrome-1, which is male lethal, Simpson-Golabi-Behmel syndrome type 2 and Joubert syndrome. We tested the effect of the IVS9+706A>G variant on OFD1 splicing in vivo. In RP23 patient-derived RNA, we detected an OFD1 transcript with the insertion of a cryptic exon spliced between exons 9 and 10 causing a frameshift, p.N313fs.X330. Correctly spliced OFD1 was also detected in patient-derived RNA, although at reduced levels (39%), hence the mutation is not male lethal. Our data suggest that photoreceptors are uniquely susceptible to reduced expression of OFD1 and that an alternative disease mechanism can cause XLRP. This disease mechanism of reduced expression for a syndromic ciliopathy gene causing isolated retinal degeneration is reminiscent of CEP290 intronic mutations that cause Leber congenital amaurosis, and we speculate that reduced dosage of correctly spliced ciliopathy genes may be a common disease mechanism in retinal degenerations. PMID:22619378

Webb, Tom R; Parfitt, David A; Gardner, Jessica C; Martinez, Ariadna; Bevilacqua, Dalila; Davidson, Alice E; Zito, Ilaria; Thiselton, Dawn L; Ressa, Jacob H C; Apergi, Marina; Schwarz, Nele; Kanuga, Naheed; Michaelides, Michel; Cheetham, Michael E; Gorin, Michael B; Hardcastle, Alison J

2012-05-22

205

Deep intronic mutation in OFD1, identified by targeted genomic next-generation sequencing, causes a severe form of X-linked retinitis pigmentosa (RP23)  

PubMed Central

X-linked retinitis pigmentosa (XLRP) is genetically heterogeneous with two causative genes identified, RPGR and RP2. We previously mapped a locus for a severe form of XLRP, RP23, to a 10.71 Mb interval on Xp22.31-22.13 containing 62 genes. Candidate gene screening failed to identify a causative mutation, so we adopted targeted genomic next-generation sequencing of the disease interval to determine the molecular cause of RP23. No coding variants or variants within or near splice sites were identified. In contrast, a variant deep within intron 9 of OFD1 increased the splice site prediction score 4 bp upstream of the variant. Mutations in OFD1 cause the syndromic ciliopathies orofaciodigital syndrome-1, which is male lethal, Simpson–Golabi–Behmel syndrome type 2 and Joubert syndrome. We tested the effect of the IVS9+706A>G variant on OFD1 splicing in vivo. In RP23 patient-derived RNA, we detected an OFD1 transcript with the insertion of a cryptic exon spliced between exons 9 and 10 causing a frameshift, p.N313fs.X330. Correctly spliced OFD1 was also detected in patient-derived RNA, although at reduced levels (39%), hence the mutation is not male lethal. Our data suggest that photoreceptors are uniquely susceptible to reduced expression of OFD1 and that an alternative disease mechanism can cause XLRP. This disease mechanism of reduced expression for a syndromic ciliopathy gene causing isolated retinal degeneration is reminiscent of CEP290 intronic mutations that cause Leber congenital amaurosis, and we speculate that reduced dosage of correctly spliced ciliopathy genes may be a common disease mechanism in retinal degenerations.

Webb, Tom R.; Parfitt, David A.; Gardner, Jessica C.; Martinez, Ariadna; Bevilacqua, Dalila; Davidson, Alice E.; Zito, Ilaria; Thiselton, Dawn L.; Ressa, Jacob H.C.; Apergi, Marina; Schwarz, Nele; Kanuga, Naheed; Michaelides, Michel; Cheetham, Michael E.; Gorin, Michael B.; Hardcastle, Alison J.

2012-01-01

206

Immunohistochemical Expression of Estrogen and Progesterone Receptors Identifies a Subset of NSCLCs and Correlates with EGFR Mutation  

PubMed Central

Purpose To determine the frequency of estrogen receptor ? and ? and progesterone receptor protein immunohistochemical expression in a large set of non–small cell lungcarcinoma (NSCLC) specimens and to compare our results with those for some of the same antibodies that have provided inconsistent results in previously published reports. Experimental Design Using multiple antibodies, we investigated the immunohistochemical expression of estrogen receptors ? and ? and progesterone receptor in 317 NSCLCs placed in tissue microarrays and correlated their expression with patients’ clinicopathologic characteristics and in adenocarcinomas with EGFR mutation status. Results Estrogen receptors ? and ? were detected in the nucleus and cytoplasm of NSCLC cells; however, the frequency of expression (nucleus, 5-36% for ? and 42-56% for ?; cytoplasm: <1-42% for ? and 20-98% for ?) varied among the different antibodies tested. Progesterone receptor was expressed in the nuclei of malignant cells in 63% of the tumors. Estrogen receptor ? nuclear expression significantly correlated with adenocarcinoma histology, female gender, and history of never smoking (P = 0.0048 to <0.0001). In NSCLC, higher cytoplasmic estrogen receptor ? expression significantly correlated with worse recurrence-free survival (hazard ratio, 1.77; 95% confidence interval, 1.12, 2.82; P = 0.015) in multivariate analysis. In adenocarcinomas, estrogen receptor ? expression correlated with EGFR mutation (P = 0.0029 to <0.0001). Estrogen receptor ? and progesterone receptor but not estrogen receptor ? expressed in the normal epithelium adjacent to lung adenocarcinomas. Conclusions Estrogen receptor ? and ? expression distinguishes a subset of NSCLC that has defined clinicopathologic and genetic features. In lung adenocarcinoma, estrogen receptor ? expression correlates with EGFR mutations.

Raso, Maria G.; Behrens, Carmen; Herynk, Matthew H.; Liu, Suyu; Prudkin, Ludmila; Ozburn, Natalie C.; Woods, Denise M.; Tang, Ximing; Mehran, Reza J.; Moran, Cesar; Lee, J. Jack; Wistuba, Ignacio I.

2010-01-01

207

A General Method for Identifying Recessive Diploid-Specific Mutations in Saccharomyces Cerevisiae, Its Application to the Isolation of Mutants Blocked at Intermediate Stages of Meiotic Prophase and Characterization of a New Gene Sae2  

PubMed Central

We describe a general new approach for identifying recessive mutations that affect diploid strains of yeast Saccharomyces cerevisiae and the application of this method to the identification of mutations that confer an intermediate block in meiotic prophase chromosome metabolism. The method uses a temperature-sensitive conjugation mutation ste7-1 in combination with homothallism. The mutations of interest confer a defect in spore formation that is dependent upon a gene required for initiation of meiotic recombination and development of meiosis-specific chromosome structure (SPO11). Identified in this screen were null mutations of the DMC1 gene, nonnull mutations of RAD50 (rad50S), and mutations in three new genes designated SAE1, SAE2 and SAE3 (Sporulation in the Absence of Spo Eleven). Molecular characterization of the SAE2 gene and characterization of meiotic and mitotic phenotypes of sae2 mutants are also presented. The phenotypes conferred by a sae2 null mutation are virtually indistinguishable from those conferred by the previously identified nonnull mutations of RAD50 (rad50S). Most notably, both mutations confer only weak sensitivity to the radiomimetic agent methyl methane sulfonate (MMS) but completely block resection and turnover of meiosis-specific double-strand breaks. These observations provide further evidence that this constellation of phenotypes identifies a specific molecular function.

McKee, AHZ.; Kleckner, N.

1997-01-01

208

Zic2 hypomorphic mutant mice as a schizophrenia model and ZIC2 mutations identified in schizophrenia patients.  

PubMed

ZIC2 is a causal gene for holoprosencephaly and encodes a zinc-finger-type transcriptional regulator. We characterized Zic2(kd/+) mice with a moderate (40%) reduction in Zic2 expression. Zic2(kd/+) mice showed increased locomotor activity in novel environments, cognitive and sensorimotor gating dysfunctions, and social behavioral abnormalities. Zic2(kd/+) brain involved enlargement of the lateral ventricle, thinning of the cerebral cortex and corpus callosum, and decreased number of cholinergic neurons in the basal forebrain. Because these features are reminiscent of schizophrenia, we examined ZIC2 variant-carrying allele frequencies in schizophrenia patients and in controls in the Japanese population. Among three novel missense mutations in ZIC2, R409P was only found in schizophrenia patients, and was located in a strongly conserved position of the zinc finger domain. Mouse Zic2 with the corresponding mutation showed lowered transcription-activating capacity and had impaired target DNA-binding and co-factor-binding capacities. These results warrant further study of ZIC2 in the pathogenesis of schizophrenia. PMID:22355535

Hatayama, Minoru; Ishiguro, Akira; Iwayama, Yoshimi; Takashima, Noriko; Sakoori, Kazuto; Toyota, Tomoko; Nozaki, Yayoi; Odaka, Yuri S; Yamada, Kazuyuki; Yoshikawa, Takeo; Aruga, Jun

2011-06-17

209

A Screen for X-Linked Mutations Affecting Drosophila Photoreceptor Differentiation Identifies Casein Kinase 1? as an Essential Negative Regulator of Wingless Signaling  

PubMed Central

The Wnt and Hedgehog signaling pathways are essential for normal development and are misregulated in cancer. The casein kinase family of serine/threonine kinases regulates both pathways at multiple levels. However, it has been difficult to determine whether individual members of this family have distinct functions in vivo, due to their overlapping substrate specificities. In Drosophila melanogaster, photoreceptor differentiation is induced by Hedgehog and inhibited by Wingless, providing a sensitive system in which to identify regulators of each pathway. We used a mosaic genetic screen in the Drosophila eye to identify mutations in genes on the X chromosome required for signal transduction. We recovered mutations affecting the transcriptional regulator CREB binding protein, the small GTPase dynamin, the cytoskeletal regulator Actin-related protein 2, and the protein kinase Casein kinase 1?. Consistent with its reported function in the ?-Catenin degradation complex, Casein Kinase 1? mutant cells accumulate ?-Catenin and ectopically induce Wingless target genes. In contrast to previous studies based on RNA interference, we could not detect any effect of the same Casein Kinase 1? mutation on Hedgehog signaling. We thus propose that Casein kinase 1? is essential to allow ?-Catenin degradation and prevent inappropriate Wingless signaling, but its effects on the Hedgehog pathway are redundant with other Casein kinase 1 family members.

Legent, Kevin; Steinhauer, Josefa; Richard, Magali; Treisman, Jessica E.

2012-01-01

210

A screen for X-linked mutations affecting Drosophila photoreceptor differentiation identifies Casein kinase 1? as an essential negative regulator of wingless signaling.  

PubMed

The Wnt and Hedgehog signaling pathways are essential for normal development and are misregulated in cancer. The casein kinase family of serine/threonine kinases regulates both pathways at multiple levels. However, it has been difficult to determine whether individual members of this family have distinct functions in vivo, due to their overlapping substrate specificities. In Drosophila melanogaster, photoreceptor differentiation is induced by Hedgehog and inhibited by Wingless, providing a sensitive system in which to identify regulators of each pathway. We used a mosaic genetic screen in the Drosophila eye to identify mutations in genes on the X chromosome required for signal transduction. We recovered mutations affecting the transcriptional regulator CREB binding protein, the small GTPase dynamin, the cytoskeletal regulator Actin-related protein 2, and the protein kinase Casein kinase 1?. Consistent with its reported function in the ?-Catenin degradation complex, Casein Kinase 1? mutant cells accumulate ?-Catenin and ectopically induce Wingless target genes. In contrast to previous studies based on RNA interference, we could not detect any effect of the same Casein Kinase 1? mutation on Hedgehog signaling. We thus propose that Casein kinase 1? is essential to allow ?-Catenin degradation and prevent inappropriate Wingless signaling, but its effects on the Hedgehog pathway are redundant with other Casein kinase 1 family members. PMID:22095083

Legent, Kevin; Steinhauer, Josefa; Richard, Magali; Treisman, Jessica E

2011-11-17

211

A Quantitative Signaling Screen Identifies CARD11 Mutations in the CARD and LATCH Domains That Induce Bcl10 Ubiquitination and Human Lymphoma Cell Survival  

PubMed Central

Antigen receptor signaling to NF-?B, essential for normal lymphocyte activation, is dysregulated in several types of lymphoma. During normal signaling, the multidomain adapter CARD11 transitions from a closed, inactive state to an open, active scaffold that assembles a multiprotein complex, leading to NF-?B activation. The regulation of CARD11 scaffold function is bypassed by lymphoma-associated oncogenic CARD11 mutations that induce spontaneous signaling. We report an unbiased high-throughput quantitative signaling screen that identifies new CARD11 hyperactive variants and defines a LATCH domain that functions with the CARD to promote CARD11 autoinhibition. Gain-of-function mutations in the LATCH or CARD disrupt inhibitory domain binding, promote Bcl10 association, and induce Bcl10 ubiquitination, NF-?B activation, and human lymphoma cell survival. Our results identify CARD11 mutations with oncogenic potential, provide a mechanistic explanation for their signaling potency, and offer a straightforward method for the discovery of variants that promote the tumorigenesis of NF-?B-dependent lymphomas.

Chan, Waipan; Schaffer, Thomas B.

2013-01-01

212

Genetic variants associated with breast cancer risk for Ashkenazi Jewish women with strong family histories but no identifiable BRCA1/2 mutation.  

PubMed

The ability to establish genetic risk models is critical for early identification and optimal treatment of breast cancer. For such a model to gain clinical utility, more variants must be identified beyond those discovered in previous genome-wide association studies (GWAS). This is especially true for women at high risk because of family history, but without BRCA1/2 mutations. This study incorporates three datasets in a GWAS analysis of women with Ashkenazi Jewish (AJ) homogeneous ancestry. Two independent discovery cohorts comprised 239 and 238 AJ women with invasive breast cancer or preinvasive ductal carcinoma in situ and strong family histories of breast cancer, but lacking the three BRCA1/2 founder mutations, along with 294 and 230 AJ controls, respectively. An independent, third cohort of 203 AJ cases with familial breast cancer history and 263 healthy controls of AJ women was used for validation. A total of 19 SNPs were identified as associated with familial breast cancer risk in AJ women. Among these SNPs, 13 were identified from a panel of 109 discovery SNPs, including an FGFR2 haplotype. In addition, six previously identified breast cancer GWAS SNPs were confirmed in this population. Seven of the 19 markers were significant in a multivariate predictive model of familial breast cancer in AJ women, three novel SNPs [rs17663555(5q13.2), rs566164(6q21), and rs11075884(16q22.2)], the FGFR2 haplotype, and three previously published SNPs [rs13387042(2q35), rs2046210(ESR1), and rs3112612(TOX3)], yielding moderate predictive power with an area under the curve (AUC) of the ROC (receiver-operator characteristic curve) of 0.74. Population-specific genetic variants in addition to variants shared with populations of European ancestry may improve breast cancer risk prediction among AJ women from high-risk families without founder BRCA1/2 mutations. PMID:23354978

Rinella, Erica S; Shao, Yongzhao; Yackowski, Lauren; Pramanik, Sreemanta; Oratz, Ruth; Schnabel, Freya; Guha, Saurav; LeDuc, Charles; Campbell, Christopher L; Klugman, Susan D; Terry, Mary Beth; Senie, Ruby T; Andrulis, Irene L; Daly, Mary; John, Esther M; Roses, Daniel; Chung, Wendy K; Ostrer, Harry

2013-01-25

213

High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency  

PubMed Central

Discovering the molecular basis of mitochondrial respiratory chain disease is challenging given the large number of both mitochondrial and nuclear genes involved. We report a strategy of focused candidate gene prediction, high-throughput sequencing, and experimental validation to uncover the molecular basis of mitochondrial complex I (CI) disorders. We created five pools of DNA from a cohort of 103 patients and then performed deep sequencing of 103 candidate genes to spotlight 151 rare variants predicted to impact protein function. We used confirmatory experiments to establish genetic diagnoses in 22% of previously unsolved cases, and discovered that defects in NUBPL and FOXRED1 can cause CI deficiency. Our study illustrates how large-scale sequencing, coupled with functional prediction and experimental validation, can reveal novel disease-causing mutations in individual patients.

Calvo, Sarah E; Tucker, Elena J; Compton, Alison G; Kirby, Denise M; Crawford, Gabriel; Burtt, Noel P; Rivas, Manuel A; Guiducci, Candace; Bruno, Damien L; Goldberger, Olga A; Redman, Michelle C; Wiltshire, Esko; Wilson, Callum J; Altshuler, David; Gabriel, Stacey B; Daly, Mark J; Thorburn, David R; Mootha, Vamsi K

2010-01-01

214

Functional outcome of a novel SLC29A3 mutation identified in a patient with H syndrome.  

PubMed

The H syndrome (OMIM 612391) is an autosomal recessive disorder characterized by hyperpigmentation, hypertrichosis, histiocytosis and short stature. It is caused by mutations in the SLC29A3 gene, which encodes for the equilibrative nucleoside transporter 3 protein (ENT3), of still uncertain subcellular localisation. Here we report a new case of H syndrome with the novel mutation c.243delA, which has been concomitantly described by others [A. Bolze, A. Abhyankar, A.V. Grant, B. Patel, R. Yadav, M. Byun, D. Caillez, J.F. Emile, M. Pastor-Anglada, L. Abel, A. Puel, R. Govindarajan, L. de Pontual, J.L. Casanova, A mild form of SLC29A3 disorder: a frameshift deletion leads to the paradoxical translation of an otherwise noncoding mRNA splice variant, PLoS ONE 7 (2012) e29708]. Patient-derived primary skin fibroblasts and B-lymphoblastoid cell lines (B-LCL) were obtained and, although no differences were found in mRNA levels of ENT3, a significant increase in plasma membrane equilibrative transport activity was found in fibroblasts from the patient. Loss of function of key proteins implicated in nucleoside metabolism can lead to mitochondrial DNA (mtDNA) depletion syndromes (MDS). Measurement of respiratory chain complex activity revealed that mitochondrial function was unaltered. Neither fibroblasts nor B-LCL showed mtDNA depletion when compared with controls. Fibroblasts and B-LCL from the patient were not particularly protected when mitochondrial damage was induced using nucleoside-derived drugs susceptible to being transported by ENT3. Analysis of mtDNA amounts in tissues obtained at autopsy proved inconclusive with respect to mitochondrial involvement in the pathogenesis of this syndrome. Overall, the data do not support the inclusion of H syndrome among the MDS and these findings are compatible with its recent inclusion among the lysosomal storage diseases. PMID:23058913

Huber-Ruano, Isabel; Errasti-Murugarren, Ekaitz; Godoy, Valeria; Vera, Ángel; Andreu, Antoni L; Garcia-Arumi, Elena; Martí, Ramon; Pastor-Anglada, Marçal

2012-10-08

215

Detection of Kanamycin-Resistant Mycobacterium tuberculosis by Identifying Mutations in the 16S rRNA Gene  

PubMed Central

In Mycobacterium smegmatis and a limited number of Mycobacterium tuberculosis strains, the involvement of alterations of the 16S rRNA gene (rrs) in resistance to kanamycin has been shown. To investigate the extent to which mutations in a specific region of the rrs gene and the kanamycin-resistant phenotype in clinically isolated M. tuberculosis strains were correlated, 43 kanamycin-resistant strains (MICs, ?200 ?g/ml), 71 kanamycin-susceptible strains, and 4 type strains were examined. The 300-bp DNA fragments carrying the rrs gene and the intervening sequence between the rrs gene and 23S rRNA (rrl) gene fragments were amplified by PCR and were subjected to PCR-based direct sequencing. By comparing the nucleotide sequences, substitutions were found in 29 of 43 (67.4%) kanamycin-resistant clinical isolates at positions 1400, 1401, and 1483 but in none of the 71 sensitive isolates or the 4 type strains. The most frequent substitution, from A to G, occurred at position 1400. A substitution from C to T at position 1401 was found once. Two clinical isolates carried the double mutation from C to A at position 1401 and from G to T at position 1483. In addition, we found that these mutants can be distinguished from wild-type strains by digestion with the restriction endonucleases TaiI and Tsp45I. Furthermore, we found that the genotypes of kanamycin-resistant strains can be discriminated from each other by digestion with a restriction endonuclease, BstUI or DdeI.

Suzuki, Yasuhiko; Katsukawa, Chihiro; Tamaru, Aki; Abe, Chiyoji; Makino, Masanao; Mizuguchi, Yasuo; Taniguchi, Hatsumi

1998-01-01

216

Gain-of-function mutations in the Caenorhabditis elegans lin-1 ETS gene identify a C-terminal regulatory domain phosphorylated by ERK MAP kinase.  

PubMed Central

Genetic analysis of lin-1 loss-of-function mutations suggests that lin-1 controls multiple cell-fate decisions during Caenorhabditis elegans development and is negatively regulated by a conserved receptor tyrosine kinase-Ras-ERK mitogen-activated protein (MAP) kinase signal transduction pathway. LIN-1 protein contains an ETS domain and presumably regulates transcription. We identified and characterized six gain-of-function mutations that define a new class of lin-1 allele. These lin-1 alleles appeared to be constitutively active and unresponsive to negative regulation. Each allele has a single-base change that affects the predicted C terminus of LIN-1, suggesting this region is required for negative regulation. The C terminus of LIN-1 was a high-affinity substrate for Erk2 in vitro, suggesting that LIN-1 is directly regulated by ERK MAP kinase. Because mpk-1 ERK MAP kinase controls at least one cell-fate decision that does not require lin-1, our results suggest that MPK-1 contributes to the specificity of this receptor tyrosine kinase-Ras-MAP kinase signal transduction pathway by phosphorylating different proteins in different developmental contexts. These lin-1 mutations all affect a four-amino-acid motif, FQFP, that is conserved in vertebrate and Drosophila ETS proteins that are also phosphorylated by ERK MAP kinase. This sequence may be a substrate recognition motif for the ERK subfamily of MAP kinases.

Jacobs, D; Beitel, G J; Clark, S G; Horvitz, H R; Kornfeld, K

1998-01-01

217

A Mutational Analysis of Killer Toxin Resistance in Saccharomyces Cerevisiae Identifies New Genes Involved in Cell Wall (1 -> 6)-?-Glucan Synthesis  

PubMed Central

Recessive mutations leading to killer resistance identify the KRE9, KRE10 and KRE11 genes. Mutations in both the KRE9 and KRE11 genes lead to reduced levels of (1 -> 6)-?-glucan in the yeast cell wall. The KRE11 gene encodes a putative 63-kD cytoplasmic protein, and disruption of the KRE11 locus leads to a 50% reduced level of cell wall (1 -> 6)-glucan. Structural analysis of the (1 -> 6)-?-glucan remaining in a kre11 mutant indicates a polymer smaller in size than wild type, but containing a similar proportion of (1 -> 6)- and (1 -> 3)-linkages. Genetic interactions among cells harboring mutations at the KRE11, KRE6 and KRE1 loci indicate lethality of kre11 kre6 double mutants and that kre11 is epistatic to kre1, with both gene products required to produce the mature glucan polymer at wild-type levels. Analysis of these KRE genes should extend knowledge of the ?-glucan biosynthetic pathway, and of cell wall synthesis in yeast.

Brown, J. L.; Kossaczka, Z.; Jiang, B.; Bussey, H.

1993-01-01

218

Mutational Profiling of Kinases in Human Tumours of Pancreatic Origin Identifies Candidate Cancer Genes in Ductal and Ampulla of Vater Carcinomas  

PubMed Central

Background Protein kinases are key regulators of cellular processes (such as proliferation, apoptosis and invasion) that are often deregulated in human cancers. Accordingly, kinase genes have been the first to be systematically analyzed in human tumors leading to the discovery that many oncogenes correspond to mutated kinases. In most cases the genetic alterations translate in constitutively active kinase proteins, which are amenable of therapeutic targeting. Tumours of the pancreas are aggressive neoplasms for which no effective therapeutic strategy is currently available. Methodology/Principal Findings We conducted a DNA-sequence analysis of a selected set of 35 kinase genes in a panel of 52 pancreatic exocrine neoplasms, including 36 pancreatic ductal adenocarcinoma, and 16 ampulla of Vater cancer. Among other changes we found somatic mutations in ATM, EGFR, EPHA3, EPHB2, and KIT, none of which was previously described in cancers. Conclusions/Significance Although the alterations identified require further experimental evaluation, the localization within defined protein domains indicates functional relevance for most of them. Some of the mutated genes, including the tyrosine kinases EPHA3 and EPHB2, are clearly amenable to pharmacological intervention and could represent novel therapeutic targets for these incurable cancers.

Corbo, Vincenzo; Ritelli, Rossana; Barbi, Stefano; Funel, Niccola; Campani, Daniela; Bardelli, Alberto; Scarpa, Aldo

2010-01-01

219

Robust full-length hepatitis C virus genotype 2a and 2b infectious cultures using mutations identified by a systematic approach applicable to patient strains.  

PubMed

Hepatitis C virus (HCV) infection is a leading cause of chronic liver diseases worldwide, but treatment options are limited. Basic HCV research required for vaccine and drug development has been hampered by inability to culture patient isolates, and to date only the JFH1 (genotype 2a) recombinant replicates spontaneously in hepatoma cells and releases infectious virus. A JFH1 chimera with the 5' end through NS2 from another genotype 2a strain, J6, had enhanced infectivity. However, the full-length J6 clone (J6CF), which we previously found to be fully functional in vivo, was replication incompetent in vitro. Through a systematic approach of culturing J6 with minimal JFH1 sequences, we identified three mutations in NS3, NS4A, and NS5B that permitted full-length J6 propagation and adaptation with infectivity titers comparable to JFH1-based systems. The most efficient recombinant, J6cc, had six adaptive mutations and did not accumulate additional changes following viral passage. We demonstrated that HCV NS3/NS4A protease-, NS5A- and NS5B polymerase-directed drugs respectively inhibited full-length J6 infection dose dependently. Importantly, the three J6-derived mutations enabled culture adaptation of the genetically divergent isolate J8 (genotype 2b), which differed from the J6 nucleotide sequence by 24%. The most efficient recombinant, J8cc, had nine adaptive mutations and was genetically stable after viral passage. The availability of these robust JFH1-independent genotype 2a and 2b culture systems represents an important advance, and the approach used might permit culture development of other isolates, with implications for improved individualized treatments of HCV patients and for development of broadly efficient vaccines. PMID:22467829

Li, Yi-Ping; Ramirez, Santseharay; Gottwein, Judith M; Scheel, Troels K H; Mikkelsen, Lotte; Purcell, Robert H; Bukh, Jens

2012-03-30

220

Whole-exome sequencing identifies homozygous AFG3L2 mutations in a spastic ataxia-neuropathy syndrome linked to mitochondrial m-AAA proteases.  

PubMed

We report an early onset spastic ataxia-neuropathy syndrome in two brothers of a consanguineous family characterized clinically by lower extremity spasticity, peripheral neuropathy, ptosis, oculomotor apraxia, dystonia, cerebellar atrophy, and progressive myoclonic epilepsy. Whole-exome sequencing identified a homozygous missense mutation (c.1847G>A; p.Y616C) in AFG3L2, encoding a subunit of an m-AAA protease. m-AAA proteases reside in the mitochondrial inner membrane and are responsible for removal of damaged or misfolded proteins and proteolytic activation of essential mitochondrial proteins. AFG3L2 forms either a homo-oligomeric isoenzyme or a hetero-oligomeric complex with paraplegin, a homologous protein mutated in hereditary spastic paraplegia type 7 (SPG7). Heterozygous loss-of-function mutations in AFG3L2 cause autosomal-dominant spinocerebellar ataxia type 28 (SCA28), a disorder whose phenotype is strikingly different from that of our patients. As defined in yeast complementation assays, the AFG3L2(Y616C) gene product is a hypomorphic variant that exhibited oligomerization defects in yeast as well as in patient fibroblasts. Specifically, the formation of AFG3L2(Y616C) complexes was impaired, both with itself and to a greater extent with paraplegin. This produced an early-onset clinical syndrome that combines the severe phenotypes of SPG7 and SCA28, in additional to other "mitochondrial" features such as oculomotor apraxia, extrapyramidal dysfunction, and myoclonic epilepsy. These findings expand the phenotype associated with AFG3L2 mutations and suggest that AFG3L2-related disease should be considered in the differential diagnosis of spastic ataxias. PMID:22022284

Pierson, Tyler Mark; Adams, David; Bonn, Florian; Martinelli, Paola; Cherukuri, Praveen F; Teer, Jamie K; Hansen, Nancy F; Cruz, Pedro; Mullikin For The Nisc Comparative Sequencing Program, James C; Blakesley, Robert W; Golas, Gretchen; Kwan, Justin; Sandler, Anthony; Fuentes Fajardo, Karin; Markello, Thomas; Tifft, Cynthia; Blackstone, Craig; Rugarli, Elena I; Langer, Thomas; Gahl, William A; Toro, Camilo

2011-10-13

221

Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation  

Microsoft Academic Search

While there have been significant advances in understanding the genetic etiology of human hair loss over the previous decade, there remain a number of hereditary disorders for which a causative gene has yet to be identified. We studied a large, consanguineous Brazilian family that presented with woolly hair at birth that progressed to severe hypotrichosis by the age of 5,

Lynn Petukhova; Edilson C. Sousa; Amalia Martinez-Mir; Anna Vitebsky; Lina G. dos Santos; Lawrence Shapiro; Chad Haynes; Derek Gordon; Yutaka Shimomura; Angela M. Christiano

2008-01-01

222

An RNA-seq protocol to identify mRNA expression changes in mouse diaphyseal bone: Applications in mice with bone property altering Lrp5 mutations.  

PubMed

Loss-of-function and certain missense mutations in the Wnt coreceptor low-density lipoprotein receptor-related protein 5 (LRP5) significantly decrease or increase bone mass, respectively. These human skeletal phenotypes have been recapitulated in mice harboring Lrp5 knockout and knock-in mutations. We hypothesized that measuring mRNA expression in diaphyseal bone from mice with Lrp5 wild-type (Lrp5(+/+) ), knockout (Lrp5(-/-) ), and high bone mass (HBM)-causing (Lrp5(p.A214V/+) ) knock-in alleles could identify genes and pathways that regulate or are regulated by LRP5 activity. We performed RNA-seq on pairs of tibial diaphyseal bones from four 16-week-old mice with each of the aforementioned genotypes. We then evaluated different methods for controlling for contaminating nonskeletal tissue (ie, blood, bone marrow, and skeletal muscle) in our data. These methods included predigestion of diaphyseal bone with collagenase and separate transcriptional profiling of blood, skeletal muscle, and bone marrow. We found that collagenase digestion reduced contamination, but also altered gene expression in the remaining cells. In contrast, in silico filtering of the diaphyseal bone RNA-seq data for highly expressed blood, skeletal muscle, and bone marrow transcripts significantly increased the correlation between RNA-seq data from an animal's right and left tibias and from animals with the same Lrp5 genotype. We conclude that reliable and reproducible RNA-seq data can be obtained from mouse diaphyseal bone and that lack of LRP5 has a more pronounced effect on gene expression than the HBM-causing LRP5 missense mutation. We identified 84 differentially expressed protein-coding transcripts between LRP5 "sufficient" (ie, Lrp5(+/+) and Lrp5(p.A214V/+) ) and "insufficient" (Lrp5(-/-) ) diaphyseal bone, and far fewer differentially expressed genes between Lrp5(p.A214V/+) and Lrp5(+/+) diaphyseal bone. © 2013 American Society for Bone and Mineral Research. PMID:23553928

Ayturk, Ugur M; Jacobsen, Christina M; Christodoulou, Danos C; Gorham, Joshua; Seidman, Jonathan G; Seidman, Christine E; Robling, Alexander G; Warman, Matthew L

2013-10-01

223

A specific screen for oligosaccharyltransferase mutations identifies the 9 kDa OST5 protein required for optimal activity in vivo and in vitro.  

PubMed Central

The central reaction in the process of N-linked protein glycosylation in eukaryotic cells, the transfer of the oligosaccharide Glc(3)Man(9)GlcNAc(2) from the lipid dolicholpyrophosphate to selected asparagine residues, is catalyzed by the oligosaccharyltransferase (OTase). This enzyme consists of multiple subunits; however, purification of the complex has revealed different results with respect to its protein composition. To determine how many different loci are required for OTase activity in vivo, we performed a novel, specific screen for mutants with altered OTase activity. Based on the synthetic lethal phenotype of OTase mutants in combination with a deficiency of dolicholphosphoglucose biosynthesis which results in non-glucosylated lipid-linked oligosaccharide, we identified seven complementation groups with decreased OTase activity. Beside the known OTase loci, STT3, OST1, WBP1, OST3, SWP1 and OST2, a novel locus, OST5, was identified. OST5 is an intron-containing gene encoding a putative membrane protein of 9.5 kDa present in highly purified OTase preparations. OST5 protein is not essential for growth but its depletion results in a reduced OTase activity. Suppression of an ost1 mutation by overexpression of OST5 indicates that this small membrane protein directly interacts with other OTase components, most likely with Ost1p. A strong genetic interaction with a stt3 mutation implies a role in complex assembly.

Reiss, G; te Heesen, S; Gilmore, R; Zufferey, R; Aebi, M

1997-01-01

224

Mutational Analysis of Aminopeptidase N, a Receptor for Several Group 1 Coronaviruses, Identifies Key Determinants of Viral Host Range  

Microsoft Academic Search

Feline coronavirus (FCoV), porcine transmissible gastroenteritis coronavirus (TGEV), canine coronavirus (CCoV), and human coronavirus HCoV-229E, which belong to the group 1 coronavirus, use aminopeptidase N (APN) of their natural host and feline APN (fAPN) as receptors. Using mouse-feline APN chimeras, we identified three small, discontinuous regions, amino acids (aa) 288 to 290, aa 732 to 746 (called R1), and aa

Sonia M. Tusell; Stephanie A. Schittone; Kathryn V. Holmes

2007-01-01

225

A novel K509I mutation of KIT identified in familial mastocytosis—in vitro and in vivo responsiveness to imatinib therapy  

Microsoft Academic Search

KIT mutation has been implicated in sporadic mastocytosis, yet clusters in only a few sites in the molecule. For those malignancies associated with KIT mutation or over-expression, imatinib offers a specific therapeutic option, yet it has no effect on D816V mutation commonly seen in sporadic mastocytosis. The majority of cases of familial mastocytosis seem to lack KIT mutation. We report

Ling Yan Zhang; Matthew L. Smith; Beate Schultheis; Jude Fitzgibbon; T. Andrew Lister; Junia V. Melo; Nicholas C. P. Cross; Jamie D. Cavenagh

2006-01-01

226

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk  

PubMed Central

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P?=?2.7×10?8, HR?=?1.14, 95% CI: 1.09–1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P?=?1.4×10?8, HR?=?1.27, 95% CI: 1.17–1.38) and 4q32.3 (rs4691139, P?=?3.4×10?8, HR?=?1.20, 95% CI: 1.17–1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific association. The 17q21.31 locus was also associated with ovarian cancer risk in 8,211 BRCA2 carriers (P?=?2×10?4). These loci may lead to an improved understanding of the etiology of breast and ovarian tumors in BRCA1 carriers. Based on the joint distribution of the known BRCA1 breast cancer risk-modifying loci, we estimated that the breast cancer lifetime risks for the 5% of BRCA1 carriers at lowest risk are 28%–50% compared to 81%–100% for the 5% at highest risk. Similarly, based on the known ovarian cancer risk-modifying loci, the 5% of BRCA1 carriers at lowest risk have an estimated lifetime risk of developing ovarian cancer of 28% or lower, whereas the 5% at highest risk will have a risk of 63% or higher. Such differences in risk may have important implications for risk prediction and clinical management for BRCA1 carriers.

Wang, Xianshu; McGuffog, Lesley; Lee, Andrew; Olswold, Curtis; Kuchenbaecker, Karoline B.; Soucy, Penny; Fredericksen, Zachary; Barrowdale, Daniel; Dennis, Joe; Gaudet, Mia M.; Dicks, Ed; Kosel, Matthew; Healey, Sue; Sinilnikova, Olga M.; Lee, Adam; Bacot, Francois; Vincent, Daniel; Hogervorst, Frans B. L.; Peock, Susan; Stoppa-Lyonnet, Dominique; Jakubowska, Anna; Investigators, kConFab; Radice, Paolo; Schmutzler, Rita Katharina; Domchek, Susan M.; Piedmonte, Marion; Singer, Christian F.; Friedman, Eitan; Thomassen, Mads; Hansen, Thomas V. O.; Neuhausen, Susan L.; Szabo, Csilla I.; Blanco, Ignacio; Greene, Mark H.; Karlan, Beth Y.; Garber, Judy; Phelan, Catherine M.; Weitzel, Jeffrey N.; Montagna, Marco; Olah, Edith; Andrulis, Irene L.; Godwin, Andrew K.; Yannoukakos, Drakoulis; Goldgar, David E.; Caldes, Trinidad; Nevanlinna, Heli; Osorio, Ana; Terry, Mary Beth; Daly, Mary B.; van Rensburg, Elizabeth J.; Hamann, Ute; Ramus, Susan J.; Ewart Toland, Amanda; Caligo, Maria A.; Olopade, Olufunmilayo I.; Tung, Nadine; Claes, Kathleen; Beattie, Mary S.; Southey, Melissa C.; Imyanitov, Evgeny N.; Tischkowitz, Marc; Janavicius, Ramunas; John, Esther M.; Kwong, Ava; Diez, Orland; Balmana, Judith; Barkardottir, Rosa B.; Arun, Banu K.; Rennert, Gad; Teo, Soo-Hwang; Ganz, Patricia A.; Campbell, Ian; van der Hout, Annemarie H.; van Deurzen, Carolien H. M.; Seynaeve, Caroline; Gomez Garcia, Encarna B.; van Leeuwen, Flora E.; Meijers-Heijboer, Hanne E. J.; Gille, Johannes J. P.; Ausems, Margreet G. E. M.; Blok, Marinus J.; Ligtenberg, Marjolijn J. L.; Rookus, Matti A.; Devilee, Peter; Verhoef, Senno; van Os, Theo A. M.; Wijnen, Juul T.; Frost, Debra; Ellis, Steve; Fineberg, Elena; Platte, Radka; Evans, D. Gareth; Izatt, Louise; Eeles, Rosalind A.; Adlard, Julian; Eccles, Diana M.; Cook, Jackie; Brewer, Carole; Douglas, Fiona; Hodgson, Shirley; Morrison, Patrick J.; Side, Lucy E.; Donaldson, Alan; Houghton, Catherine; Rogers, Mark T.; Dorkins, Huw; Eason, Jacqueline; Gregory, Helen; McCann, Emma; Murray, Alex; Calender, Alain; Hardouin, Agnes; Berthet, Pascaline; Delnatte, Capucine; Nogues, Catherine; Lasset, Christine; Houdayer, Claude; Leroux, Dominique; Rouleau, Etienne; Prieur, Fabienne; Damiola, Francesca; Sobol, Hagay; Coupier, Isabelle; Venat-Bouvet, Laurence; Castera, Laurent; Gauthier-Villars, Marion; Leone, Melanie; Pujol, Pascal; Mazoyer, Sylvie; Bignon, Yves-Jean; Zlowocka-Perlowska, Elzbieta; Gronwald, Jacek; Lubinski, Jan; Durda, Katarzyna; Jaworska, Katarzyna; Huzarski, Tomasz; Spurdle, Amanda B.; Viel, Alessandra; Peissel, Bernard; Bonanni, Bernardo; Melloni, Giulia; Ottini, Laura; Papi, Laura; Varesco, Liliana; Tibiletti, Maria Grazia; Peterlongo, Paolo; Volorio, Sara; Manoukian, Siranoush; Pensotti, Valeria; Arnold, Norbert; Engel, Christoph; Deissler, Helmut; Gadzicki, Dorothea; Gehrig, Andrea; Kast, Karin; Rhiem, Kerstin; Meindl, Alfons; Niederacher, Dieter; Ditsch, Nina; Plendl, Hansjoerg; Preisler-Adams, Sabine; Engert, Stefanie; Sutter, Christian; Varon-Mateeva, Raymonda; Wappenschmidt, Barbara; Weber, Bernhard H. F.; Arver, Brita; Stenmark-Askmalm, Marie; Loman, Niklas; Rosenquist, Richard; Einbeigi, Zakaria; Nathanson, Katherine L.; Rebbeck, Timothy R.; Blank, Stephanie V.; Cohn, David E.; Rodriguez, Gustavo C.; Small, Laurie; Friedlander, Michael; Bae-Jump, Victoria L.; Fink-Retter, Anneliese; Rappaport, Christine; Gschwantler-Kaulich, Daphne; Pfeiler, Georg; Tea, Muy-Kheng; Lindor, Noralane M.; Kaufman, Bella; Shimon Paluch, Shani; Laitman, Yael; Skytte, Anne-Bine; Gerdes, Anne-Marie; Pedersen, Inge Sokilde; Moeller, Sanne Traasdahl; Kruse, Torben A.; Jensen, Uffe Birk; Vijai, Joseph; Sarrel, Kara; Robson, Mark; Kauff, Noah; Mulligan, Anna Marie; Glendon, Gord; Ozcelik, Hilmi; Ejlertsen, Bent; Nielsen, Finn C.; J?nson, Lars; Andersen, Mette K.; Ding, Yuan Chun; Steele, Linda; Foretova, Lenka; Teule, Alex; Lazaro, Conxi; Brunet, Joan; Pujana, Miquel Angel; Mai, Phuong L.; Loud, Jennifer T.; Walsh, Christine; Lester, Jenny; Orsulic, Sandra; Narod, Steven A.; Herzog, Josef; Sand, Sharon R.; Tognazzo, Silvia; Agata, Simona; Vaszko, Tibor; Weaver, Joellen; Stavropoulou, Alexandra V.; Buys, Saundra S.; Romero, Atocha; de la Hoya, Miguel; Aittomaki, Kristiina; Muranen, Taru A.; Duran, Mercedes; Chung, Wendy K.; Lasa, Adriana; Dorfling, Cecilia M.; Miron, Alexander; Benitez, Javier; Senter, Leigha; Huo, Dezheng; Chan, Salina B.; Sokolenko, Anna P.; Chiquette, Jocelyne; Tihomirova, Laima; Friebel, Tara M.; Agnarsson, Bjarni A.; Lu, Karen H.; Lejbkowicz, Flavio; James, Paul A.; Hall, Per

2013-01-01

227

Genome-wide association study in BRCA1 mutation carriers identifies novel loci associated with breast and ovarian cancer risk.  

PubMed

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7 × 10(-8), HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4 × 10(-8), HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4 × 10(-8), HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific association. The 17q21.31 locus was also associated with ovarian cancer risk in 8,211 BRCA2 carriers (P = 2×10(-4)). These loci may lead to an improved understanding of the etiology of breast and ovarian tumors in BRCA1 carriers. Based on the joint distribution of the known BRCA1 breast cancer risk-modifying loci, we estimated that the breast cancer lifetime risks for the 5% of BRCA1 carriers at lowest risk are 28%-50% compared to 81%-100% for the 5% at highest risk. Similarly, based on the known ovarian cancer risk-modifying loci, the 5% of BRCA1 carriers at lowest risk have an estimated lifetime risk of developing ovarian cancer of 28% or lower, whereas the 5% at highest risk will have a risk of 63% or higher. Such differences in risk may have important implications for risk prediction and clinical management for BRCA1 carriers. PMID:23544013

Couch, Fergus J; Wang, Xianshu; McGuffog, Lesley; Lee, Andrew; Olswold, Curtis; Kuchenbaecker, Karoline B; Soucy, Penny; Fredericksen, Zachary; Barrowdale, Daniel; Dennis, Joe; Gaudet, Mia M; Dicks, Ed; Kosel, Matthew; Healey, Sue; Sinilnikova, Olga M; Lee, Adam; Bacot, François; Vincent, Daniel; Hogervorst, Frans B L; Peock, Susan; Stoppa-Lyonnet, Dominique; Jakubowska, Anna; Radice, Paolo; Schmutzler, Rita Katharina; Domchek, Susan M; Piedmonte, Marion; Singer, Christian F; Friedman, Eitan; Thomassen, Mads; Hansen, Thomas V O; Neuhausen, Susan L; Szabo, Csilla I; Blanco, Ignacio; Greene, Mark H; Karlan, Beth Y; Garber, Judy; Phelan, Catherine M; Weitzel, Jeffrey N; Montagna, Marco; Olah, Edith; Andrulis, Irene L; Godwin, Andrew K; Yannoukakos, Drakoulis; Goldgar, David E; Caldes, Trinidad; Nevanlinna, Heli; Osorio, Ana; Terry, Mary Beth; Daly, Mary B; van Rensburg, Elizabeth J; Hamann, Ute; Ramus, Susan J; Toland, Amanda Ewart; Caligo, Maria A; Olopade, Olufunmilayo I; Tung, Nadine; Claes, Kathleen; Beattie, Mary S; Southey, Melissa C; Imyanitov, Evgeny N; Tischkowitz, Marc; Janavicius, Ramunas; John, Esther M; Kwong, Ava; Diez, Orland; Balmaña, Judith; Barkardottir, Rosa B; Arun, Banu K; Rennert, Gad; Teo, Soo-Hwang; Ganz, Patricia A; Campbell, Ian; van der Hout, Annemarie H; van Deurzen, Carolien H M; Seynaeve, Caroline; Gómez Garcia, Encarna B; van Leeuwen, Flora E; Meijers-Heijboer, Hanne E J; Gille, Johannes J P; Ausems, Margreet G E M; Blok, Marinus J; Ligtenberg, Marjolijn J L; Rookus, Matti A; Devilee, Peter; Verhoef, Senno; van Os, Theo A M; Wijnen, Juul T; Frost, Debra; Ellis, Steve; Fineberg, Elena; Platte, Radka; Evans, D Gareth; Izatt, Louise; Eeles, Rosalind A; Adlard, Julian; Eccles, Diana M; Cook, Jackie; Brewer, Carole; Douglas, Fiona; Hodgson, Shirley; Morrison, Patrick J; Side, Lucy E; Donaldson, Alan; Houghton, Catherine; Rogers, Mark T; Dorkins, Huw; Eason, Jacqueline; Gregory, Helen; McCann, Emma; Murray, Alex; Calender, Alain; Hardouin, Agnès; Berthet, Pascaline; Delnatte, Capucine; Nogues, Catherine; Lasset, Christine; Houdayer, Claude; Leroux, Dominique; Rouleau, Etienne; Prieur, Fabienne; Damiola, Francesca; Sobol, Hagay; Coupier, Isabelle; Venat-Bouvet, Laurence; Castera, Laurent; Gauthier-Villars, Marion; Léoné, Mélanie; Pujol, Pascal; Mazoyer, Sylvie; Bignon, Yves-Jean; Z?owocka-Per?owska, El?bieta; Gronwald, Jacek; Lubinski, Jan; Durda, Katarzyna; Jaworska, Katarzyna; Huzarski, Tomasz; Spurdle, Amanda B; Viel, Alessandra; Peissel, Bernard; Bonanni, Bernardo; Melloni, Giulia; Ottini, Laura; Papi, Laura; Varesco, Liliana; Tibiletti, Maria Grazia; Peterlongo, Paolo; Volorio, Sara; Manoukian, Siranoush; Pensotti, Valeria; Arnold, Norbert; Engel, Christoph; Deissler, Helmut; Gadzicki, Dorothea; Gehrig, Andrea; Kast, Karin; Rhiem, Kerstin; Meindl, Alfons; Niederacher, Dieter; Ditsch, Nina; Plendl, Hansjoerg; Preisler-Adams, Sabine; Engert, Stefanie; Sutter, Christian; Varon-Mateeva, Raymonda; Wappenschmidt, Barbara; Weber, Bernhard H F; Arver, Brita; Stenmark-Askmalm, Marie; Loman, Niklas; Rosenquist, Richard; Einbeigi, Zakaria; Nathanson, Katherine L; Rebbeck, Timothy R; Blank, Stephanie V; Cohn, David E; Rodriguez, Gustavo C; Small, Laurie; Friedlander, Michael; Bae-Jump, Victoria L; Fink-Retter, Anneliese; Rappaport, Christine; Gschwantler-Kaulich, Daphne; Pfeiler, Georg; Tea, Muy-Kheng; Lindor, Noralane M; Kaufman, Bella; Shimon Paluch, Shani; Laitman, Yael; Skytte, Anne-Bine; Gerdes, Anne-Marie; Pedersen, Inge Sokilde; Moeller, Sanne Traasdahl; Kruse, Torben A; Jensen, Uffe Birk; Vijai, Joseph; Sarrel, Kara; Robson, Mark; Kauff, Noah; Mulligan, Anna Marie; Glendon, Gord; Ozcelik, Hilmi; Ejlertsen, Bent; Nielsen, Finn C; Jønson, Lars; Andersen, Mette K; Ding, Yuan Chun; Steele, Linda; Foretova, Lenka; Teulé, Alex; Lazaro, Conxi; Brunet, Joan; Pujana, Miquel Angel; Mai, Phuong L; Loud, Jennifer T; Walsh, Christine; Lester, Jenny; Orsulic, Sandra; Narod, Steven A; Herzog, Josef; Sand, Sharon R; Tognazzo, Silvia; Agata, Simona; Vaszko, Tibor; Weaver, Joellen; Stavropoulou, Alexandra V; Buys, Saundra S; Romero, Atocha; de la Hoya, Miguel; Aittomäki, Kristiina; Muranen, Taru A; Duran, Mercedes; Chung, Wendy K; Lasa, Adriana; Dorfling, Cecilia M; Miron, Alexander; Benitez, Javier; Senter, Leigha; Huo, Dezheng; Chan, Salina B; Sokolenko, Anna P; Chiquette, Jocelyne; Tihomirova, Laima; Friebel, Tara M; Agnarsson, Bjarni A; Lu, Karen H; Lejbkowicz, Flavio; James, Paul A; Hall, Per; Dunning, Alison M; Tessier, Daniel; Cunningham, Julie; Slager, Susan L; Wang, Chen; Hart, Steven

2013-03-27

228

Use of reporter genes to identify recessive trans-acting mutations specifically involved in the regulation of Aspergillus nidulans penicillin biosynthesis genes.  

PubMed Central

Starting from three amino acid precursors, penicillin biosynthesis is catalyzed by three enzymes which are encoded by the following three genes: acvA (pcbAB), ipnA (pcbC), and aat (penDE). To identify trans-acting mutations which are specifically involved in the regulation of these secondary metabolism genes, a molecular approach was employed by using an Aspergillus nidulans strain (AXTII9) carrying acvA-uidA and ipnA-lacZ gene fusions integrated in double copies at the chromosomal argB gene. On minimal agar plates supplemented with X-Gal (5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside), colonies of such a strain stained blue, which is indicative of ipnA-lacZ expression. After mutagenesis with UV light, colonies were isolated on agar plates with lactose as the carbon source, which produced only a faint blue color or no color at all. Such mutants (named Prg for penicillin regulation) most likely were defective in trans-acting genes. Control experiments revealed that the mutants studied still carried the correct number of gene fusions. In a fermentation run, mutants Prg-1 and Prg-6 exhibited only 20 to 50% of the ipnA-lacZ expression of the wild-type strain and produced only 20 to 30% of the penicillin produced by the wild-type strain. Western blot (immunoblot) analysis showed that these mutants contained reduced amounts of ipnA gene product, i.e., isopenicillin N synthase. Both mutant Prg-1 and mutant Prg-6 also differed in acvA-uidA expression levels from the wild type. Segregation analysis indicated that for both mutants the Prg phenotype resulted from mutation of a single gene. Two different complementation groups, which were designated prgA1 and prgB1, were identified. However, the specific activity of the aat (penDE) gene product, i.e., acyl coenzyme A:6-aminopenicillanic acid acyltransferase, was essentially the same for the mutants as for the wild-type strain, implying that the last step of the penicillin biosynthetic pathway is not affected by the trans-acting mutations identified.

Brakhage, A A; Van den Brulle, J

1995-01-01

229

A screen for dominant modifiers of ro(Dom), a mutation that disrupts morphogenetic furrow progression in Drosophila, identifies groucho and hairless as regulators of atonal expression.  

PubMed Central

ro(Dom) is a dominant allele of rough (ro) that results in reduced eye size due to premature arrest in morphogenetic furrow (MF) progression. We found that the ro(Dom) stop-furrow phenotype was sensitive to the dosage of genes known to affect retinal differentiation, in particular members of the hedgehog (hh) signaling cascade. We demonstrate that ro(Dom) interferes with Hh's ability to induce the retina-specific proneural gene atonal (ato) in the MF and that normal eye size can be restored by providing excess Ato protein. We used ro(Dom) as a sensitive genetic background in which to identify mutations that affect hh signal transduction or regulation of ato expression. In addition to mutations in several unknown loci, we recovered multiple alleles of groucho (gro) and Hairless (H). Analysis of their phenotypes in somatic clones suggests that both normally act to restrict neuronal cell fate in the retina, although they control different aspects of ato's complex expression pattern.

Chanut, F; Luk, A; Heberlein, U

2000-01-01

230

Exome Sequencing Identifies a DYNC1H1 Mutation in a Large Pedigree with Dominant Axonal Charcot-Marie-Tooth Disease  

PubMed Central

Charcot-Marie-Tooth disease is characterized by length-dependent axonal degeneration with distal sensory loss and weakness, deep-tendon-reflex abnormalities, and skeletal deformities. It is caused by mutations in more than 40 genes. We investigated a four-generation family with 23 members affected by the axonal form (type 2), for which the common causes had been excluded by Sanger sequencing. Exome sequencing of three affected individuals separated by eight meioses identified a single shared novel heterozygous variant, c.917A>G, in DYNC1H1, which encodes the cytoplasmic dynein heavy chain 1 (here, novel refers to a variant that has not been seen in dbSNP131or the August 2010 release of the 1000 Genomes project). Testing of six additional affected family members showed cosegregation and a maximum LOD score of 3.6. The shared DYNC1H1 gene variant is a missense substitution, p.His306Arg, at a highly conserved residue within the homodimerization domain. Three mouse models with different mutations within this domain have previously been reported with age-related progressive loss of muscle bulk and locomotor ability. Cytoplasmic dynein is a large multisubunit motor protein complex and has a key role in retrograde axonal transport in neurons. Our results highlight the importance of dynein and retrograde axonal transport in neuronal function in humans.

Weedon, Michael N.; Hastings, Robert; Caswell, Richard; Xie, Weijia; Paszkiewicz, Konrad; Antoniadi, Thalia; Williams, Maggie; King, Cath; Greenhalgh, Lynn; Newbury-Ecob, Ruth; Ellard, Sian

2011-01-01

231

Targeted Capture and Next-Generation Sequencing Identifies C9orf75, Encoding Taperin, as the Mutated Gene in Nonsyndromic Deafness DFNB79  

PubMed Central

Targeted genome capture combined with next-generation sequencing was used to analyze 2.9 Mb of the DFNB79 interval on chromosome 9q34.3, which includes 108 candidate genes. Genomic DNA from an affected member of a consanguineous family segregating recessive, nonsyndromic hearing loss was used to make a library of fragments covering the DFNB79 linkage interval defined by genetic analyses of four pedigrees. Homozygosity for eight previously unreported variants in transcribed sequences was detected by evaluating a library of 402,554 sequencing reads and was later confirmed by Sanger sequencing. Of these variants, six were determined to be polymorphisms in the Pakistani population, and one was in a noncoding gene that was subsequently excluded genetically from the DFNB79 linkage interval. The remaining variant was a nonsense mutation in a predicted gene, C9orf75, renamed TPRN. Evaluation of the other three DFNB79-linked families identified three additional frameshift mutations, for a total of four truncating alleles of this gene. Although TPRN is expressed in many tissues, immunolocalization of the protein product in the mouse cochlea shows prominent expression in the taper region of hair cell stereocilia. Consequently, we named the protein taperin.

Rehman, Atteeq Ur; Morell, Robert J.; Belyantseva, Inna A.; Khan, Shahid Y.; Boger, Erich T.; Shahzad, Mohsin; Ahmed, Zubair M.; Riazuddin, Saima; Khan, Shaheen N.; Riazuddin, Sheikh; Friedman, Thomas B.

2010-01-01

232

Autosomal recessive mental retardation: homozygosity mapping identifies 27 single linkage intervals, at least 14 novel loci and several mutation hotspots.  

PubMed

Mental retardation (MR) has a worldwide prevalence of around 2% and is a frequent cause of severe disability. Significant excess of MR in the progeny of consanguineous matings as well as functional considerations suggest that autosomal recessive forms of MR (ARMR) must be relatively common. To shed more light on the causes of autosomal recessive MR (ARMR), we have set out in 2003 to perform systematic clinical studies and autozygosity mapping in large consanguineous Iranian families with non-syndromic ARMR (NS-ARMR). As previously reported (Najmabadi et al. in Hum Genet 121:43-48, 2007), this led us to the identification of 12 novel ARMR loci, 8 of which had a significant LOD score (OMIM: MRT5-12). In the meantime, we and others have found causative gene defects in two of these intervals. Moreover, as reported here, tripling the size of our cohort has enabled us to identify 27 additional unrelated families with NS-ARMR and single-linkage intervals; 14 of these define novel loci for non-syndromic ARMR. Altogether, 13 out of 39 single linkage intervals observed in our cohort were found to cluster at 6 different loci on chromosomes, i.e., 1p34, 4q27, 5p15, 9q34, 11p11-q13 and 19q13, respectively. Five of these clusters consist of two significantly overlapping linkage intervals, and on chr 1p34, three single linkage intervals coincide, including the previously described MRT12 locus. The probability for this distribution to be due to chance is only 1.14 × 10(-5), as shown by Monte Carlo simulation. Thus, in contrast to our previous conclusions, these novel data indicate that common molecular causes of NS-ARMR do exist, and in the Iranian population, the most frequent ones may well account for several percent of the patients. These findings will be instrumental in the identification of the underlying genes. PMID:21063731

Kuss, Andreas Walter; Garshasbi, Masoud; Kahrizi, Kimia; Tzschach, Andreas; Behjati, Farkhondeh; Darvish, Hossein; Abbasi-Moheb, Lia; Puettmann, Lucia; Zecha, Agnes; Weissmann, Robert; Hu, Hao; Mohseni, Marzieh; Abedini, Seyedeh Sedigheh; Rajab, Anna; Hertzberg, Christoph; Wieczorek, Dagmar; Ullmann, Reinhard; Ghasemi-Firouzabadi, Saghar; Banihashemi, Susan; Arzhangi, Sanaz; Hadavi, Valeh; Bahrami-Monajemi, Gholamreza; Kasiri, Mahboubeh; Falah, Masoumeh; Nikuei, Pooneh; Dehghan, Atefeh; Sobhani, Masoumeh; Jamali, Payman; Ropers, Hans Hilger; Najmabadi, Hossein

2010-11-10

233

The tamas gene, identified as a mutation that disrupts larval behavior in Drosophila melanogaster, codes for the mitochondrial DNA polymerase catalytic subunit (DNApol-gamma125).  

PubMed

From a screen of pupal lethal lines of Drosophila melanogaster we identified a mutant strain that displayed a reproducible reduction in the larval response to light. Moreover, this mutant strain showed defects in the development of the adult visual system and failure to undergo behavioral changes characteristic of the wandering stage. The foraging third instar larvae remained in the food substrate for a prolonged period and died at or just before pupariation. Using a new assay for individual larval photobehavior we determined that the lack of response to light in these mutants was due to a primary deficit in locomotion. The mutation responsible for these phenotypes was mapped to the lethal complementation group l(2)34Dc, which we renamed tamas (translated from Sanskrit as "dark inertia"). Sequencing of mutant alleles demonstrated that tamas codes for the mitochondrial DNA polymerase catalytic subunit (DNApol-gamma125). PMID:10581287

Iyengar, B; Roote, J; Campos, A R

1999-12-01

234

Mutagenesis and Analysis of Genetic Mutations in the GC-rich KISS1 Receptor Sequence Identified in Humans with Reproductive Disorders  

PubMed Central

The kisspeptin receptor (KISS1R) is a G protein-coupled receptor recognized as the trigger of puberty and a regulator of reproductive competence in adulthood 1,2,3. Inactivating mutations in KISS1R identified in patients have been associated with iodiopathic hypogonadotropic hypogonadism (IHH) 1,2 and precocious puberty 4. Functional studies of these mutants are crucial for our understanding of the mechanisms underlying the regulation of reproduction by this receptor as well as those shaping the disease outcomes, which result from abnormal KISS1R signaling and function. However, the highly GC-rich sequence of the KISS1R gene makes it rather difficult to introduce mutations or amplify the gene encoding this receptor by PCR. Here we describe a method to introduce mutations of interest into this highly GC-rich sequence that has been used successfully to generate over a dozen KISS1R mutants in our laboratory. We have optimized the PCR conditions to facilitate the amplification of a range of KISS1R mutants that include substitutions, deletions or insertions in the KISS1R sequence. The addition of a PCR enhancer solution, as well as of a small percentage of DMSO were especially helpful to improve amplification. This optimized procedure may be useful for other GC-rich templates as well. The expression vector encoding the KISS1R is been used to characterize signaling and function of this receptor in order to understand how mutations may change KISS1R function and lead to the associated reproductive phenotypes. Accordingly, potential applications of KISS1R mutants generated by site-directed mutagenesis can be illustrated by many studies 1,4,5,6,7,8. As an example, the gain-of-function mutation in the KISS1R (Arg386Pro), which is associated with precocious puberty, has been shown to prolong responsiveness of the receptor to ligand stimulation 4 as well as to alter the rate of degradation of KISS1R 9. Interestingly, our studies indicate that KISS1R is degraded by the proteasome, as opposed to the classic lysosomal degradation described for most G protein-coupled receptors 9. In the example presented here, degradation of the KISS1R is investigated in Human Embryonic Kidney Cells (HEK-293) transiently expressing Myc-tagged KISS1R (MycKISS1R) and treated with proteasome or lysosome inhibitors. Cell lysates are immunoprecipitated using an agarose-conjugated anti-myc antibody followed by western blot analysis. Detection and quantification of MycKISS1R on blots is performed using the LI-COR Odyssey Infrared System. This approach may be useful in the study of the degradation of other proteins of interest as well.

da Silva, Luciana Madeira; Vandepas, Lauren; Bianco, Suzy D.C.

2011-01-01

235

The JAK2(V617F) tyrosine kinase mutation identifies clinically latent myeloproliferative disorders in patients presenting with hepatic or portal vein thrombosis.  

PubMed

Clinically latent myeloproliferative disorders (MPDs) are important causes of what would otherwise be considered idiopathic hepatic (HVT) or portal vein thrombosis (PVT). They may be difficult to diagnose initially because the peripheral blood count may be normal at the time of thrombosis. A strong association between an activating mutation of the gene encoding one of the Janus kinase family of tyrosine kinases (JAK2(V617F)) and the Philadelphia chromosome-negative MPDs has been identified. We have studied 19 patients with unexplained HVT or PVT and tested for JAK2(V617F). Fourteen (74%) of the 19 patients were heterozygous for JAK2(V617F) but did not meet diagnostic criteria for a MPD at the time of presentation with thrombosis. Prolonged follow-up established the presence of an overt MPD in 13 of the 14 patients after a median duration of 38 months. We recommend testing for JAK2(V617F) in all patients with unexplained HVT or PVT, to identify latent MPDs and prevent potential complications. PMID:19046316

Goulding, C; Uttenthal, B; Foroni, L; Duke, V; Traore, A; Kottaridis, P; Hoffbrand, A V; Patch, D; McNamara, C

2008-10-01

236

Mutational Analysis Identifies Residues Crucial for Homodimerization of Myeloid Differentiation Factor 88 (MyD88) and for Its Function in Immune Cells.  

PubMed

Myeloid differentiation factor 88 (MyD88) is an adaptor protein that transduces intracellular signaling pathways evoked by the Toll-like receptors (TLRs) and interleukin-1 receptors (IL-1Rs). MyD88 is composed of an N-terminal death domain (DD) and a C-terminal Toll/IL-1 receptor (TIR) domain, separated by a short region. Upon ligand binding, TLR/IL-1Rs hetero- or homodimerize and recruit MyD88 through their respective TIR domains. Then, MyD88 oligomerizes via its DD and TIR domain and interacts with the interleukin-1 receptor-associated kinases (IRAKs) to form the Myddosome complex. We performed site-directed mutagenesis of conserved residues that are located in exposed regions of the MyD88-TIR domain and analyzed the effect of the mutations on MyD88 signaling. Our studies revealed that mutation of Glu(183), Ser(244), and Arg(288) impaired homodimerization of the MyD88-TIR domain, recruitment of IRAKs, and activation of NF-?B. Moreover, overexpression of two green fluorescent protein (GFP)-tagged MyD88 mini-proteins (GFP-MyD88151-189 and GFP-MyD88168-189), comprising the Glu(183) residue, recapitulated these effects. Importantly, expression of these dominant negative MyD88 mini-proteins competed with the function of endogenous MyD88 and interfered with TLR2/4-mediated responses in a human monocytic cell line (THP-1) and in human primary monocyte-derived dendritic cells. Thus, our studies identify novel residues of the TIR domain that are crucially involved in MyD88 homodimerization and TLR signaling in immune cells. PMID:24019529

Loiarro, Maria; Volpe, Elisabetta; Ruggiero, Vito; Gallo, Grazia; Furlan, Roberto; Maiorino, Chiara; Battistini, Luca; Sette, Claudio

2013-09-09

237

Kinase domain mutations of BCR-ABL identified at diagnosis before imatinib-based therapy are associated with progression in patients with high Sokal risk chronic phase chronic myeloid leukemia.  

PubMed

Acquired resistance to imatinib in the advanced phase of chronic myeloid leukemia (CML) has been associated with mutations in the kinase domain (KD) of BCR-ABL. On the contrary, the prognostic implication of KD mutations in early chronic phase (CP) patients at diagnosis before imatinib-based therapy has not yet been established. We have reviewed the status of mutations in 43 patients with early CP-CML on the samples collected at diagnosis. Mutations were identified by direct sequencing (DS) with BidDye Terminator v 1.1. cycle sequencing kit and analyzed with a 3130 ABI capillary electrophoresis system. Eight out 13 (61.5%) high Sokal risk patients showed the following mutations: Y253C, S265R, E255K, F359Y, N374S, E255V, E255V, E255V. Three patients progressed during imatinib and second-line inhibitors and died of blastic phase CML at 23, 33, and 69 months. Another patient with intermediate Sokal risk showed D363G mutation at diagnosis, progressed under imatinib, was allografted and he is now alive in major molecular remission (MMR). No low-risk patient carried KD mutation at diagnosis. In conclusion, KD mutations conferring high-level imatinib resistance are present in patients with de novo CML and in some of them lead to disease progression. PMID:20038234

Carella, Angelo M; Garuti, Anna; Cirmena, Gabriella; Catania, Gioacchino; Rocco, Ilaria; Palermo, Claudia; Pica, Gianmatteo; Pierri, Ivana; Miglino, Maurizio; Ballestrero, Alberto; Gobbi, Marco; Patrone, Franco

2010-02-01

238

High throughput fluorescence-based conformation-sensitive gel electrophoresis (F-CSGE) identifies six unique BRCA2 mutations and an overall low incidence of BRCA2 mutations in high-risk BRCA1-negative breast cancer families  

Microsoft Academic Search

Mutational analysis of cancer susceptibility genes has opened up a new era in clinical genetics. In this report we present\\u000a the results of mutational analysis of the BRCA2 coding sequences in 105 high-risk individuals affected with breast cancer\\u000a and\\/or ovarian cancer and previously found to be negative for mutations of the BRCA1 coding sequence in our laboratory. These\\u000a individuals have

Tapan Ganguly; Rohini Dhulipala; Lynn Godmilow; Arupa Ganguly

1998-01-01

239

Enzymatic analysis of the effect of naturally occurring Leu138Pro mutation identified in SHV ?-lactamase on hydrolysis of penicillin and ampicillin  

PubMed Central

Background The aim of this study was to analyze the significance of leucine to proline substitution at position 138(Leu138Pro) on the hydrolysis of penicillin and ampicillin that we identified in the blaSHV gene of clinical Escherichia coli swine isolate. Results Kinetic analysis of the mutant proteins showed that Km value of the purified L138P mutant was comparatively higher than SHV-1, SHV-33 and SHV-33(L138P) enzyme for penicillin and ampicillin. Docking simulation of the SHV-1 and SHV-(L138P) enzymes also confirmed that ?-lactamases preferred penicillin to ampicillin and the SHV-1 had a higher binding affinity for antibiotics compared to the SHV-(L138P) and other mutants. Conclusions Our result demonstrated that L138P has a reduced role in penicillin and ampicillin hydrolyzing properties of SHV ?-lactamases. These naturally occurring mutations rendering reduced function of the existing protein could trigger the emergence or acquisition of more effective alternative mechanisms for ?-lactam hydrolysis.

2011-01-01

240

Targeted next-generation sequencing detects point mutations, insertions, deletions and balanced chromosomal rearrangements as well as identifies novel leukemia-specific fusion genes in a single procedure  

Microsoft Academic Search

DNA sequence enrichment from complex genomic samples using microarrays enables targeted next-generation sequencing (NGS). In this study, we combined 454 shotgun pyrosequencing with long oligonucleotide sequence capture arrays. We demonstrate the detection of mutations including point mutations, deletions and insertions in a cohort of 22 patients presenting with acute leukemias and myeloid neoplasms. Importantly, this one-step methodological procedure also allowed

V Grossmann; A Kohlmann; H-U Klein; S Schindela; S Schnittger; F Dicker; M Dugas; W Kern; T Haferlach; C Haferlach

2011-01-01

241

A new approach for identifying non-pathogenic mutations. An analysis of the cystic fibrosis transmembrane regulator gene in normal individuals  

Microsoft Academic Search

Given q as the global frequency of the alleles causing a disease, any allele with a frequency higher than q minus the cumulative frequency of the previously known disease-causing mutations (threshold) cannot be the cause of that disease. This principle was applied to the analysis of cystic fibrosis transmembrane conductance regulator (CFTR) mutations in order to decide whether they are

Cristina Bombieri; Silvia Giorgi; Soukeyna Carles; Rafael de Cid; Francesca Belpinati; Caterina Tandoi; Nathalie Pallares-Ruiz; Conxi Lazaro; Bianca Maria Ciminelli; Marie-Catherine Romey; Teresa Casals; Fiorenza Pompei; Giorgio Gandini; Mireille Claustres; Xavier Estivill; Pier Franco Pignatti; Guido Modiano

2000-01-01

242

Somatic mosaicism for a newly identified splice-site mutation in a patient with adenosine deaminase-deficient immunodeficiency and spontaneous clinical recovery  

SciTech Connect

Absent or severely reduced adenosine deaminase (ADA) activity produces inherited immunodeficiency of varying severity, with defects of both cellular and humoral immunity. The authors report somatic mosaicism as the basis for a delayed presentation and unusual course of a currently healthy young adult receiving no therapy. He was diagnosed at age 2[1/2] years because of life-threatening pneumonia, recurrent infections, failure of normal growth, and lymphopenia, but he retained significant cellular immune function. A fibroblast cell line and a B cell line, established at diagnosis, lacked ADA activity and were heteroallelic for a splice-donor-site mutation in IVS 1 (+1GT[yields]CT) and a missense mutation (Arg101Gln). All clones (17/17) isolated from the B cell mRNA carried the missense mutation, indicating that the allele with the splice-site mutation produced unstable mRNA. In striking contrast, a B cell line established at age 16 years expressed 50% of normal ADA; 50% had the missense mutation. Genomic DNA contained the missense mutation but not the splice-site mutation. All three cell lines were identical for multiple polymorphic markers and the presence of a Y chromosome. In vivo somatic mosaicism was demonstrated in genomic DNA from peripheral blood cells obtained at 16 years of age, in that less than half the DNA carried the splice-site mutation (P<.0.02, vs. original B cell line). Consistent with mosaicism, erythrocyte content of the toxic metabolite deoxyATP was only minimally elevated. Somatic mosaicism could have arisen either by somatic mutation or by reversion at the site of mutation. Selection in vivo for ADA normal hematopoietic cells may have played a role in the return to normal health, in the absence of therapy. 57 refs., 4 figs., 2 tabs.

Hirschhorn, R.; Yang, D.R.; Israni, A.; Huie, M.L. (New York Univ. Medical Center, NY (United States)); Ownby, D.R. (Henry Ford Hospital, Detroit, MI (United States))

1994-07-01

243

Medium-Chain Acyl-CoA Dehydrogenase (MCAD) Mutations Identified by MS/MS-Based Prospective Screening of Newborns Differ from Those Observed in Patients with Clinical Symptoms: Identification and Characterization of a New, Prevalent Mutation That Results in Mild MCAD Deficiency*  

PubMed Central

Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is the most frequently diagnosed mitochondrial ?-oxidation defect, and it is potentially fatal. Eighty percent of patients are homozygous for a common mutation, 985A?G, and a further 18% have this mutation in only one disease allele. In addition, a large number of rare disease-causing mutations have been identified and characterized. There is no clear genotype-phenotype correlation. High 985A?G carrier frequencies in populations of European descent and the usual avoidance of recurrent disease episodes by patients diagnosed with MCAD deficiency who comply with a simple dietary treatment suggest that MCAD deficiency is a candidate in prospective screening of newborns. Therefore, several such screening programs employing analysis of acylcarnitines in blood spots by tandem mass spectrometry (MS/MS) are currently used worldwide. No validation of this method by mutation analysis has yet been reported. We investigated for MCAD mutations in newborns from US populations who had been identified by prospective MS/MS-based screening of 930,078 blood spots. An MCAD-deficiency frequency of 1/15,001 was observed. Our mutation analysis shows that the MS/MS-based method is excellent for detection of MCAD deficiency but that the frequency of the 985A?G mutant allele in newborns with a positive acylcarnitine profile is much lower than that observed in clinically affected patients. Our identification of a new mutation, 199T?C, which has never been observed in patients with clinically manifested disease but was present in a large proportion of the acylcarnitine-positive samples, may explain this skewed ratio. Overexpression experiments showed that this is a mild folding mutation that exhibits decreased levels of enzyme activity only under stringent conditions. A carrier frequency of 1/500 in the general population makes the 199T?C mutation one of the three most prevalent mutations in the enzymes of fatty-acid oxidation.

Andresen, Brage Storstein; Dobrowolski, Steve F.; O'Reilly, Linda; Muenzer, Joseph; McCandless, Shawn E.; Frazier, Dianne M.; Udvari, Szabolcs; Bross, Peter; Knudsen, Inga; Banas, Rick; Chace, Donald H.; Engel, Paul; Naylor, Edwin W.; Gregersen, Niels

2001-01-01

244

Mutational analysis of NM23-H2/NDP kinase identifies the structural domains critical to recognition of a c-myc regulatory element.  

PubMed Central

NM23-H2, a presumed regulator of tumor metastasis in humans, is a hexameric protein with both enzymatic (NDP kinase) and regulatory (transcriptional activation) activity. While the structure and catalytic mechanisms have been well characterized, the mode of DNA binding is not known. We examined this latter function in a site-directed mutational study and identified residues and domains essential for the recognition of a c-myc regulatory sequence. Three amino acids, Arg-34, Asn-69, and Lys-135, were found among 30 possibilities to be critical for DNA binding. Two of these, Asn-69 and Lys-135, are not conserved between NM23 variants differing in DNA-binding potential, suggesting that DNA recognition resides partly in nonconserved amino acids. All three DNA-binding defective mutant proteins are active enzymatically and appear to be stable hexamers, suggesting that they perform at the level of DNA recognition and that separate functional domains exist for enzyme catalysis and DNA binding. In the context of the known crystal structure of NM23-H2, the DNA-binding residues are located within distinct structural motifs in the monomer, which are exposed to the surface near the 2-fold axis of adjacent subunits in the hexamer. These findings are explained by a model in which NM23-H2 binds DNA with a combinatorial surface consisting of the "outer" face of the dimer. Chemical crosslinking data support a dimeric DNA-binding mode by NM23-H2. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5

Postel, E H; Weiss, V H; Beneken, J; Kirtane, A

1996-01-01

245

Selection for intragenic suppressors of lethal 23S rRNA mutations in Escherichia coli identifies residues important for ribosome assembly and function  

Microsoft Academic Search

Mutations in several functionally important regions of the 23S rRNA of E. coli increase the levels of frameshifting and readthrough of stop codons. These mutations include U2555A, U2555G, ?A1916 and U2493C.\\u000a The mutant rRNAs are lethal when expressed at high levels from a plasmid, in strains also expressing wild type rRNA from chromosomal\\u000a rrn operons. The lethal phenotype can be

Michael O’Connor

2007-01-01

246

A Newly Identified Mutation in the Complement Factor I Gene Not Associated With Early Post-transplant Recurrence of Atypical Hemolytic-Uremic Syndrome: A Case Report.  

PubMed

Atypical hemolytic uremic syndrome (aHUS), which can recur after renal transplantation, is associated with poor graft outcomes. The underlying genetic defect, namely, mutations in genes coding for the complement factor H, I (CFI), or membrane cofactor protein, greatly impacts the risk of aHUS recurrence. We report here the case of a patient with chronic renal failure due to aHUS in which screening for complement mutations, performed before wait-listing for kidney transplantation, showed a never described previously heterozygous mutation in the exon II of the CFI gene. Specifically, this mutation leads to a substitution of cytosine for guanosine at nucleotide 148, resulting in the change at amino acid 50 from arginine to proline. Subsequently, he received a renal allograft from deceased donor. Good graft function was established immediately, without clinical features of aHUS. Due to a lack of data on this mutation, we avoided prophylactic treatment for aHUS but closely monitored biochemical markers of aHUS to treat a possible recurrence. Immunosuppressive treatment was based on basiliximab, tacrolimus, steroids, and mycophenolic acid. At the time of discharge the serum creatinine was 1.4 mg/dL. Ten months after transplantation the patient is doing well without evidence of aHUS. Our case suggested that a heterozygous mutation in exon II of the CFI gene was not associated with a risk of early post-transplant aHUs recurrence adding new knowledge on complement mutations implicated in aHUS post-transplant recurrences. PMID:24034049

Ranghino, A; Tognarelli, G; Basso, E; Messina, M; Manzione, A M; Daidola, G; Segoloni, G P

2013-09-01

247

Use of the Ligase Detection Reaction-Polymerase Chain Reaction to Identify Point Mutations in Extended-Spectrum Beta-Lactamases  

Microsoft Academic Search

The aim of this study was to detect point mutations in extended-spectrum ?-lactamase (ESBL) genes in a background of wild-type\\u000a (non-ESBL-producing) bacteria using a highly sensitive and specific method developed for this purpose. The ligase detection\\u000a reaction-polymerase chain reaction (LDR-PCR) method was used to test different ESBL-producing strains and clinical isolates\\u000a for a specific point mutation in the bla SHV-ESBL

C. Niederhauser; L. Kaempf; I. Heinzer

2000-01-01

248

KRAS Mutation  

PubMed Central

Treatment of colon carcinoma with the anti-epidermal growth factor receptor antibody Cetuximab is reported to be ineffective in KRAS-mutant tumors. Mutation testing techniques have therefore become an urgent concern. We have compared three methods for detecting KRAS mutations in 59 cases of colon carcinoma: 1) high resolution melting, 2) the amplification refractory mutation system using a bifunctional self-probing primer (ARMS/Scorpion, ARMS/S), and 3) direct sequencing. We also evaluated the effects of the methods of sectioning and coring of paraffin blocks to obtain tumor DNA on assay sensitivity and specificity. The most sensitive and specific combination of block sampling and mutational analysis was ARMS/S performed on DNA derived from 1-mm paraffin cores. This combination of tissue sampling and testing method detected KRAS mutations in 46% of colon tumors. Four samples were positive by ARMS/S, but initially negative by direct sequencing. Cloned DNA samples were retested by direct sequencing, and in all four cases KRAS mutations were identified in the DNA. In six cases, high resolution melting abnormalities could not be confirmed as specific mutations either by ARMS/S or direct sequencing. We conclude that coring of the paraffin blocks and testing by ARMS/S is a sensitive, specific, and efficient method for KRAS testing.

Franklin, Wilbur A.; Haney, Jerry; Sugita, Michio; Bemis, Lynne; Jimeno, Antonio; Messersmith, Wells A.

2010-01-01

249

Whole-Exome-Sequencing Identifies Mutations in Histone Acetyltransferase Gene KAT6B in Individuals with the Say-Barber-Biesecker Variant of Ohdo Syndrome  

PubMed Central

Say-Barber-Biesecker-Young-Simpson syndrome (SBBYSS or Ohdo syndrome) is a multiple anomaly syndrome characterized by severe intellectual disability, blepharophimosis, and a mask-like facial appearance. A number of individuals with SBBYSS also have thyroid abnormalities and cleft palate. The condition usually occurs sporadically and is therefore presumed to be due in most cases to new dominant mutations. In individuals with SBBYSS, a whole-exome sequencing approach was used to demonstrate de novo protein-truncating mutations in the highly conserved histone acetyltransferase gene KAT6B (MYST4/MORF)) in three out of four individuals sequenced. Sanger sequencing was used to confirm truncating mutations of KAT6B, clustering in the final exon of the gene in all four individuals and in a further nine persons with typical SBBYSS. Where parental samples were available, the mutations were shown to have occurred de novo. During mammalian development KAT6B is upregulated specifically in the developing central nervous system, facial structures, and limb buds. The phenotypic features seen in the Qkf mouse, a hypomorphic Kat6b mutant, include small eyes, ventrally placed ears and long first digits that mirror the human phenotype. This is a further example of how perturbation of a protein involved in chromatin modification might give rise to a multisystem developmental disorder.

Clayton-Smith, Jill; O'Sullivan, James; Daly, Sarah; Bhaskar, Sanjeev; Day, Ruth; Anderson, Beverley; Voss, Anne K.; Thomas, Tim; Biesecker, Leslie G.; Smith, Philip; Fryer, Alan; Chandler, Kate E.; Kerr, Bronwyn; Tassabehji, May; Lynch, Sally-Ann; Krajewska-Walasek, Malgorzata; McKee, Shane; Smith, Janine; Sweeney, Elizabeth; Mansour, Sahar; Mohammed, Shehla; Donnai, Dian; Black, Graeme

2011-01-01

250

Clinical and mutational characteristics of X-linked agammaglobulinemia and its carrier identified by flow cytometric assessment combined with genetic analysis  

Microsoft Academic Search

Background: X-linked agammaglobulinemia (XLA), caused by mutations in Bruton's tyrosine kinase (BTK), is the most common form of inherited antibody deficiency. We previously reported that a flow cytometric evaluation of BTK expression in monocytes could easily detect XLA as well as its carrier. Objective: Our purpose was to perform further flow cytometric analysis in additional XLA families in Japan. Methods:

Hirokazu Kanegane; Takeshi Futatani; Yue Wang; Keiko Nomura; Kentaro Shinozaki; Hiroyoshi Matsukura; Takeo Kubota; Satoshi Tsukada; Toshio Miyawaki

2001-01-01

251

Mutational Profiling of Kinases in Human Tumours of Pancreatic Origin Identifies Candidate Cancer Genes in Ductal and Ampulla of Vater Carcinomas  

Microsoft Academic Search

BackgroundProtein kinases are key regulators of cellular processes (such as proliferation, apoptosis and invasion) that are often deregulated in human cancers. Accordingly, kinase genes have been the first to be systematically analyzed in human tumors leading to the discovery that many oncogenes correspond to mutated kinases. In most cases the genetic alterations translate in constitutively active kinase proteins, which are

Vincenzo Corbo; Rossana Ritelli; Stefano Barbi; Niccola Funel; Daniela Campani; Alberto Bardelli; Aldo Scarpa; Hana Algül

2010-01-01

252

Novel CIC Point Mutations and an Exon-Spanning, Homozygous Deletion Identified in Oligodendroglial Tumors by a Comprehensive Genomic Approach Including Transcriptome Sequencing.  

PubMed

Oligodendroglial tumors form a distinct subgroup of gliomas, characterized by a better response to treatment and prolonged overall survival. Most oligodendrogliomas and also some oligoastrocytomas are characterized by a unique and typical unbalanced translocation, der(1,19), resulting in a 1p/19q co-deletion. Candidate tumor suppressor genes targeted by these losses, CIC on 19q13.2 and FUBP1 on 1p31.1, were only recently discovered. We analyzed 17 oligodendrogliomas and oligoastrocytomas by applying a comprehensive approach consisting of RNA expression analysis, DNA sequencing of CIC, FUBP1, IDH1/2, and array CGH. We confirmed three different genetic subtypes in our samples: i) the "oligodendroglial" subtype with 1p/19q co-deletion in twelve out of 17 tumors; ii) the "astrocytic" subtype in three tumors; iii) the "other" subtype in two tumors. All twelve tumors with the 1p/19q co-deletion carried the most common IDH1 R132H mutation. In seven of these tumors, we found protein-disrupting point mutations in the remaining allele of CIC, four of which are novel. One of these tumors also had a deleterious mutation in FUBP1. Only by integrating RNA expression and array CGH data, were we able to discover an exon-spanning homozygous microdeletion within the remaining allele of CIC in an additional tumor with 1p/19q co-deletion. Therefore we propose that the mutation rate might be underestimated when looking at sequence variants alone. In conclusion, the high frequency and the spectrum of CIC mutations in our 1p/19q-codeleted tumor cohort support the hypothesis that CIC acts as a tumor suppressor in these tumors, whereas FUBP1 might play only a minor role. PMID:24086756

Eisenreich, Sophie; Abou-El-Ardat, Khalil; Szafranski, Karol; Campos Valenzuela, Jaime A; Rump, Andreas; Nigro, Janice M; Bjerkvig, Rolf; Gerlach, Eva-Maria; Hackmann, Karl; Schröck, Evelin; Krex, Dietmar; Kaderali, Lars; Schackert, Gabriele; Platzer, Matthias; Klink, Barbara

2013-09-27

253

Novel CIC Point Mutations and an Exon-Spanning, Homozygous Deletion Identified in Oligodendroglial Tumors by a Comprehensive Genomic Approach Including Transcriptome Sequencing  

PubMed Central

Oligodendroglial tumors form a distinct subgroup of gliomas, characterized by a better response to treatment and prolonged overall survival. Most oligodendrogliomas and also some oligoastrocytomas are characterized by a unique and typical unbalanced translocation, der(1,19), resulting in a 1p/19q co-deletion. Candidate tumor suppressor genes targeted by these losses, CIC on 19q13.2 and FUBP1 on 1p31.1, were only recently discovered. We analyzed 17 oligodendrogliomas and oligoastrocytomas by applying a comprehensive approach consisting of RNA expression analysis, DNA sequencing of CIC, FUBP1, IDH1/2, and array CGH. We confirmed three different genetic subtypes in our samples: i) the “oligodendroglial” subtype with 1p/19q co-deletion in twelve out of 17 tumors; ii) the “astrocytic” subtype in three tumors; iii) the “other” subtype in two tumors. All twelve tumors with the 1p/19q co-deletion carried the most common IDH1 R132H mutation. In seven of these tumors, we found protein-disrupting point mutations in the remaining allele of CIC, four of which are novel. One of these tumors also had a deleterious mutation in FUBP1. Only by integrating RNA expression and array CGH data, were we able to discover an exon-spanning homozygous microdeletion within the remaining allele of CIC in an additional tumor with 1p/19q co-deletion. Therefore we propose that the mutation rate might be underestimated when looking at sequence variants alone. In conclusion, the high frequency and the spectrum of CIC mutations in our 1p/19q-codeleted tumor cohort support the hypothesis that CIC acts as a tumor suppressor in these tumors, whereas FUBP1 might play only a minor role.

Eisenreich, Sophie; Abou-El-Ardat, Khalil; Szafranski, Karol; Campos Valenzuela, Jaime A.; Rump, Andreas; Nigro, Janice M.; Bjerkvig, Rolf; Gerlach, Eva-Maria; Hackmann, Karl; Schrock, Evelin; Krex, Dietmar; Kaderali, Lars; Schackert, Gabriele; Platzer, Matthias; Klink, Barbara

2013-01-01

254

Whole Exome Sequencing and Homozygosity Mapping Identify Mutation in the Cell Polarity Protein GPSM2 as the Cause of Nonsyndromic Hearing Loss DFNB82  

PubMed Central

Massively parallel sequencing of targeted regions, exomes, and complete genomes has begun to dramatically increase the pace of discovery of genes responsible for human disorders. Here we describe how exome sequencing in conjunction with homozygosity mapping led to rapid identification of the causative allele for nonsyndromic hearing loss DFNB82 in a consanguineous Palestinian family. After filtering out worldwide and population-specific polymorphisms from the whole exome sequence, only a single deleterious mutation remained in the homozygous region linked to DFNB82. The nonsense mutation leads to an early truncation of the G protein signaling modulator GPSM2, a protein that is essential for maintenance of cell polarity and spindle orientation. In the mouse inner ear, GPSM2 is localized to apical surfaces of hair cells and supporting cells and is most highly expressed during embryonic development. Identification of GPSM2 as essential to the development of normal hearing suggests dysregulation of cell polarity as a mechanism underlying hearing loss.

Walsh, Tom; Shahin, Hashem; Elkan-Miller, Tal; Lee, Ming K.; Thornton, Anne M.; Roeb, Wendy; Abu Rayyan, Amal; Loulus, Suheir; Avraham, Karen B.; King, Mary-Claire; Kanaan, Moien

2010-01-01

255

Switch-domain mutations in the Saccharomycescerevisiae G protein ? -subunit Gpa1p identify a receptor subtype-biased mating defect  

Microsoft Academic Search

The response to pheromone in Saccharomyces cerevisiae involves a heterotrimeric G protein composed of Gpa1p (? subunit), Ste4p (?) and Ste18p (?). The switch II region of G? subunits\\u000a is involved in several protein-protein interactions and an intrinsic GTPase activity. To investigate the role of this region\\u000a of Gpa1p, we have analyzed the effect of switch II mutations. The Q323

S. M. DeSimone; J. Kurjan

1998-01-01

256

Next-Generation Sequencing Identifies Mutations of SMPX, which Encodes the Small Muscle Protein, X-Linked, as a Cause of Progressive Hearing Impairment  

Microsoft Academic Search

In a Dutch family with an X-linked postlingual progressive hearing impairment, a critical linkage interval was determined to span a region of 12.9 Mb flanked by the markers DXS7108 and DXS7110. This interval overlaps with the previously described DFNX4 locus and contains 75 annotated genes. Subsequent next-generation sequencing (NGS) detected one variant within the linkage interval, a nonsense mutation in

Margit Schraders; Jaap Oostrik; Hao Hu; Sriram Kannan; Hannie Kremer

2011-01-01

257

Metaplastic mammary carcinoma with osteoclast-like giant cells: identical point mutation of p53 gene only identified in both the intraductal and sarcomatous components  

Microsoft Academic Search

Metaplastic mammary carcinoma with osteoclast-like giant cells is a rare neoplasm, and the histogenesis of this tumor remains controversial. A case of metaplastic mammary carcinoma with osteoclast-like giant cells in a 72-year-old woman is reported with p53 mutational analysis. Microscopically, the tumor was composed of a dominant sarcomatous stromal component containing osteoclast-like giant cells and a minor component of intraductal

JiShin Lee; YoungBog Kim; KyungWhan Min

2004-01-01

258

A novel deletion–insertion mutation identified in exon 3 of FXN in two siblings with a severe Friedreich ataxia phenotype  

Microsoft Academic Search

Friedreich ataxia (FRDA) is an autosomal recessive neurodegenerative disease most commonly caused by a GAA trinucleotide repeat\\u000a expansion in the first intron of FXN, which reduces expression of the mitochondrial protein frataxin. Approximately 98% of individuals with FRDA are homozygous\\u000a for GAA expansions, with the remaining 2% compound heterozygotes for a GAA expansion and a point mutation within FXN. Two

Marguerite V. Evans-Galea; Louise A. Corben; Justin Hasell; Charles A. Galea; Michael C. Fahey; Desirée du Sart; Martin B. Delatycki

259

Use of expression data and the CGEMS genome-wide breast cancer association study to identify genes that may modify risk in BRCA1\\/2 mutation carriers  

Microsoft Academic Search

Germline mutations in BRCA1 or BRCA2 confer an increased lifetime risk of developing breast or ovarian cancer, but variable penetrance suggests that cancer susceptibility\\u000a is influenced in part by modifier genes. Microarray expression profiling was conducted for 69 irradiated lymphoblastoid cell\\u000a lines derived from healthy controls, or from cancer-affected women with a strong family history of breast and ovarian cancer

Logan C. Walker; Nic Waddell; Anette Ten Haaf; Sean Grimmond; Amanda B. Spurdle

2008-01-01

260

The Cancer Genome Atlas Reports First Results of Comprehensive Study of Brain Tumors: Large-Scale Effort Identifies New Genetic Mutations, Core Pathways  

Cancer.gov

The Cancer Genome Atlas (TCGA) Research Network today reported the first results of its large-scale, comprehensive study of the most common form of brain cancer, glioblastoma (GBM). In a paper published Sept. 4, 2008, in the advance online edition of the journal Nature, the TCGA team describes the discovery of new genetic mutations and other types of DNA alterations with potential implications for the diagnosis and treatment of GBM.

261

The Cpx proteins of Escherichia coli K-12: evidence that cpxA, ecfB, ssd, and eup mutations all identify the same gene.  

PubMed Central

An existing cpxA(Ts) mutant was resistant to amikacin at levels that inhibited completely the growth of a cpxA+ and a cpxA deletion strain and failed to grow as efficiently on exogenous proline. These properties are similar to those of mutants altered in a gene mapped to the cpxA locus and variously designated as ecfB, ssd, and eup. The amikacin resistance phenotype of the cpxA mutant was inseparable by recombination from the cpxA mutant phenotype (inability to grow at 41 degrees C without exogenous isoleucine and valine) and was recessive to the cpxA+ allele of a recombinant plasmid. Using methods that ensured independent mutations in the cpxA region of the chromosome, we isolated six new amikacin-resistant mutants following nitrosoguanidine mutagenesis. Three-factor crosses mapped the mutations to the cpxA locus. When transferred by P1 transduction to a cpxB11 Hfr strain, each of the mutations conferred the Tra- and Ilv- phenotypes characteristic of earlier cpxA mutants. Two of the new mutations led to a significantly impaired ability to utilize exogenous proline, and four led to partial resistance to colicin A. Two of the new cpxA alleles were recessive to the cpxA+ allele, and four were dominant, albeit to different degrees. On the basis of these data, we argue that cpxA, ecfB, eup, and ssd are all the same gene. We discuss the cellular function of the cpxA gene product in that light.

Rainwater, S; Silverman, P M

1990-01-01

262

Functional and molecular genetic analyses of nine newly identified XPD-deficient patients reveal a novel mutation resulting in TTD as well as in XP/CS complex phenotypes.  

PubMed

The xeroderma pigmentosum (XP) group D protein is involved in nucleotide excision repair (NER) as well as in basal transcription. Determined by the type of XPD mutation, six different clinical entities have been distinguished: XP, XP with neurological symptoms, trichothiodystrophy (TTD), XP?TTD complex, XP?Cockayne syndrome (CS) complex or the cerebro-oculo-facio-skeletal syndrome (COFS). We identified nine new XPD-deficient patients. Their fibroblasts showed reduced post-UV cell survival, reduced NER capacity, normal XPD mRNA expression and partly reduced XPD protein expression. Six patients exhibited a XP phenotype in accordance with established XP-causing mutations (c.2079G>A, p.R683Q; c.2078G>T, p.R683W; c.1833G>T, p.R601L; c.1878G>C, p.R616P; c.1878G>A, p.R616Q). One TTD patient was homozygous for the known TTD-causing mutation p.R722W (c.2195C>T). Two patients were compound heterozygous for a TTD-causing mutation (c.366G>A, p.R112H) and a novel p.D681H (c.2072G>C) amino acid exchange, but exhibited different TTD and XP/CS complex phenotypes, respectively. Interestingly, the XP/CS patient's cells exhibited a reduced but well detectable XPD protein expression compared with hardly detectable XPD expression of the TTD patient's cells. Same mutations with different clinical outcomes in NER-defective patients demonstrate the complexity of phenotype-genotype correlations, for example relating to additional genetic variations (parental consanguinity), different allelic expression due to SNPs or differences in the methylation status. PMID:23800062

Schäfer, Annika; Gratchev, Alexei; Seebode, Christina; Hofmann, Lars; Schubert, Steffen; Laspe, Petra; Apel, Antje; Ohlenbusch, Andreas; Tzvetkov, Mladen; Weishaupt, Carsten; Oji, Vinzenz; Schön, Michael P; Emmert, Steffen

2013-07-01

263

Patient-specific induced-pluripotent stem cells-derived cardiomyocytes recapitulate the pathogenic phenotypes of dilated cardiomyopathy due to a novel DES mutation identified by whole exome sequencing.  

PubMed

In this paper, we report a novel heterozygous mutation of A285V codon conversion on exon 4 of the desmin (DES), using whole exome sequencing (WES) in an isolated proband with documented dilated cardiomyopathy (DCM). This mutation is predicted to cause three-dimensional structure changes of DES. Immunohistological and electron microscopy studies demonstrated diffuse abnormal DES aggregations in DCM-induced-pluripotent stem cell (iPSC)-derived cardiomyocytes, and control-iPSC-derived cardiomyocytes transduced with A285V-DES. DCM-iPSC-derived cardiomyocytes also exhibited functional abnormalities in vitro. This is the first demonstration that patient-specific iPSC-derived cardiomyocytes can be used to provide histological and functional confirmation of a suspected genetic basis for DCM identified by WES. PMID:23300193

Tse, Hung-Fat; Ho, Jenny C Y; Choi, Shing-Wan; Lee, Yee-Ki; Butler, Amy W; Ng, Kwong-Man; Siu, Chung-Wah; Simpson, Michael A; Lai, Wing-Hon; Chan, Yau-Chi; Au, Ka-Wing; Zhang, Jinqiu; Lay, Kenneth W J; Esteban, Miguel A; Nicholls, John M; Colman, Alan; Sham, Pak C

2013-01-08

264

Inverse Correlation between Cyclin A1 Hypermethylation and p53 Mutation in Head and Neck Cancer Identified by Reversal of Epigenetic Silencing  

Microsoft Academic Search

Aberrant promoter hypermethylation of tumor suppressor genes is proposed to be a common feature of primary cancer cells. We recently developed a pharmacological unmasking microarray approach to screen unknown tumor suppressor gene candidates epigenetically silenced in human cancers. In this study, we applied this method to identify such genes in head and neck squamous cell carcinoma (HNSCC). We identified 12

Yutaka Tokumaru; Keishi Yamashita; Motonobu Osada; Shuji Nomoto; Dong-Il Sun; Yan Xiao; Mohammad Obaidul Hoque; William H. Westra; Joseph A. Califano; David Sidransky

2004-01-01

265

Mutational analysis of the EMCV 2A protein identifies a nuclear localization signal and an eIF4E binding site  

SciTech Connect

Cardioviruses have a unique 2A protein (143 aa). During genome translation, the encephalomyocarditis virus (EMCV) 2A is released through a ribosome skipping event mitigated through C-terminal 2A sequences and by subsequent N-terminal reaction with viral 3C{sup pro}. Although viral replication is cytoplasmic, mature 2A accumulates in nucleoli shortly after infection. Some protein also transiently associates with cytoplasmic 40S ribosomal subunits, an activity contributing to inhibition of cellular cap-dependent translation. Cardiovirus sequences predict an eIF4E binding site (aa 126-134) and a nuclear localization signal (NLS, aa 91-102), within 2A, both of which are functional during EMCV infection. Point mutations preventing eIF4E:2A interactions gave small-plaque phenotype viruses, but still inhibited cellular cap-dependent translation. Deletions within the NLS motif relocalized 2A to the cytoplasm and abrogated the inhibition of cap-dependent translation. A fusion protein linking the 2A NLS to eGFP was sufficient to redirect the reporter to the nucleus but not into nucleoli.

Groppo, Rachel; Brown, Bradley A.; Palmenberg, Ann C., E-mail: acpalmen@wisc.ed

2011-02-05

266

Mutational Analysis of the EMCV 2A Protein Identifies a Nuclear Localization Signal and an eIF4E Binding Site  

PubMed Central

Cardioviruses have a unique 2A protein (143 aa). During genome translation, the encephalomyocarditis virus (EMCV) 2A is released through a ribosome skipping event mitigated through C-terminal 2A sequences and by subsequent N-terminal reaction with viral 3Cpro. Although viral replication is cytoplasmic, mature 2A accumulates in nucleoli shortly after infection. Some protein also transiently associates with cytoplasmic 40S ribosomal subunits, an activity contributing to inhibition of cellular cap-dependent translation. Cardiovirus sequences predict an eIF4E binding site (aa 126–134) and a nuclear localization signal (NLS, aa 91–102), within 2A, both of which are functional during EMCV infection. Point mutations preventing eIF4E:2A interactions gave small-plaque phenotype viruses, but still inhibited cellular cap-dependent translation. Deletions within the NLS motif relocalized 2A to the cytoplasm and abrogated the inhibition of cap-dependent translation. A fusion protein linking the 2A NLS to eGFP was sufficient to redirect the reporter to the nucleus but not into nucleoli.

Groppo, Rachel; Brown, Bradley A.; Palmenberg, Ann C.

2010-01-01

267

Lampe1: An ENU-Germline Mutation Causing Spontaneous Hepatosteatosis Identified through Targeted Exon-Enrichment and Next-Generation Sequencing  

Microsoft Academic Search

Using a small scale ENU mutagenesis approach we identified a recessive germline mutant, designated Lampe1 that exhibited growth retardation and spontaneous hepatosteatosis. Low resolution mapping based on 20 intercrossed Lampe1 mice revealed linkage to a ?14 Mb interval on the distal site of chromosome 11 containing a total of 285 genes. Exons and 50 bp flanking sequences within the critical

Rachel Sheridan; Kristin Lampe; Shiva Kumar Shanmukhappa; Patrick Putnam; Mehdi Keddache; Senad Divanovic; Jorge Bezerra; Kasper Hoebe

2011-01-01

268

250K Single Nucleotide Polymorphism Array Karyotyping Identifies Acquired Uniparental Disomy and Homozygous Mutations, Including Novel Missense Substitutions of c-Cbl, in Myeloid Malignancies  

Microsoft Academic Search

Two types of acquired loss of heterozygosity are possible in cancer: deletions and copy-neutral uniparental disomy (UPD). Conventionally, copy number losses are identified using metaphase cytogenetics, whereas detection of UPD is accom- plished by microsatellite and copy number analysis and as such, is not often used clinically. Recently, introduction of single nucleotide polymorphism (SNP) microarrays has allowed for the systematic

Andrew J. Dunbar; Lukasz P. Gondek; Christine L. O'Keefe; Hideki Makishima; Manjot S. Rataul; Hadrian Szpurka; Xiao Fei Wang; Michael A. McDevitt; Jaroslaw P. Maciejewski

269

The removal from plasma of chylomicrons and remnants is reduced in heterozygous familial hypercholesterolemia subjects with identified LDL receptor mutations: study with artificial emulsions.  

PubMed

Chylomicron remnants bind to both their specific receptors (LRP) and to the LDL receptor (LDLR) in the liver. There is controversy whether disturbances of chylomicron metabolism occur in subjects with familial hypercholesterolemia (FH). The aim of this study was to evaluate whether there are defects on the removal from plasma of chylomicrons and their remnants in heterozygous FH patients with determined LDLR mutations. We studied 20 heterozygous FH patients (43.2±12 years old, 60% males) and 50 normolipidemic subjects matched for age and gender. FH subjects were not in use of LDL-lowering drugs for at least 6 weeks. The removal from plasma of chylomicrons and their remnants was measured by isotopic decay after venous injection of a chylomicron-like emulsion radiolabeled with (14)C-cholesteryl ester ((14)C-CE) and (3)H-triolein ((3)H-TO). These track respectively removal from plasma of chylomicrons and remnants and lipolysis. There was a significant reduction in the fractional catabolic rates (FCR in h(-1)) of (14)C-CE in FH in comparison with normolipidemics: 0.048 (1.46.10(-7); 0.57) vs. 0.71(0.049; 1.62), [median (25th-75th percentile)], p=0.003. No differences were found in FCR of (3)H-TO between FH and controls, respectively 1.62 (1.02; 2.331) and 1.914 (1.34; 2.878), p=0.405. In conclusion heterozygous FH subjects had a significant decrease on the removal from plasma of chylomicrons and their remnants compared with normolipidemics. PMID:22257824

Carneiro, Marcia M; Miname, Marcio H; Gagliardi, Ana C; Pereira, Carolina; Pereira, Alexandre C; Krieger, Jose E; Maranhão, Raul C; Santos, Raul D

2011-12-29

270

Prediction of conformational changes by single mutation in the hepatitis B virus surface antigen (HBsAg) identified in HBsAg-negative blood donors  

PubMed Central

Background Selection of hepatitis B virus (HBV) by host immunity has been suggested to give rise to variants with amino acid substitutions at or around the 'a' determinant of the surface antigen (HBsAg), the main target of antibody neutralization and diagnostic assays. However, there have never been successful attempts to provide evidence for this hypothesis, partly because the 3 D structure of HBsAg molecules has not been determined. Tertiary structure prediction of HBsAg solely from its primary amino acid sequence may reveal the molecular energetic of the mutated proteins. We carried out this preliminary study to analyze the predicted HBsAg conformation changes of HBV variants isolated from Indonesian blood donors undetectable by HBsAg assays and its significance, compared to other previously-reported variants that were associated with diagnostic failure. Results Three HBV variants (T123A, M133L and T143M) and a wild type sequence were analyzed together with frequently emerged variants T123N, M133I, M133T, M133V, and T143L. Based on the Jameson-Wolf algorithm for calculating antigenic index, the first two amino acid substitutions resulted in slight changes in the antigenicity of the 'a' determinant, while all four of the comparative variants showed relatively more significant changes. In the pattern T143M, changes in antigenic index were more significant, both in its coverage and magnitude, even when compared to variant T143L. These data were also partially supported by the tertiary structure prediction, in which the pattern T143M showed larger shift in the HBsAg second loop structure compared to the others. Conclusions Single amino acid substitutions within or near the 'a' determinant of HBsAg may alter antigenicity properties of variant HBsAg, which can be shown by both its antigenic index and predicted 3 D conformation. Findings in this study emphasize the significance of variant T143M, the prevalent isolate with highest degree of antigenicity changes found in Indonesian blood donors. This highlights the importance of evaluating the effects of protein structure alterations on the sensitivity of screening methods being used in detection of ongoing HBV infection, as well as the use of vaccines and immunoglobulin therapy in contributing to the selection of HBV variants.

2010-01-01

271

Mutation analysis of peroxisome proliferator-activated receptor-? coactivator-1 (PGC1) and relationships of identified amino acid polymorphisms to Type II diabetes mellitus  

Microsoft Academic Search

.\\u000a Aim\\/hypothesis:   This study aimed to investigate if variability in the peroxisome proliferator-activated receptor-? coactivator-1 (PGC-1) gene is associated with Type II (non-insulin-dependent) diabetes mellitus. \\u000a \\u000a \\u000a \\u000a Methods:   The PGC-1 gene was examined in 53 Type II diabetic patients applying single strand conformational polymorphism analysis followed by\\u000a nucleotide sequencing. Identified variants were genotyped in an association study comprising 483 Type II diabetic

J. Ek; G. Andersen; S. A. Urhammer; P. H. Gæde; T. Drivsholm; K. Borch-Johnsen; T. Hansen; O. Pedersen

2001-01-01

272

Mutational analysis of the L1 neuronal cell adhesion molecule identifies membrane-proximal amino acids of the cytoplasmic domain that are required for cytoskeletal anchorage.  

PubMed

The preferential localization of the L1 cell adhesion molecule in the axons and growth cones of differentiating neurons suggests the existence of a mechanism for targeting or anchoring the molecule to these locations. We have used B28 glioma cells, which have an extremely flattened morphology, as a model system to study the organization of L1 on the cell structure. Transfection of L1 cDNA into B28 cells results in expression of the L1 protein in organized linear cell surface arrays which are codistributed with cytoskeletal stress fibers, but not with microtubles or intermediate filaments. Transfection studies with L1 deletion mutants identify the juxtamembrane segment of the cytoplasmic domain as the critical entity for arrangement of L1 into ordered cell surface arrays. The seventh cytoplasmic amino acid of L1, lysine 1150, and to a lesser extent the fourth cytoplasmic amino acid, lysine 1147, appear to be critical residues for maintaining normal L1 anchorage and distribution. PMID:9245498

Dahlin-Huppe, K; Berglund, E O; Ranscht, B; Stallcup, W B

1997-01-01

273

Modeling, Substrate Docking, and Mutational Analysis Identify Residues Essential for the Function and Specificity of a Eukaryotic Purine-Cytosine NCS1 Transporter*  

PubMed Central

The recent elucidation of crystal structures of a bacterial member of the NCS1 family, the Mhp1 benzyl-hydantoin permease from Microbacterium liquefaciens, allowed us to construct and validate a three-dimensional model of the Aspergillus nidulans purine-cytosine/H+ FcyB symporter. The model consists of 12 transmembrane ?-helical, segments (TMSs) and cytoplasmic N- and C-tails. A distinct core of 10 TMSs is made of two intertwined inverted repeats (TMS1–5 and TMS6–10) that are followed by two additional TMSs. TMS1, TMS3, TMS6, and TMS8 form an open cavity that is predicted to host the substrate binding site. Based on primary sequence alignment, three-dimensional topology, and substrate docking, we identified five residues as potentially essential for substrate binding in FcyB; Ser-85 (TMS1), Trp-159, Asn-163 (TMS3), Trp-259 (TMS6), and Asn-354 (TMS8). To validate the role of these and other putatively critical residues, we performed a systematic functional analysis of relevant mutants. We show that the proposed substrate binding residues, plus Asn-350, Asn-351, and Pro-353 are irreplaceable for FcyB function. Among these residues, Ser-85, Asn-163, Asn-350, Asn-351, and Asn-354 are critical for determining the substrate binding affinity and/or the specificity of FcyB. Our results suggest that Ser-85, Asn-163, and Asn-354 directly interact with substrates, Trp-159 and Trp-259 stabilize binding through ?-? stacking interactions, and Pro-353 affects the local architecture of substrate binding site, whereas Asn-350 and Asn-351 probably affect substrate binding indirectly. Our work is the first systematic approach to address structure-function-specificity relationships in a eukaryotic member of NCS1 family by combining genetic and computational approaches.

Krypotou, Emilia; Kosti, Vasiliki; Amillis, Sotiris; Myrianthopoulos, Vassilios; Mikros, Emmanuel; Diallinas, George

2012-01-01

274

NUP98-NSD1 fusion in association with FLT3-ITD mutation identifies a prognostically relevant subgroup of pediatric acute myeloid leukemia patients suitable for monitoring by real time quantitative PCR.  

PubMed

The cytogenetically cryptic t(5;11)(q35;p15) leading to the NUP98-NSD1 fusion is a rare but recurrent gene rearrangement recently reported to identify a group of young AML patients with poor prognosis. We used reverse transcription polymerase chain reaction (PCR) to screen retrospectively diagnostic samples from 54 unselected pediatric AML patients and designed a real time quantitative PCR assay to track individual patient response to treatment. Four positive cases (7%) were identified; three arising de novo and one therapy related AML. All had intermediate risk cytogenetic markers and a concurrent FLT3-ITD but lacked NPM1 and CEBPA mutations. The patients had a poor response to therapy and all proceeded to hematopoietic stem cell transplant. These data lend support to the adoption of screening for NUP98-NSD1 in pediatric AML without otherwise favorable genetic markers. The role of quantitative PCR is also highlighted as a potential tool for managing NUP98-NSD1 positive patients post-treatment. © 2013 Wiley Periodicals, Inc. PMID:23999921

Akiki, Susanna; Dyer, Sara A; Grimwade, David; Ivey, Adam; Abou-Zeid, Nervana; Borrow, Julian; Jeffries, Sally; Caddick, Judith; Newell, Hayley; Begum, Suriya; Tawana, Kiran; Mason, Joanne; Velangi, Mark; Griffiths, Michael

2013-09-02

275

Real-time quantitative PCR analysis can be used as a primary screen to identify patients with CML treated with imatinib who have BCR-ABL kinase domain mutations  

Microsoft Academic Search

Mutations within the BCR-ABL kinase do- main in imatinib-treated chronic myeloid leukemia (CML) are the main mechanism of acquired resistance. The early detec- tion of mutations should provide clinical benefit by allowing early intervention. Quantitative polymerase chain reaction (RQ-PCR) results ofBCR-ABLmRNAwere correlated with mutation analysis in 214 patients treated with imatinib. We deter- mined whether there was a difference in

Susan Branford; Zbigniew Rudzki; Ian Parkinson; Andrew Grigg; Kerry Taylor; John F. Seymour; Simon Durrant; Peter Browett; Anthony P. Schwarer; Chris Arthur; John Catalano; Michael F. Leahy; Robin Filshie; Kenneth Bradstock; Richard Herrmann; David Joske; Kevin Lynch; Tim Hughes

2004-01-01

276

The androgen receptor gene mutations database.  

PubMed

The androgen receptor gene mutations database is a comprehensive listing of mutations published in journals and meetings proceedings. The majority of mutations are point mutations identified in patients with androgen insensitivity syndrome. Information is included regarding the phenotype, the nature and location of the mutations, as well as the effects of the mutations on the androgen binding activity of the receptor. The current version of the database contains 149 entries, of which 114 are unique mutations. The database is available from EMBL (NetServ@EMBL-Heidelberg.DE) or as a Macintosh Filemaker file (mc33001@musica.mcgill.ca). PMID:7937057

Patterson, M N; Hughes, I A; Gottlieb, B; Pinsky, L

1994-09-01

277

Biochemical analyses are instrumental in identifying the impact of mutations on holo and/or apo-forms and on the region(s) of alanine:glyoxylate aminotransferase variants associated with Primary Hyperoxaluria Type I?  

PubMed Central

Primary Hyperoxaluria Type I (PH1) is a disorder of glyoxylate metabolism caused by mutations in the human AGXT gene encoding liver peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5?-phosphate (PLP) dependent enzyme. Previous investigations highlighted that, although PH1 is characterized by a significant variability in terms of enzymatic phenotype, the majority of the pathogenic variants are believed to share both structural and functional defects, as mainly revealed by data on AGT activity and expression level in crude cellular extracts. However, the knowledge of the defects of the AGT variants at a protein level is still poor. We therefore performed a side-by-side comparison between normal AGT and nine purified recombinant pathogenic variants in terms of catalytic activity, coenzyme binding mode and affinity, spectroscopic features, oligomerization, and thermal stability of both the holo- and apo-forms. Notably, we chose four variants in which the mutated residues are located in the large domain of AGT either within the active site and interacting with the coenzyme or in its proximity, and five variants in which the mutated residues are distant from the active site either in the large or in the small domain. Overall, this integrated analysis of enzymatic activity, spectroscopic and stability information is used to (i) reassess previous data obtained with crude cellular extracts, (ii) establish which form(s) (i.e. holoenzyme and/or apoenzyme) and region(s) (i.e. active site microenvironment, large and/or small domain) of the protein are affected by each mutation, and (iii) suggest the possible therapeutic approach for patients bearing the examined mutations.

Oppici, Elisa; Montioli, Riccardo; Lorenzetto, Antonio; Bianconi, Silvia; Borri Voltattorni, Carla; Cellini, Barbara

2012-01-01

278

Biochemical analyses are instrumental in identifying the impact of mutations on holo and/or apo-forms and on the region(s) of alanine:glyoxylate aminotransferase variants associated with primary hyperoxaluria type I.  

PubMed

Primary Hyperoxaluria Type I (PH1) is a disorder of glyoxylate metabolism caused by mutations in the human AGXT gene encoding liver peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5'-phosphate (PLP) dependent enzyme. Previous investigations highlighted that, although PH1 is characterized by a significant variability in terms of enzymatic phenotype, the majority of the pathogenic variants are believed to share both structural and functional defects, as mainly revealed by data on AGT activity and expression level in crude cellular extracts. However, the knowledge of the defects of the AGT variants at a protein level is still poor. We therefore performed a side-by-side comparison between normal AGT and nine purified recombinant pathogenic variants in terms of catalytic activity, coenzyme binding mode and affinity, spectroscopic features, oligomerization, and thermal stability of both the holo- and apo-forms. Notably, we chose four variants in which the mutated residues are located in the large domain of AGT either within the active site and interacting with the coenzyme or in its proximity, and five variants in which the mutated residues are distant from the active site either in the large or in the small domain. Overall, this integrated analysis of enzymatic activity, spectroscopic and stability information is used to (i) reassess previous data obtained with crude cellular extracts, (ii) establish which form(s) (i.e. holoenzyme and/or apoenzyme) and region(s) (i.e. active site microenvironment, large and/or small domain) of the protein are affected by each mutation, and (iii) suggest the possible therapeutic approach for patients bearing the examined mutations. PMID:22018727

Oppici, Elisa; Montioli, Riccardo; Lorenzetto, Antonio; Bianconi, Silvia; Borri Voltattorni, Carla; Cellini, Barbara

2011-10-05

279

Mucopolysaccharidosis IVA mutations in Chinese patients: 16 novel mutations.  

PubMed

Mucopolysaccharidosis IVA (MPS IVA; Morquio A syndrome) is a lysosomal storage disease caused by deficiency of N-acetylgalactosamine-6-sulfatase (GALNS) and transmitted as an autosomal recessive trait. This is the first systematic mutation screen in Chinese MPS IVA patients. Mutation detections in 24 unrelated Chinese MPS IVA patients were performed by PCR and direct sequencing of exons or the mRNA of GALNS. A total of 42 mutant alleles were identified, belonging to 27 different mutations. Out of the 27 mutations, 16 were novel, including 2 splicing mutations (c.567-1G>T and c.634-1G>A), 2 nonsense mutations (p.W325X and p.Q422X) and 12 missense mutations (p.T88I, p.H142R, p.P163H, p.G168L, p.H236D, p.N289S, p.T312A, p.G316V, p.A324E, p.L366P, p.Q422K and p.F452L). p.G340D was found to be a common mutation in the Chinese MPS IVA patients, accounting for 16.7% of the total number of mutant alleles. The results show that the mutations in Chinese MPS IVA patients are also family specific but have a different mutation spectrum as compared to those of other populations. PMID:20574428

Wang, Zheng; Zhang, Weimin; Wang, Yun; Meng, Yan; Su, Liang; Shi, Huiping; Huang, Shangzhi

2010-06-24

280

Exome sequencing identifies a founder frameshift mutation in an alternative exon of USH1C as the cause of autosomal recessive retinitis pigmentosa with late-onset hearing loss.  

PubMed

We used a combined approach of homozygosity mapping and whole exome sequencing (WES) to search for the genetic cause of autosomal recessive retinitis pigmentosa (arRP) in families of Yemenite Jewish origin. Homozygosity mapping of two arRP Yemenite Jewish families revealed a few homozygous regions. A subsequent WES analysis of the two index cases revealed a shared homozygous novel nucleotide deletion (c.1220delG) leading to a frameshift (p.Gly407Glufs*56) in an alternative exon (#15) of USH1C. Screening of additional Yemenite Jewish patients revealed a total of 16 homozygous RP patients (with a carrier frequency of 0.008 in controls). Funduscopic and electroretinography findings were within the spectrum of typical RP. While other USH1C mutations usually cause Usher type I (including RP, vestibular dysfunction and congenital deafness), audiometric screening of 10 patients who are homozygous for c.1220delG revealed that patients under 40 years of age had normal hearing while older patients showed mild to severe high tone sensorineural hearing loss. This is the first report of a mutation in a known USH1 gene that causes late onset rather than congenital sensorineural hearing loss. The c.1220delG mutation of USH1C accounts for 23% of RP among Yemenite Jewish patients in our cohort. PMID:23251578

Khateb, Samer; Zelinger, Lina; Ben-Yosef, Tamar; Merin, Saul; Crystal-Shalit, Ornit; Gross, Menachem; Banin, Eyal; Sharon, Dror

2012-12-12

281

Exome Sequencing Identifies a Founder Frameshift Mutation in an Alternative Exon of USH1C as the Cause of Autosomal Recessive Retinitis Pigmentosa with Late-Onset Hearing Loss  

PubMed Central

We used a combined approach of homozygosity mapping and whole exome sequencing (WES) to search for the genetic cause of autosomal recessive retinitis pigmentosa (arRP) in families of Yemenite Jewish origin. Homozygosity mapping of two arRP Yemenite Jewish families revealed a few homozygous regions. A subsequent WES analysis of the two index cases revealed a shared homozygous novel nucleotide deletion (c.1220delG) leading to a frameshift (p.Gly407Glufs*56) in an alternative exon (#15) of USH1C. Screening of additional Yemenite Jewish patients revealed a total of 16 homozygous RP patients (with a carrier frequency of 0.008 in controls). Funduscopic and electroretinography findings were within the spectrum of typical RP. While other USH1C mutations usually cause Usher type I (including RP, vestibular dysfunction and congenital deafness), audiometric screening of 10 patients who are homozygous for c.1220delG revealed that patients under 40 years of age had normal hearing while older patients showed mild to severe high tone sensorineural hearing loss. This is the first report of a mutation in a known USH1 gene that causes late onset rather than congenital sensorineural hearing loss. The c.1220delG mutation of USH1C accounts for 23% of RP among Yemenite Jewish patients in our cohort.

Khateb, Samer; Zelinger, Lina; Ben-Yosef, Tamar; Crystal-Shalit, Ornit; Gross, Menachem; Banin, Eyal; Sharon, Dror

2012-01-01

282

A role for helix 3 of the TRbeta ligand-binding domain in coactivator recruitment identified by characterization of a third cluster of mutations in resistance to thyroid hormone.  

PubMed Central

Resistance to thyroid hormone (RTH) has hitherto been associated with thyroid hormone beta receptor (TRbeta) mutations which cluster in two regions (alphaalpha 310-353 and alphaalpha 429-461) of the hormone-binding domain and closely approximate the ligand-binding cavity. Here, we describe a third cluster of RTH mutations extending from alphaalpha 234-282 which constitute a third boundary of the ligand pocket. One mutant, T277A, exhibits impaired transactivation which is disproportionate to its mildly reduced ligand affinity (Ka). T3-dependent recruitment of coactivators (SRC-1, ACTR) by mutant receptor-RXR heterodimers was reduced in comparison with wild-type. Cotransfection of SRC-1 restored transactivation by T277A. In the TRbeta crystal structure this helix 3 residue is surface-exposed and is in close proximity to residues L454 and E457 in helix 12 which are known to be critical for coactivator interaction, suggesting that they all constitute part of a receptor-coactivator interface. The transcriptional function of other mutants (A234T, R243W/Q, A268D, Delta276I, A279V, R282S) in this cluster correlated with their reduced Ka and they inhibited wild-type TRbeta action in a dominant negative manner. DNA binding, heterodimerization and corepressor recruitment were preserved in all mutants, signifying the importance of these attributes for dominant negative activity and correlating with the absence of natural mutations in regions bordering the third cluster which mediate these functions.

Collingwood, T N; Wagner, R; Matthews, C H; Clifton-Bligh, R J; Gurnell, M; Rajanayagam, O; Agostini, M; Fletterick, R J; Beck-Peccoz, P; Reinhardt, W; Binder, G; Ranke, M B; Hermus, A; Hesch, R D; Lazarus, J; Newrick, P; Parfitt, V; Raggatt, P; de Zegher, F; Chatterjee, V K

1998-01-01

283

Domain landscapes of somatic mutations in cancer  

PubMed Central

Background Large-scale tumor sequencing projects are now underway to identify genetic mutations that drive tumor initiation and development. Most studies take a gene-based approach to identifying driver mutations, highlighting genes mutated in a large percentage of tumor samples as those likely to contain driver mutations. However, this gene-based approach usually does not consider the position of the mutation within the gene or the functional context the position of the mutation provides. Here we introduce a novel method for mapping mutations to distinct protein domains, not just individual genes, in which they occur, thus providing the functional context for how the mutation contributes to disease. Furthermore, aggregating mutations from all genes containing a specific protein domain enables the identification of mutations that are rare at the gene level, but that occur frequently within the specified domain. These highly mutated domains potentially reveal disruptions of protein function necessary for cancer development. Results We mapped somatic mutations from the protein coding regions of 100 colon adenocarcinoma tumor samples to the genes and protein domains in which they occurred, and constructed topographical maps to depict the “mutational landscapes” of gene and domain mutation frequencies. We found significant mutation frequency in a number of genes previously known to be somatically mutated in colon cancer patients including APC, TP53 and KRAS. In addition, we found significant mutation frequency within specific domains located in these genes, as well as within other domains contained in genes having low mutation frequencies. These domain “peaks” were enriched with functions important to cancer development including kinase activity, DNA binding and repair, and signal transduction. Conclusions Using our method to create the domain landscapes of mutations in colon cancer, we were able to identify somatic mutations with high potential to drive cancer development. Interestingly, the majority of the genes involved have a low mutation frequency. Therefore, themethod shows good potential for identifying rare driver mutations in current, large-scale tumor sequencing projects. In addition, mapping mutations to specific domains provides the necessary functional context for understanding how the mutations contribute to the disease, and may reveal novel or more refined gene and domain target regions for drug development.

2012-01-01

284

Identifying harms.  

PubMed

Moral disagreements often revolve around the issue of harm to others. Identifying harms, however, is a contested enterprise. This paper provides a conceptual toolbox for identifying harms, and so possible wrongdoing, by drawing several distinctions. First, I distinguish between four modes of human vulnerability, forming four ways in which one can be in a harmed state. Second, I argue for the intrinsic disvalue of harm and so distinguish the presence of harm from the fact that it is instrumental to or constitutive of a valued act, practice or way of life. Finally, I distinguish between harm and wrongdoing, arguing that while harm is a normative concept requiring justification, not all harmed states are automatically unjustified. The advantage of this view is that it refocuses the moral debate on the normative issues involved while establishing a common basis to which both sides can agree: the presence of harm to others. PMID:21434956

Harrosh, Shlomit

2011-03-25

285

Identify Symmetry  

NSDL National Science Digital Library

This unit will teach you how to identify symmetry in everyday objects and mathematical shapes in lines and rotational symmetry. What is line symmetry? Click on the link to find out: Line Symmetry Here is a line activity to see if you understand it: Line Symmetry Class Zone See if you understand the concepts by doing the following quiz: Line Symmetry Work Now for rotational symmetry: Rotational Symmetry See if you understand rotational symmetry by taking this quiz: Rotational Symmetry Work ...

Neubert, Mrs.

2011-03-03

286

Identifying Erosion  

NSDL National Science Digital Library

In this environmental science activity (page 3 of the PDF), leaners will identify and explain the causes of erosion. They will observe the effects of erosion on the surrounding area and further explore examples of erosion online. An extension activity allows learners to make a hands-on model of soil erosion. Though this was created as a pre-visit activity for a workshop about water flow and erosion, it makes a great stand-alone activity as well!

Cosi

2009-01-01

287

Identification of HRAS mutations and absence of GNAQ or GNA11 mutations in deep penetrating nevi.  

PubMed

HRAS is mutated in ?15% of Spitz nevi, and GNAQ or GNA11 is mutated in blue nevi (46-83% and ?7% respectively). Epithelioid blue nevi and deep penetrating nevi show features of both blue nevi (intradermal location, pigmentation) and Spitz nevi (epithelioid morphology). Epithelioid blue nevi and deep penetrating nevi can also show overlapping features with melanoma, posing a diagnostic challenge. Although epithelioid blue nevi are considered blue nevic variants, no GNAQ or GNA11 mutations have been reported. Classification of deep penetrating nevi as blue nevic variants has also been proposed, however, no GNAQ or GNA11 mutations have been reported and none have been tested for HRAS mutations. To better characterize these tumors, we performed mutational analysis for GNAQ, GNA11, and HRAS, with blue nevi and Spitz nevi as controls. Within deep penetrating nevi, none demonstrated GNAQ or GNA11 mutations (0/38). However, 6% revealed HRAS mutation (2/32). Twenty percent of epithelioid blue nevi contained a GNAQ mutation (2/10), while none displayed GNA11 or HRAS mutation. Eighty-seven percent of blue nevi contained a GNAQ mutation (26/30), 4% a GNA11 mutation (1/28), and none an HRAS mutation. Within Spitz nevi, none demonstrated GNAQ or GNA11 mutations (0/30). Seventeen percent contained an HRAS mutation (5/30). All GNAQ and GNA11 mutations were p.Q209L (c.626A>T) point mutations, except 2 GNAQ mutations, which contained novel c.625_626CA>TT double mutations. Four HRAS mutations were in exon 2, and three in exon 3. This is the first study to identify HRAS mutations in deep penetrating nevi. The presence of HRAS mutations and absence of GNAQ or GNA11 mutations in deep penetrating nevi suggests classification of these unusual nevi within the Spitz nevus category of melanocytic tumors, rather than the blue nevus category. PMID:23599145

Bender, Ryan P; McGinniss, Matthew J; Esmay, Paula; Velazquez, Elsa F; Reimann, Julie Dr

2013-04-19

288

Strategy of mutual compensation of green and red mutants of firefly luciferase identifies a mutation of the highly conservative residue E457 with a strong red shift of bioluminescence.  

PubMed

Bioluminescence spectra of firefly luciferases demonstrate highly pH-sensitive spectra changing the color from green to red light when pH is lowered from alkaline to acidic. This reflects a change of ratio of the green and red emitters in the bimodal spectra of bioluminescence. We show that the mutations strongly stabilizing green (Y35N) or red (H433Y) emission compensate each other leading to the WT color of firefly luciferase. We further used this compensating ability of Y35N to search for strong red-shifting mutations in the C-domain of firefly luciferase by random mutagenesis. The discovered mutation E457K substantially increased the contribution of the red emitter and caused a 12 nm red shift of the green emitter as well. E457 is highly conservative not only in beetle luciferases but also in a whole ANL superfamily of adenylating enzymes and forms a conservative structural hydrogen bond with V471. Our results suggest that the removal of this hydrogen bond only mildly affects luciferase properties and that most of the effect of E457K is caused by the introduction of positive charge. E457 forms a salt bridge with R534 in most ANL enzymes including pH-insensitive luciferases which is absent in pH-sensitive firefly luciferases. The mutant A534R shows that this salt bridge is not important for pH-sensitivity but considerably improves in vivo thermostability. Although E457 is located far from the oxyluciferin-binding site, the properties of the mutant E457K suggest that it affects color by influencing the AMP binding. PMID:24057044

Koksharov, Mikhail I; Ugarova, Natalia N

2013-10-16

289

Identifying Species  

NSDL National Science Digital Library

This two part activity will allow students to investigate biological diversity in the area of their school. They will first prepare a taxonomic key to distinguish between the four insects or spiders that they have selected. All of the keys are combined and students then perform a transect study of a neighborhood field or school playing ground. Finally as a class students will compile a list of the animals and plants that are found within a mile of their school. They may need to use field guides, local resources, taxonomic keys, and species lists to help identify these organisms. Once they have compiled their list they will organize the species into the taxonomic groups they have studied.

Dispezio, Michael

290

Use of DNA arrays to identify a mutation in the negative regulator, csrR, responsible for the high virulence of a naturally occurring type M3 group A streptococcus clinical isolate.  

PubMed

We previously reported that type M3 group A streptococcus (GAS) showed a wide range of 50% lethal dose values in mice. Analysis using DNA arrays indicated that the most virulent strain, M3-f, expressed significantly higher levels of the products of several virulence genes than did the other M3 isolates. Sequencing of the csrS, csrR, luxS, and rgg genes in the isolates showed that the M-3f csrR gene contained a specific point mutation. Disruption of wild-type (wt) csrR in an M3 strain increased its virulence and the expression of hyaluronic acid, whereas complementation with wt but not type M3-f csrR attenuated these changes. Expression experiments showed that type M3-f CsrR counteracted the effects of wt CsrR. Although wt CsrR bound to the hasA promoter region, type M3-f CsrR did not. Thus, the high virulence of the type M3-f strain is associated with the decreased binding of type M3-f CsrR to its target sequences. PMID:16703511

Miyoshi-Akiyama, Tohru; Ikebe, Tadayoshi; Watanabe, Haruo; Uchiyama, Takehiko; Kirikae, Teruo; Kawamura, Yoshiaki

2006-05-10

291

Expanding the phenotype of LMNA mutations in dilated cardiomyopathy and functional consequences of these mutations  

PubMed Central

Aims: Mutations in the lamin A/C gene (LMNA) have been reported to be involved in dilated cardiomyopathy (DCM) associated with conduction system disease and/or skeletal myopathy. The aim of this study was to perform a mutational analysis of LMNA in a large white population of patients affected by dilated cardiomyopathy with or without associated symptoms. Methods: We performed screening of the coding sequence of LMNA on DNA samples from 66 index cases, and carried out cell transfection experiments to examine the functional consequences of the mutations identified. Results: A new missense (E161K) mutation was identified in a family with early atrial fibrillation and a previously described (R377H) mutation in another family with a quadriceps myopathy associated with DCM. A new mutation (28insA) leading to a premature stop codon was identified in a family affected by DCM with conduction defects. No mutation in LMNA was found in cases with isolated dilated cardiomyopathy. Functional analyses have identified potential physiopathological mechanisms involving identified mutations, such as haploinsufficiency (28insA) or intermediate filament disorganisation (E161K, R377H). Conclusion: For the first time, a specific phenotype characterised by early atrial fibrillation is associated with LMNA mutation. Conversely, mutations in LMNA appear as a rare cause of isolated dilated cardiomyopathy. The variable phenotypes observed in LMNA-DCM might be explained by the variability of functional consequences of LMNA mutations.

Sebillon, P; Bouchier, C; Bidot, L; Bonne, G; Ahamed, K; Charron, P; Drouin-Garraud, V; Millaire, A; Desrumeaux, G; Benaiche, A; Charniot, J; Schwartz, K; Villard, E; Komajda, M

2003-01-01

292

Jagged1 (JAG1) mutations in Alagille syndrome: increasing the mutation detection rate.  

PubMed

Alagille syndrome (AGS) is caused by heterozygous mutations in JAG1, and mutations have been previously reported in about 70% of patients who meet clinical diagnostic criteria. We studied a cohort of 247 clinically well-defined patients, and using an aggressive and sequential screening approach we identified JAG1 mutations in 94% of individuals. Mutations were found in 232 out of 247 patients studied and 83 of the mutations were novel. This increase in the mutation rate was accomplished by combining rigorous clinical phenotyping, with a combination of mutation detection techniques, including fluorescence in situ hybridization (FISH), genomic and cDNA sequencing, and quantitative PCR. This higher rate of mutation identification has implications for clinical practice, facilitating genetic counseling, prenatal diagnosis, and evaluation of living-related liver transplant donors. Our results suggest that more aggressive screening may similarly increase the rate of mutation detection in other dominant and recessive disorders. PMID:16575836

Warthen, D M; Moore, E C; Kamath, B M; Morrissette, J J D; Sanchez-Lara, P A; Sanchez, P; Piccoli, D A; Krantz, I D; Spinner, N B

2006-05-01

293

Somatic mutation, genomic variation, and neurological disease.  

PubMed

Genetic mutations causing human disease are conventionally thought to be inherited through the germ line from one's parents and present in all somatic (body) cells, except for most cancer mutations, which arise somatically. Increasingly, somatic mutations are being identified in diseases other than cancer, including neurodevelopmental diseases. Somatic mutations can arise during the course of prenatal brain development and cause neurological disease-even when present at low levels of mosaicism, for example-resulting in brain malformations associated with epilepsy and intellectual disability. Novel, highly sensitive technologies will allow more accurate evaluation of somatic mutations in neurodevelopmental disorders and during normal brain development. PMID:23828942

Poduri, Annapurna; Evrony, Gilad D; Cai, Xuyu; Walsh, Christopher A

2013-07-01

294

Genetic identifiers of epilepsy.  

PubMed

Epilepsy affects >0.5% of the world's population and has a large genetic component. The most common human genetic epilepsies display a complex pattern of inheritance, and the identity of the susceptibility genes is largely unknown despite recent advances in molecular biology. However, genetic identifiers of certain types of epilepsy with neurodegenerative characteristics and of a small number of familial idiopathic epilepsies have been uncovered to date. This article reviews recent progress made in molecular genetics of epilepsy, focusing mostly on idiopathic epilepsy together with our own discovery of novel mutations in the genes of autosomal dominant nocturnal frontal lobe epilepsy and benign familial neonatal convulsions (BFNCs), and the genetic locus of benign adult familial myoclonic epilepsy. Pathogenesis of epilepsy as a channelopathy and of BFNC also is discussed. PMID:12383274

Kaneko, Sunao; Iwasa, Hiroto; Okada, Motohiro

2002-01-01

295

Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole-genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes.  

PubMed

Chlamydia trachomatis is the most common bacterial sexually transmitted infection worldwide and the leading cause of preventable blindness in developing countries. Tetracycline is commonly the drug of choice for treating C. trachomatis infections, but cases of antibiotic resistance in clinical isolates have previously been reported. Here, we used antibiotic resistance assays and whole-genome sequencing to interrogate the hypothesis that two clinical isolates (IU824 and IU888) have acquired mechanisms of antibiotic resistance. Immunofluorescence staining was used to identify C. trachomatis inclusions in cell cultures grown in the presence of tetracycline; however, only antibiotic-free control cultures yielded the strong fluorescence associated with the presence of chlamydial inclusions. Infectivity was lost upon passage of harvested cultures grown in the presence of tetracycline into antibiotic-free medium, so we conclude that these isolates were phenotypically sensitive to tetracycline. Comparisons of the genome and plasmid sequences for the two isolates with tetracycline-sensitive strains did not identify regions of low sequence identity that could accommodate horizontally acquired resistance genes, and the tetracycline binding region of the 16S rRNA gene was identical to that of the sensitive control strains. The porB gene of strain IU824, however, was found to contain a premature stop codon not previously identified, which is noteworthy but unlikely to be related to tetracycline resistance. In conclusion, we found no evidence of tetracycline resistance in the two strains investigated, and it seems most likely that the small, aberrant inclusions previously identified resulted from the high chlamydial load used in the original antibiotic resistance assays. PMID:23378575

O'Neill, C E; Seth-Smith, H M B; Van Der Pol, B; Harris, S R; Thomson, N R; Cutcliffe, L T; Clarke, I N

2013-02-01

296

A novel missense mutation in SLC34A3 that causes hereditary hypophosphatemic rickets with hypercalciuria in humans identifies threonine 137 as an important determinant of sodium-phosphate cotransport in NaPi-IIc  

PubMed Central

The present study describes two novel compound heterozygous mutations, c.410C>T(p.T137M) (T137M) on the maternal and g.4225_50del on the paternal allele of SLC34A3, in a previously reported male with hereditary hypophosphatemic rickets with hypercalciuria (HHRH) and recurrent kidney stones (Chen C, Carpenter T, Steg N, Baron R, Anast C. Pediatrics 84: 276–280, 1989). For functional analysis in vitro, we generated expression plasmids encoding enhanced green fluorescence protein (EGFP) concatenated to the NH2 terminus of wild-type or mutant human type IIc Na-Pi cotransporter (NaPi-IIc), i.e., EGFP-hNaPi-IIc, EGFP-[M137]hNaPi-IIc, or EGFP-[Stop446]hNaPi-IIc. The V446Stop mutant showed complete loss of expression and function when assayed for apical patch expression in opossum kidney (OK) cells and sodium-dependent 33P uptake into Xenopus laevis oocytes. Conversely, EGFP-[M137]hNaPi-IIc was inserted into apical patches of OK cells and into oocyte membranes. However, when quantified by confocal microscopy, surface fluorescence was reduced to 40% compared with wild-type. After correction for surface expression, the rate of 33P uptake by oocytes mediated by EGFP-[M137]hNaPi-IIc was decreased by an additional 60%. The resulting overall reduction of function of this NaPi-IIc mutant to 16%, taken together with complete loss of expression and function of g.4225_50del(V446Stop), thus appears to be sufficient to explain the phenotype in our patient. Furthermore, the stoichiometric ratio of 22Na and 33P uptake was increased to 7.1 ± 3.65 for EGFP-[M137]hNaPi-IIc compared with wild-type. Two-electrode studies indicate that EGFP-[M137]hNaPi-IIc is nonelectrogenic but displayed a significant phosphate-independent inward-rectified sodium current, which appears to be insensitive to phosphonoformic acid. M137 thus may uncouple sodium-phosphate cotransport, suggesting that this amino acid residue has an important functional role in human NaPi-IIc.

Jaureguiberry, Graciana; Carpenter, Thomas O.; Forman, Stuart; Juppner, Harald; Bergwitz, Clemens

2008-01-01

297

Stress, Mutators, Mutations and Stress Resistance  

Microsoft Academic Search

\\u000a Organisms need genetic mechanisms to rapidly adapt to changing, stressful environments. Having a high mutation frequency would\\u000a have a drag on a population due to the deleterious nature of mutations, but having a sub-population with high mutation rate\\u000a due to the presence of mutator genes seems to be nature’s solution. Far more is known about mutator genes in bacteria than

Jonathan Gressel; Avraham A. Levy

298

KRAS mutations in lung cancer.  

PubMed

Epidermal growth factor receptor (EGFR) gene mutations and increased EGFR copy numbers have been associated with a favorable response to EGFR tyrosine kinase inhibitors (TKI) in patients with non-small-cell lung cancer (NSCLC), and several markers have been identified that predict response to treatment. Lung adenocarcinomas also harbor activating mutations in the downstream GTPase, v-Ki-ras2 Kirsten rat sarcoma viral oncogene (KRAS), and mutations in EGFR and KRAS appear to be mutually exclusive. Even though KRAS mutations were identified in NSCLC tumors more than 20 years ago, we have only just begun to appreciate the clinical value of determining KRAS tumor status. Recent studies indicate that patients with mutant KRAS tumors fail to benefit from adjuvant chemotherapy and do not respond to EGFR inhibitors. There is a clear need for therapies specifically developed for patients with KRAS-mutant NSCLC. In this review, we summarize the clinical and pathologic characteristics of patients with NSCLC and with KRAS mutations, describe work that explores the predictive and prognostic influence of KRAS mutations, and provide an overview of the "synthetic lethal" interactions and current approaches to targeting KRAS-mutant NSCLC. PMID:23122493

Karachaliou, Niki; Mayo, Clara; Costa, Carlota; Magrí, Ignacio; Gimenez-Capitan, Ana; Molina-Vila, Miguel Angel; Rosell, Rafael

2012-11-01

299

TOX3 Mutations in Breast Cancer  

PubMed Central

TOX3 maps to 16q12, a region commonly lost in breast cancers and recently implicated in the risk of developing breast cancer. However, not much is known of the role of TOX3 itself in breast cancer biology. This is the first study to determine the importance of TOX3 mutations in breast cancers. We screened TOX3 for mutations in 133 breast tumours and identified four mutations (three missense, one in-frame deletion of 30 base pairs) in six primary tumours, corresponding to an overall mutation frequency of 4.5%. One potentially deleterious missense mutation in exon 3 (Leu129Phe) was identified in one tumour (genomic DNA and cDNA). Whilst copy number changes of 16q12 are common in breast cancer, our data show that mutations of TOX3 are present at low frequency in tumours. Our results support that TOX3 should be further investigated to elucidate its role in breast cancer biology.

Jones, James Owain; Chin, Suet-Feung; Wong-Taylor, Li-An; Leaford, Donna; Ponder, Bruce A. J.; Caldas, Carlos; Maia, Ana-Teresa

2013-01-01

300

Mutation and the environment  

Microsoft Academic Search

This book is covered under the following topics: Somatic Mutation: Animal Model; Somatic Mutation: Human; Heritable Mutation: Animal Model; Heritable Mutation: Approaches to Human Induction Rates; Heritable Mutation: Human Risk; Epidemiology: Population Studies on Genotoxicity; and Epidemiology: Workplace Studies of Genotoxicity.

M. L. Mendelsohn; R. J. Albertini

1990-01-01

301

CBFA1 mutation analysis and functional correlation with phenotypic variability in cleidocranial dysplasia  

Microsoft Academic Search

Cleidocranial dysplasia (CCD) is a dominantly inherited skeletal dysplasia caused by mutations in the osteoblast-specific transcription factor CBFA1 .T o correlate CBFA1 mutations in different functional domains with the CCD clinical spectrum, we studied 26 independent cases of CCD and a total of 16 new mutations were identified in 17 families. The majority of mutations were de novo missense mutations

Guang Zhou; Yuqing Chen; Lei Zhou; Kannan Thirunavukkarasu; Jacqueline Hecht; David Chitayat; D. Gelb; Sinikka Pirinen; Susan A. Berry; Cheryl R. Greenberg; Gerard Karsenty; Brendan Lee

1999-01-01

302

Mutations affecting development of the zebrafish ear  

Microsoft Academic Search

In a large scale screen for genetic defects in zebrafish embryogenesis we identified mutations affecting several aspects of ear development, including: specification of the otic placode, growth of the otic vesicle (otocyst), otolith formation, morphogenesis of the semicircular canals and differentiation of the otic capsule. Here we report initial phenotypic and genetic characterization of 20 of these mutations defining 13

Jarema Malicki; Alexander F. Schier; Lilianna Solnica-Krezel; Derek L. Stemple; Stephan C. F. Neuhauss; Didier Y. R. Stainier; Salim Abdelilah; Zehava Rangini; Fried Zwartkruis; Wolfgang Driever

303

exo1-Dependent Mutator Mutations: Model System for Studying Functional Interactions in Mismatch Repair  

PubMed Central

EXO1 interacts with MSH2 and MLH1 and has been proposed to be a redundant exonuclease that functions in mismatch repair (MMR). To better understand the role of EXO1 in mismatch repair, a genetic screen was performed to identify mutations that increase the mutation rates caused by weak mutator mutations such as exo1? and pms1-A130V mutations. In a screen starting with an exo1 mutation, exo1-dependent mutator mutations were obtained in MLH1, PMS1, MSH2, MSH3, POL30 (PCNA), POL32, and RNR1, whereas starting with the weak pms1 allele pms1-A130V, pms1-dependent mutator mutations were identified in MLH1, MSH2, MSH3, MSH6, and EXO1. These mutations only cause weak MMR defects as single mutants but cause strong MMR defects when combined with each other. Most of the mutations obtained caused amino acid substitutions in MLH1 or PMS1, and these clustered in either the ATP-binding region or the MLH1-PMS1 interaction regions of these proteins. The mutations showed two other types of interactions: specific pairs of mutations showed unlinked noncomplementation in diploid strains, and the defect caused by pairs of mutations could be suppressed by high-copy-number expression of a third gene, an effect that showed allele and overexpressed gene specificity. These results support a model in which EXO1 plays a structural role in MMR and stabilizes multiprotein complexes containing a number of MMR proteins. A similar role is proposed for PCNA based on the data presented.

Amin, Neelam S.; Nguyen, My-Nga; Oh, Scott; Kolodner, Richard D.

2001-01-01

304

Progressive hearing loss, and recurrent sudden sensorineural hearing loss associated with GJB2 mutations - phenotypic spectrum and frequencies of GJB2 mutations in Austria  

Microsoft Academic Search

Mutations of GJB2 (encoding connexin 26) are the most common cause of hearing loss (HL) in different populations, and a broad spectrum of GJB2 mutations has been identified. We screened 204 consecutive patients with non-syndromic sensorineural hearing loss for GJB2 mutations. Causative GJB2 mutations were identified in 31 (15.2%) patients, and two common mutations, c.35delG and L90P (c.269T>C), accounted for

Andreas R. Janecke; Almut Hirst-Stadlmann; Barbara Günther; Barbara Utermann; Thomas Müller; Judith Löffler; Gerd Utermann; Doris Nekahm-Heis

2002-01-01

305

Novel PORCN mutations in focal dermal hypoplasia.  

PubMed

Focal dermal hypoplasia (FDH), Goltz or Goltz-Gorlin syndrome, is an X-linked dominant multisystem disorder characterized primarily by involvement of the skin, skeletal system and eyes. We screened for mutations in the PORCN gene in eight patients of Belgian and Finnish origin with firm clinical suspicion of FDH. First, we performed quantitative PCR (qPCR) analysis to define the copy number at this locus. Next, we sequenced the coding regions and flanking intronic sequences of the PORCN gene. Three de novo mutations were identified in our patients with FDH: a 150-kb deletion removing six genes including PORCN, as defined by qPCR and X-array-CGH, and two heterozygous missense mutations; c.992T>G (p.L331R) in exon 11 and c.1094G>A (p.R365Q) in exon 13 of the gene. Both point mutations changed highly conserved amino acids and were not found in 300 control X chromosomes. The three patients in whom mutations were identified all present with characteristic dermal findings together with limb manifestations, which were not seen in our mutation-negative patients. The clinical characteristics of our patients with PORCN mutations were compared with the previously reported mutation-positive cases. In this report, we summarize the literature on PORCN mutations and associated phenotypes. PMID:19863546

Froyen, G; Govaerts, K; Van Esch, H; Verbeeck, J; Tuomi, M-L; Heikkilä, H; Torniainen, S; Devriendt, K; Fryns, J-P; Marynen, P; Järvelä, I; Ala-Mello, S

2009-10-23

306

Identification of six new Gaucher disease mutations  

SciTech Connect

The four most common mutations account for 97% of the Gaucher disease-producing alleles in Jewish patients and 75% of the alleles in non-Jewish patients. Although at least 15 other mutations and some examples of gene conversion and/or fusion genes have been described, a number of mutations remain unidentified. We have now identified six new mutations, a deletion of a C at the 72 position of the cDNA, a 481C[yields]T mutation (122p[sup Gly[yields]Ser]), a 751T [yields] C (212 [sup Tyr[yields]His]), a 1549G [yields] A (478[sup Gly[yields]Ser]), a 1604G [yields] A (496 [sup Arg[yields]His]), and a 55-bp deletion. All but one of these were found in single families. The 1604A mutation, however, was observed in four unrelated individuals. 7 refs., 2 tabs.

Beutler, E.; Gelbart, T.; West, C. (Scripps Research Institute, La Jolla, CA (United States))

1993-01-01

307

High Frequency of FGFR3 Mutations in Adenoid Seborrheic Keratoses  

Microsoft Academic Search

FGFR3 germline mutations cause autosomal dominant skeletal disorders including achondroplasia, thanatophoric dysplasia, severe achondroplasia with developmental delay and acanthosis nigricans, and Crouzon syndrome. Somatic mutations of FGFR3 have been identified in bladder cancer, multiple myeloma, and other neoplasms. FGFR3 mutations have also been detected in 40% of seborrheic keratoses (SKs) of the hyperkeratotic and acanthotic subtype, which are very common

Christian Hafner; Johanna M M van Oers; Arndt Hartmann; Michael Landthaler; Robert Stoehr; Hagen Blaszyk; Ferdinand Hofstaedter; Ellen C Zwarthoff; Thomas Vogt

2006-01-01

308

A Haplotype Framework for Cystic Fibrosis Mutations in Iran  

PubMed Central

This is the first comprehensive profile of cystic fibrosis transmembrane conductance regulator (CFTR) mutations and their corresponding haplotypes in the Iranian population. All of the 27 CFTR exons of 60 unrelated Iranian CF patients were sequenced to identify disease-causing mutations. Eleven core haplotypes of CFTR were identified by genotyping six high-frequency simple nucleotide polymorphisms. The carrier frequency of 2.5 in 100 (1 in 40) was estimated from the frequency of heterozygous patients and suggests that contrary to popular belief, cystic fibrosis may be a common, under-diagnosed disease in Iran. A heterogeneous mutation spectrum was observed at the CFTR locus in 60 cystic fibrosis (CF) patients from Iran. Twenty putative disease-causing mutations were identified on 64 (53%) of the 120 chromosomes. The five most common Iranian mutations together represented 37% of the expected mutated alleles. The most frequent mutation, ?F508 (p.F508del), represented only 16% of the expected mutated alleles. The next most frequent mutations were c.1677del2 (p.515fs) at 7.5%, c.4041C>G (p.N1303K) at 5.6%, c.2183AA>G (p.684fs) at 5%, and c.3661A>T (p.K1177X) at 2.5%. Three of the five most frequent Iranian mutations are not included in a commonly used panel of CF mutations, underscoring the importance of identifying geographic-specific mutations in this population.

Elahi, Elahe; Khodadad, Ahmad; Kupershmidt, Ilya; Ghasemi, Fereshteh; Alinasab, Babak; Naghizadeh, Ramin; Eason, Robert G.; Amini, Mahshid; Esmaili, Mehran; Esmaeili Dooki, Mohammad R.; Sanati, Mohammad H.; Davis, Ronald W.; Ronaghi, Mostafa; Thorstenson, Yvonne R.

2006-01-01

309

Mutations in EZH2 Cause Weaver Syndrome  

PubMed Central

We used trio-based whole-exome sequencing to analyze two families affected by Weaver syndrome, including one of the original families reported in 1974. Filtering of rare variants in the affected probands against the parental variants identified two different de novo mutations in the enhancer of zeste homolog 2 (EZH2). Sanger sequencing of EZH2 in a third classically-affected proband identified a third de novo mutation in this gene. These data show that mutations in EZH2 cause Weaver syndrome.

Gibson, William T.; Hood, Rebecca L.; Zhan, Shing Hei; Bulman, Dennis E.; Fejes, Anthony P.; Moore, Richard; Mungall, Andrew J.; Eydoux, Patrice; Babul-Hirji, Riyana; An, Jianghong; Marra, Marco A.; Chitayat, David; Boycott, Kym M.; Weaver, David D.; Jones, Steven J.M.

2012-01-01

310

Rare occurrence of DNMT3A mutations in myelodysplastic syndromes  

PubMed Central

Gene mutations and epigenetic changes have been shown to play significant roles in the pathogenesis of myelodysplastic syndromes. Recently, mutations in DNMT3A were identified in 22.1% of patients with acute myeloid leukemia. In this study, we analyzed the frequency and clinical impact of DNMT3A mutations in a cohort of 193 patients with myelodysplastic syndromes. Mutations in DNMT3A were found in 2.6% of patients. The majority of mutations were heterozygous missense mutations affecting codon R882. Patients with DNMT3A mutations were found to have a higher rate of transformation to acute myeloid leukemia. When assessing the global methylation levels in patients with mutated versus unmutated DNMT3A and healthy controls no difference in global DNA methylation levels between the two groups was seen. Our data show that in patients with myelodysplastic syndromes, DNMT3A mutations occur at a low frequency and may be a risk factor for leukemia progression.

Thol, Felicitas; Winschel, Claudia; Ludeking, Andrea; Yun, Haiyang; Friesen, Inna; Damm, Frederik; Wagner, Katharina; Krauter, Jurgen; Heuser, Michael; Ganser, Arnold

2011-01-01

311

Risks of lynch syndrome cancers for msh6 mutation carriers  

Microsoft Academic Search

Background: Germline mutations in MSH6 account for 10%-20% of Lynch syndrome colorectal cancers caused by hereditary DNA mismatch repair gene mutations. Because there have been only a few studies of mutation carriers, their cancer risks are uncertain. Methods: We identified 113 families of MSH6 mutation carriers from five countries that we ascertained through family cancer clinics and population-based cancer registries.

L. Baglietto; N. M. Lindor; J. G. Dowty; D. M. White; A. Wagner; E. B. Gómez García; A. H. J. T. Vriends; N. R. Cartwright; R. A. Barnetson; S. M. Farrington; A. Tenesa; H. Hampel; D. Buchanan; S. Arnold; J. Young; M. D. Walsh; J. Jass; F. A. Macrae; Y. Antill; I. M. Winship; G. G. Giles; J. Goldblatt; S. Parry; G. Suthers; B. Leggett; M. Butz; M. Aronson; J. N. Poynter; J. A. Baron; L. Le Marchand; R. Haile; S. Gallinger; J. L. Hopper; J. Potter; La Chapelle de A; H. F. Vasen; M. G. Dunlop; S. N. Thibodeau; M. A. Jenkins

2010-01-01

312

Functional analysis of PTPN11\\/SHP2 mutants identified in Noonan syndrome and childhood leukemia  

Microsoft Academic Search

Noonan syndrome (NS) is characterized by short stature, characteristic facial features, and heart defects. Recently, missense mutations of PTPN11, the gene encoding protein tyrosine phosphatase (PTP) SHP-2, were identified in patients with NS. Further, somatic mutations in PTPN11 were detected in childhood leukemia. Recent studies showed that the phosphatase activities of five mutations identified in NS and juvenile myelomonocytic leukemia

Tetsuya Niihori; Yoko Aoki; Hirofumi Ohashi; Kenji Kurosawa; Tatsuro Kondoh; Satoshi Ishikiriyama; Hiroshi Kawame; Hotaka Kamasaki; Tsutomu Yamanaka; Fumio Takada; Kimio Nishio; Masahiro Sakurai; Hiroshi Tamai; Tatsuro Nagashima; Yoichi Suzuki; Shigeo Kure; Kunihiro Fujii; Masue Imaizumi; Yoichi Matsubara

2005-01-01

313

Keap1 mutations in lung cancer patients  

PubMed Central

Kelch-like ECH-associated protein 1 (Keap1) inhibits nuclear factor erythroid 2-related 2 (NEF2L2; also named NRF2)-induced cytoprotection and has been hypothesized to represent a candidate tumor suppressor. We have previously reported the somatic mutations of the NRF2 gene (NFE2L2), however, the correlation between the Keap1 mutation and the clinicopathological features of lung cancer has not been well investigated. Therefore, in the present study, the Keap1 mutational status in non-small cell lung cancer (NSCLC) patients was investigated by reverse transcription PCR and direct sequencing. The study included 76 surgically-removed lung cancer cases from patients of the Nagoya City University Hospital in which the EGFR and NFE2L2 mutation status was already established. Keap1 mutations were identified in 2 (2.6%) adenocarcinoma patients with a history of heavy smoking. These mutations were identified to exist exclusively. The Keap1 mutation was only detected in patients with advanced adenocarcinoma (4.3%) and the completely exclusive status of this mutation and others, including EGFR, Kas, erbB2 and NRF2L2, is likely to improve the selection of personalized therapy for lung cancer.

SASAKI, HIDEFUMI; SUZUKI, AYUMI; SHITARA, MASAYUKI; OKUDA, KATSUHIRO; HIKOSAKA, YU; MORIYAMA, SATORU; YANO, MOTOKI; FUJII, YOSHITAKA

2013-01-01

314

Spectrum of mutations in alpha-mannosidosis.  

PubMed Central

alpha-Mannosidosis is an autosomal recessive disorder caused by deficiency of lysosomal alpha-mannosidase (LAMAN). The resulting intracellular accumulation of mannose-containing oligosaccharides leads to mental retardation, hearing impairment, skeletal changes, and immunodeficiency. Recently, we reported the first alpha-mannosidosis-causing mutation affecting two Palestinian siblings. In the present study 21 novel mutations and four polymorphic amino acid positions were identified by the screening of 43 patients, from 39 families, mainly of European origin. Disease-causing mutations were identified in 72% of the alleles and included eight splicing, six missense, and three nonsense mutations, as well as two small insertions and two small deletions. In addition, Southern blot analysis indicated rearrangements in some alleles. Most mutations were private or occurred in two or three families, except for a missense mutation resulting in an R750W substitution. This mutation was found in 13 patients, from different European countries, and accounted for 21% of the disease alleles. Although there were clinical variations among the patients, no significant LAMAN activity could be detected in any of the fibroblast cultures. In addition, no correlation between the types of mutations and the clinical manifestations was evident.

Berg, T; Riise, H M; Hansen, G M; Malm, D; Tranebjaerg, L; Tollersrud, O K; Nilssen, O

1999-01-01

315

Spectrum of small mutations in the dystrophin coding region  

SciTech Connect

Duchenne and Becker muscular dystrophies (DMD and BMD) are caused by defects in the dystrophin gene. About two-thirds of the affected patients have large deletions or duplications, which occur in the 5` and central portion of the gene. The nondeletion/duplication cases are most likely the result of smaller mutations that cannot be identified by current diagnostic screening strategies. We screened {approximately} 80% of the dystrophin coding sequence for small mutations in 158 patients without deletions or duplications and identified 29 mutations. The study indicates that many of the DMD and the majority of the BMD small mutations lie in noncoding regions of the gene. All of the mutations identified were unique to single patients, and most of the mutations resulted in protein truncation. We did not find a clustering of small mutations similar to the deletion distribution but found > 40% of the small mutations 3` of exon 55. The extent of protein truncation caused by the 3` mutations did not determine the phenotype, since even the exon 76 nonsense mutation resulted in the severe DMD phenotype. Our study confirms that the dystrophin gene is subject to a high rate of mutation in CpG sequences. As a consequence of not finding any hotspots or prevalent small mutations, we conclude that it is presently not possible to perform direct carrier and prenatal diagnostics for many families without deletions or duplications. 71 refs., 2 figs., 2 tabs.

Prior, T.W.; Bartolo, C.; Pearl, D.K. [Ohio State Univ., Columbus, OH (United States)] [and others

1995-07-01

316

Two frequent missense mutations in Pendred syndrome.  

PubMed

Pendred syndrome is an autosomal recessive disorder characterized by early childhood deafness and goiter. A century after its recognition as a syndrome by Vaughan Pendred, the disease gene ( PDS ) was mapped to chromosome 7q22-q31.1 and, recently, found to encode a putative sulfate transporter. We performed mutation analysis of the PDS gene in patients from 14 Pendred families originating from seven countries and identified all mutations. The mutations include three single base deletions, one splice site mutation and 10 missense mutations. One missense mutation (L236P) was found in a homozygous state in two consanguineous families and in a heterozygous state in five additional non-consanguineous families. Another missense mutation (T416P) was found in a homozygous state in one family and in a heterozygous state in four families. Pendred patients in three non-consanguineous families were shown to be compound heterozygotes for L236P and T416P. In total, one or both of these mutations were found in nine of the 14 families analyzed. The identification of two frequent PDS mutations will facilitate the molecular diagnosis of Pendred syndrome. PMID:9618166

Van Hauwe, P; Everett, L A; Coucke, P; Scott, D A; Kraft, M L; Ris-Stalpers, C; Bolder, C; Otten, B; de Vijlder, J J; Dietrich, N L; Ramesh, A; Srisailapathy, S C; Parving, A; Cremers, C W; Willems, P J; Smith, R J; Green, E D; Van Camp, G

1998-07-01

317

Evidence for mutation showers  

PubMed Central

Mutants in the Big Blue transgenic mouse system show spontaneous clustered multiple mutations with unexpectedly high frequency, consistent with chronocoordinate events. We tested the prediction that the multiple mutations seen within the lacI mutation target sometimes occur in the context of chronocoordinate multiple mutations spanning multiple kilobases (mutation showers). Additional sequencing of mutants was performed in regions immediately flanking the lacI region (total of 10.7 kb). Nineteen additional mutations were found outside the lacI region (“ectomutations”) from 10 mutants containing two or more lacI mutations, whereas only one ectomutation was found in 130 mutants with a single mutation (P < 0.0001). The mutation showers had an average of approximately one mutation per 3 kb. Four mutants showed closely spaced double mutations in the new sequence, and analysis of the spacing between these mutations revealed significant clustering (P = 0.0098). To determine the extent of the mutation showers, regions (8.5 kb total) remote from the lacI region (?16–17 kb away) were sequenced. Only two additional ectomutations were found in these remote regions, consistent with mutation showers that generally do not extend more than ?30 kb. We conclude that mutation showers exist and that they constitute at least 0.2% and possibly 1% or more of mutational events observed in this system. The existence of mutation showers has implications for oncogenesis and evolution, raising the possibilities of “cancer in an instant” and “introns as sponges to reduce the deleterious impact of mutation showers.”

Wang, Jicheng; Gonzalez, Kelly D.; Scaringe, William A.; Tsai, Kimberly; Liu, Ning; Gu, Dongqing; Li, Wenyan; Hill, Kathleen A.; Sommer, Steve S.

2007-01-01

318

THAP1 Mutations and Dystonia Phenotypes: Genotype Phenotype Correlations  

PubMed Central

THAP1 mutations have been shown to be the cause of DYT6. A number of different mutation types and locations in the THAP1 gene have been associated with a range of severity and dystonia phenotypes, but, as yet, it has been difficult to identify clear genotype phenotype patterns. Here, we screened the THAP1 gene in a further series of dystonia cases and evaluated the mutation pathogenicity in this series as well as previously reported mutations to investigate possible phenotype-genotype correlations. THAP1 mutations have been identified throughout the coding region of the gene, with the greatest concentration of variants localized to the THAP1 domain. In the additional cases analyzed here, a further two mutations were found. No obvious, indisputable genotype-phenotype correlation emerged from these data. However, we managed to find a correlation between the pathogenicity of mutations, distribution, and age of onset of dystonia. THAP1 mutations are an important cause of dystonia, but, as yet, no clear genotype-phenotype correlations have been identified. Greater mutation numbers in different populations will be important and mutation-specific functional studies will be essential to identify the pathogenicity of the various THAP1 mutations. © 2012 Movement Disorder Society

Xiromerisiou, Georgia; Houlden, Henry; Scarmeas, Nikolaos; Stamelou, Maria; Kara, Eleanna; Hardy, John; Lees, Andrew J; Korlipara, Prasad; Limousin, Patricia; Paudel, Reema; Hadjigeorgiou, Georgios M; Bhatia, Kailash P

2012-01-01

319

Mutator phenotypes of yeast strains heterozygous for mutations in the MSH2 gene  

PubMed Central

Heterozygosity for germ-line mutations in the DNA mismatch repair gene MSH2 predisposes humans to cancer. Here we use a highly sensitive reporter to describe a spontaneous mutator phenotype in diploid yeast cells containing a deletion of only one MSH2 allele. We also identify five MSH2 missense mutations that have dominant mutator effects in heterozygous cells when expressed at normal levels from the natural MSH2 promoter. For example, a 230-fold mutator effect is observed in an MSH2/msh2 diploid strain in which Gly693, which is invariant in MutS homologs and involved in ATP hydrolysis, is changed to alanine. DNA binding data suggest that mismatch repair is suppressed by binding of a mutant Msh2–Msh6 heterodimer to a mismatch with subsequent inability to dissociate from the mismatch in the presence of ATP. A dominant mutator effect also is observed in yeast when Gly693 is changed to serine. An early onset colorectal tumor is heterozygous for the analogous Gly ? Ser mutation in hMSH2, and a second hMSH2 mutation was not found, suggesting that this missense mutation may predispose to cancer via a dominant mutator effect. The mutator effects of the deletion mutant and the Gly ? Ala missense mutant in yeast MSH2 are enhanced by heterozygosity for a missense mutation in DNA polymerase ? that reduces its proofreading activity but is not a mutator in the heterozygous state. The synergistic effects of heterozygosity for mutations in two different genes that act in series to correct replication errors may be relevant to cancer predisposition.

Drotschmann, Karin; Clark, Alan B.; Tran, Hiep T.; Resnick, Michael A.; Gordenin, Dmitry A.; Kunkel, Thomas A.

1999-01-01

320

DNA Sequence Fragment Containing C to A Mutation as a Convenient Mutation Standard for DHPLC Analysis.  

PubMed

Objective(s): Denaturing high performance liquid chromatography (DHPLC) is a high throughput approach for screening DNA sequence variations. To assess oven calibration, cartridge performance, buffer composition and stability, the WAVE Low and High Range Mutation Standards are employed to ensure reproducibility and accuracy of the chromatographic analysis. The purpose of this study was to provide a cost-effective homemade mutation standard for DHPLC analysis. Materials and Methods: DHPLC was performed to evaluate different elution temperatures of a 374 bp DNA fragment with C>A mutation at position of 59 to achieve a peak profile similar to the Low Mutation Standard. In order to verify the reproducibility of the homemade mutation standard using DHPLC, 15 different experiments were performed to compare the homemade mutation standard, the WAVE Low Range Mutation Standard with a positive DNA control sample. Results: We identified a comparable elution temperature and a peak profile with the WAVE Low Range Mutation Standard. Conclusion: This study confirmed the reproducibility of the peak profile of our homemade mutation standard compared to the Low Mutation Standard using DHPLC analysis. PMID:24106601

Dastsooz, Hassan; Vahedi, Nazanin; Fardaei, Majid

2013-08-01

321

Cancer-specific High-throughput Annotation of Somatic Mutations: computational prediction of driver missense mutations  

PubMed Central

Large-scale sequencing of cancer genomes has uncovered thousands of DNA alterations, but the functional relevance of the majority of these mutations to tumorigenesis is unknown. We have developed a computational method, called CHASM (Cancer-specific High-throughput Annotation of Somatic Mutations), to identify and prioritize those missense mutations most likely to generate functional changes that enhance tumor cell proliferation. The method has high sensitivity and specificity when discriminating between known driver missense mutations and randomly generated missense mutations (area under ROC curve > 0.91, area under Precision-Recall curve > 0.79). CHASM substantially outperformed previously described missense mutation function prediction methods at discriminating known oncogenic mutations in TP53 and the tyrosine kinase EGFR. We applied the method to 607 missense mutations found in a recent glioblastoma multiforme sequencing (GBM) study. Based on a model that assumed the GBM mutations are a mixture of drivers and passengers, we estimate that 8% of these mutations are drivers, causally contributing to tumorigenesis.

Carter, Hannah; Chen, Sining; Isik, Leyla; Tyekucheva, Svitlana; Velculescu, Victor E.; Kinzler, Kenneth W.; Vogelstein, Bert; Karchin, Rachel

2009-01-01

322

DNA Sequence Fragment Containing C to A Mutation as a Convenient Mutation Standard for DHPLC Analysis  

PubMed Central

Objective(s): Denaturing high performance liquid chromatography (DHPLC) is a high throughput approach for screening DNA sequence variations. To assess oven calibration, cartridge performance, buffer composition and stability, the WAVE Low and High Range Mutation Standards are employed to ensure reproducibility and accuracy of the chromatographic analysis. The purpose of this study was to provide a cost-effective homemade mutation standard for DHPLC analysis. Materials and Methods: DHPLC was performed to evaluate different elution temperatures of a 374 bp DNA fragment with C>A mutation at position of 59 to achieve a peak profile similar to the Low Mutation Standard. In order to verify the reproducibility of the homemade mutation standard using DHPLC, 15 different experiments were performed to compare the homemade mutation standard, the WAVE Low Range Mutation Standard with a positive DNA control sample. Results: We identified a comparable elution temperature and a peak profile with the WAVE Low Range Mutation Standard. Conclusion: This study confirmed the reproducibility of the peak profile of our homemade mutation standard compared to the Low Mutation Standard using DHPLC analysis.

Dastsooz, Hassan; Vahedi, Nazanin; Fardaei, Majid

2013-01-01

323

Mutation screening of the RYR1 gene in malignant hyperthermia: Detection of a novel Tyr to ser mutation in a pedigree with associated centrl cores  

Microsoft Academic Search

The ryanodine receptor gene (RYR1) has been shown to be mutated in a small number of malignant hyperthermia (MH) predigrees. Missense mutations in this gene have also been identified in two families with central core disease (CCD), a rare myopathy closely associated with MH. In an effort to identify other RYR1 mutations responsible for MH and CCD, we used a

K. A. Quane; K. E. Keating; J. M. S. Healy

1994-01-01

324

Desmin Mutations and Arrhythmogenic Right Ventricular Cardiomyopathy  

PubMed Central

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disease characterized by fibrofatty replacement of the myocardium and ventricular arrhythmias, associated with mutations in the desmosomal genes. Only a missense mutation in the DES gene coding for desmin, the intermediate filament protein expressed by cardiac and skeletal muscle cells, has been recently associated with ARVC. We screened 91 ARVC index cases (53 negative for mutations in desmosomal genes and an additional 38 carrying desmosomal gene mutations) for DES mutations. Two rare missense variants were identified. The heterozygous p.K241E substitution was detected in 1 patient affected with a severe form of ARVC who also carried the p.T816RfsX10 mutation in plakophilin-2 gene. This DES substitution, showing an allele frequency of <0.01 in the control population, is predicted to cause an intolerant amino acid change in a highly conserved protein domain. Thus, it can be considered a rare variant with a possible modifier effect on the phenotypic expression of the concomitant mutation. The previously known p.A213V substitution was identified in 1 patient with ARVC who was negative for mutations in the desmosomal genes. Because a greater prevalence of p.A213V has been reported in patients with heart dilation than in control subjects, the hypothesis that this rare variant could have an unfavorable effect on cardiac remodeling cannot be ruled out. In conclusion, our data help to establish that, in the absence of skeletal muscle involvement suggestive of a desminopathy, the probability of DES mutations in ARVC is very low. These findings have important implications in the mutation screening strategy for patients with ARVC.

Lorenzon, Alessandra; Beffagna, Giorgia; Bauce, Barbara; De Bortoli, Marzia; Li Mura, Ilena E.A.; Calore, Martina; Dazzo, Emanuela; Basso, Cristina; Nava, Andrea; Thiene, Gaetano; Rampazzo, Alessandra

2013-01-01

325

Mutation analysis of BRCA1 and BRCA2 genes in Iranian high risk breast cancer families  

Microsoft Academic Search

Purpose: Germline mutations in either BRCA1 or BRCA2 genes are responsible for the majority of hereditary breast and ovarian cancers. At present, over thousand distinct BRCA1 and BRCA2 mutations have been identified. Specific mutations are found to be common within particular populations, resulting from genetic founder effects. To investigate the contribution of germline mutations in these two genes to inherited

Andrea Pietschmann; Parvin Mehdipour; Morteza Atri; Wera Hofmann; S. Said Hosseini-Asl; Siegfried Scherneck; Stefan Mundlos; Hartmut Peters

2005-01-01

326

Automatic Extraction of Protein Point Mutations Using a Graph Bigram Association  

Microsoft Academic Search

Protein point mutations are an essential component of the evolutionary and experimental analysis of protein structure and function. While many manually curated databases attempt to index point mutations, most experimentally generated point mutations and the biological impacts of the changes are described in the peer-reviewed published literature. We describe an application, Mutation GraB (Graph Bigram), that identifies, extracts, and verifies

Lawrence C. Lee; Florence Horn; Fred E. Cohen

2007-01-01

327

PTPN11, RAS and FLT3 mutations in childhood acute lymphoblastic leukemia  

Microsoft Academic Search

PTPN11, the gene which encodes protein tyrosine phosphatase SHP-2, plays an important role in regulating intracellular signaling. Germline mutations in PTPN11 were first observed in Noonan syndrome, while somatic mutations were identified in hematological myeloid malignancies. Recently, PTPN11 mutations have been reported in children with acute lymphoblastic leukemia (ALL). In the present study, we investigated the prevalence of mutations in

Tomoko Yamamoto; Mariko Isomura; Yinyan Xu; Juan Liang; Hiroshi Yagasaki; Yoshiro Kamachi; Kazuko Kudo; Hitoshi Kiyoi; Tomoki Naoe; Seiji Kojma

2006-01-01

328

Rates of Spontaneous Mutation  

Microsoft Academic Search

Rates of spontaneous mutation per genome as measured in the laboratory are remarkably similar within broad groups of organisms but differ strikingly among groups. Mutation rates in RNA viruses, whose genomes contain ca. 10 4 bases, are roughly 1 per genome per replication for lytic viruses and roughly 0.1 per genome per replication for retroviruses and a retrotransposon. Mutation rates

John W. Drake; Brian Charlesworth; Deborah Charlesworth; James F. Crow

1998-01-01

329

Mutational process and microevolution  

Microsoft Academic Search

Long term observations of the gene pool of the same and geographically separated populations of Drosophila melanogaster forced us to return to the old idea of De Vries about the existence of mutation periods and fluctuations in the mutation rate with time. A 3- to 5-fold increase of the total mutation rate was estimated by the frequency of lethals, and

M. D. Golubovsky

1984-01-01

330

?-Tubulin mutations that cause severe neuropathies disrupt axonal transport.  

PubMed

Microtubules are fundamental to neuronal morphogenesis and function. Mutations in tubulin, the major constituent of microtubules, result in neuronal diseases. Here, we have analysed ?-tubulin mutations that cause neuronal diseases and we have identified mutations that strongly inhibit axonal transport of vesicles and mitochondria. These mutations are in the H12 helix of ?-tubulin and change the negative charge on the surface of the microtubule. This surface is the interface between microtubules and kinesin superfamily motor proteins (KIF). The binding of axonal transport KIFs to microtubules is dominant negatively disrupted by these mutations, which alters the localization of KIFs in neurons and inhibits axon elongation in vivo. In humans, these mutations induce broad neurological symptoms, such as loss of axons in the central nervous system and peripheral neuropathy. Thus, our data identified the critical region of ?-tubulin required for axonal transport and suggest a molecular mechanism for human neuronal diseases caused by tubulin mutations. PMID:23503589

Niwa, Shinsuke; Takahashi, Hironori; Hirokawa, Nobutaka

2013-03-15

331

Mutations in GNAL cause primary torsion dystonia  

PubMed Central

Dystonia is a movement disorder characterized by repetitive twisting muscle contractions and postures1,2. Its molecular pathophysiology is poorly understood, in part due to limited knowledge of the genetic basis of the disorder. Only three genes for primary torsion dystonia (PTD), TOR1A (DYT1)3, THAP1 (DYT6)4, and CIZ15 have been identified. Using exome sequencing in two PTD families we identified a novel causative gene, GNAL, with a nonsense p.S293X mutation resulting in premature stop codon in one family and a missense p.V137M mutation in the other. Screening of GNAL in 39 PTD families, revealed six additional novel mutations in this gene. Impaired function of several of the mutations was shown by bioluminescence resonance energy transfer (BRET) assays.

Fuchs, Tania; Saunders-Pullman, Rachel; Masuho, Ikuo; Luciano, Marta San; Raymond, Deborah; Factor, Stewart; Lang, Anthony E.; Liang, Tsao-Wei; Trosch, Richard M.; White, Sierra; Ainehsazan, Edmond; Herve, Denis; Sharma, Nutan; Ehrlich, Michelle E.; Martemyanov, Kirill A.; Bressman, Susan B.; Ozelius, Laurie J.

2012-01-01

332

FLT3 Mutations in Myeloproliferative Neoplasms: The Beaumont Experience.  

PubMed

FLT3 is one of the most frequently mutated genes in acute myeloid leukemia. Previous studies have reported FLT3 mutation in as many as 9.2% of myeloproliferative neoplasms (MPNs) and myelodysplastic/myeloproliferative neoplasms (MDS/MPNs), as well as in chronic myelogenous leukemia, that are negative for the JAK2 V617F gene mutation; no FLT3 mutation has been found in JAK2-positive MPNs, suggesting that the mutations are mutually exclusive. The goal of our study is to evaluate the mutational status of the FLT3 gene in patients with an MPN or MDS/MPN, in correlation with the JAK2 mutational status. Patient specimens were retrospectively identified on the basis of MPN or MDS/MPN diagnosis and JAK2 analysis from February 2006 to December 2011. FLT3 mutation analysis was performed on DNA extracted from 152 patients using polymerase chain reaction amplification and analysis of amplicons by gel electrophoresis for internal tandem duplication mutations and by restriction endonuclease digestion fragment analysis for the D835 point mutation. FLT3 mutation analysis was performed on 90 cases of JAK2-negative MPN or MDS/MPN and 62 cases of JAK2-positive MPN. One FLT3 internal tandem duplication mutation was identified in the JAK2-negative group (1.1%), and none were identified in the JAK2-positive group, confirming the absence of FLT3 mutations in JAK2-positive specimens. The FLT3-positive MPN patient was diagnosed with MPN, unclassifiable, and was later found to have myeloid sarcoma; thus, FLT3 mutation was not seen in the usual types of MPN in our series. Our result of 1.1% FLT3 mutations in JAK2-negative MPN and MDS/MPN cases is lower than the 9.2% previously reported. PMID:23846442

Williams, Lindsay; Kelley, Harlan H; Meng, Xiuling; Prada, Anne; Crisan, Domnita

2013-09-01

333

MITOCHONDRIAL DNA MUTATIONS IN HUMAN DISEASE  

PubMed Central

The human mitochondrial genome is extremely small compared with the nuclear genome, and mitochondrial genetics presents unique clinical and experimental challenges. Despite the diminutive size of the mitochondrial genome, mitochondrial DNA (mtDNA) mutations are an important cause of inherited disease. Recent years have witnessed considerable progress in understanding basic mitochondrial genetics and the relationship between inherited mutations and disease phenotypes, and in identifying acquired mtDNA mutations in both ageing and cancer. However, many challenges remain, including the prevention and treatment of these diseases. This review explores the advances that have been made and the areas in which future progress is likely.

Taylor, Robert W.; Turnbull, Doug M.

2006-01-01

334

Novel pathogenic mutations in the glucocerebrosidase locus  

PubMed Central

To determine the frequency of mutations responsible for Gaucher's disease, we systematically sequenced the GBA1 gene as part of a molecular characterization of 73 adult patients in the United Kingdom. Five hitherto unknown pathogenic variants were identified, one of which is a splice site change; the others are novel missense mutations. Given that GBA1 gene mutations are an important risk factor for the development of Parkinson's disease, we contend that a complete analysis and molecular characterization of both the known and novel GBA1 variants will be needed before the biochemical processes underlying this genetic association can be fully understood.

Duran, Raquel; McNeill, Alisdair; Mehta, Atul; Hughes, Derralyn; Cox, Timothy; Deegan, Patrick; Schapira, Anthony H.V.; Hardy, John

2012-01-01

335

Mining mutation chains in biological sequences  

Microsoft Academic Search

The increasing infectious disease outbreaks has led to a need for new research to better understand the disease's origins, epidemiological features and pathogenicity caused by fast-mutating, fast-spreading viruses. Traditional sequence anal- ysis methods do not take into account the spatio-temporal dynamics of rapidly evolving and spreading viral species. They are also focused on identifying single-point mutations. In this paper, we

Chang Sheng; Wynne Hsu; Mong-Li Lee; Joo Chuan Tong; See-Kiong Ng

2010-01-01

336

New KIT mutations in patients with piebaldism  

Microsoft Academic Search

Background: Piebaldism is an autosomal dominantly inherited disorder characterized by congenital leukoderma, typically on the forehead, abdomen, and knees. The leukoderma is usually stable throughout life. KIT mutations have been demonstrated in about 75% of patients with piebaldism. Objectives: To identify KIT mutations of the family with piebaldism and examine genotype-phenotype correlations in this disorder. Methods: PCR-direct-sequencing technique using genomic

Tomoko Murakami; Kazuyoshi Fukai; Naoki Oiso; Naoko Hosomi; Atsushi Kato; Cheryl Garganta; Angela Barnicoat; Francis Poppelaars; Robert Aquaron; Amy S Paller; Masamitsu Ishii

2004-01-01

337

Mutation update for the PORCN gene.  

PubMed

Mutations in the PORCN gene were first identified in Goltz-Gorlin syndrome patients in 2007. Since then, several reports have been published describing a large variety of genetic defects resulting in the Goltz-Gorlin syndrome, and mutations or deletions were also reported in angioma serpiginosum, the pentalogy of Cantrell and Limb-Body Wall Complex. Here we present a review of the published mutations in the PORCN gene to date and report on seven new mutations together with the corresponding clinical data. Based on the review we have created a Web-based locus-specific database that lists all identified variants and allows the inclusion of future reports. The database is based on the Leiden Open (source) Variation Database (LOVD) software, and is accessible online at http://www.lovd.nl/porcn. At present, the database contains 106 variants, representing 68 different mutations, scattered along the whole coding sequence of the PORCN gene, and 12 large gene rearrangements, which brings up to 80 the number of unique mutations identified in Goltz-Gorlin syndrome patients. PMID:21472892

Lombardi, Maria Paola; Bulk, Saskia; Celli, Jacopo; Lampe, Anne; Gabbett, Michael T; Ousager, Lillian Bomme; van der Smagt, Jasper J; Soller, Maria; Stattin, Eva-Lena; Mannens, Marcel A M M; Smigiel, Robert; Hennekam, Raoul C

2011-06-21

338

Toward unique identifiers  

Microsoft Academic Search

This paper discusses the creation and use of unique identifiers for intellectual property. General concepts applicable to unique identifiers are defined and discussed [identifier, digital object, dumb and intelligent identifiers, readability, affordance or computability, multiple identification, resolution, metadata, persistence, granularity, derivatives (e.g., versions, formats, manifestations, and copies), check digits, and intermediate objects]. Requirements for unique identifiers are reviewed. Capacity issues

NORMAN PASKIN

1999-01-01

339

A Highly Sensitive Genetic Protocol to Detect NF1 Mutations  

PubMed Central

Neurofibromatosis type 1 (NF1) is a hereditary disorder caused by mutations in the NF1 gene. Detecting mutation in NF1 is hindered by the gene's large size, the lack of mutation hotspots, the presence of pseudogenes, and the wide variety of possible lesions. We developed a method for detecting germline mutations by combining an original RNA-based cDNA-PCR mutation detection method and denaturing high-performance liquid chromatography (DHPLC) with multiplex ligation-dependent probe amplification (MLPA). The protocol was validated in a cohort of 56 blood samples from NF1 patients who fulfilled NIH diagnostic criteria, identifying the germline mutation in 53 cases (95% sensitivity). The efficiency and reliability of this approach facilitated detection of different types of mutations, including single-base substitutions, deletions or insertions of one to several nucleotides, microdeletions, and changes in intragenic copy number. Because mutational screening for minor lesions was performed using cDNA and the characterization of mutated alleles was performed at both the RNA and genomic DNA level, the analysis provided insight into the nature of the different mutations and their effect on NF1 mRNA splicing. After validation, we implemented the protocol as a routine test. Here we present the overall unbiased spectrum of NF1 mutations identified in 93 patients in a cohort of 105. The results indicate that this protocol is a powerful new tool for the molecular diagnosis of NF1.

Carmen Valero, Maria; Martin, Yolanda; Hernandez-Imaz, Elisabete; Marina Hernandez, Alba; Melean, German; Maria Valero, Ana; Javier Rodriguez-Alvarez, Francisco; Telleria, Dolores; Hernandez-Chico, Concepcion

2011-01-01

340

RFLP analysis for APP 717 mutations associated with Alzheimer's disease.  

PubMed Central

Familial Alzheimer's disease (FAD) has been shown to be associated with three distinct point mutations within the same codon of the amyloid precursor protein (APP) gene. The mutation identified in the Indiana kindred is a G-->T transversion at the first position of the codon for amino acid 717, resulting in a substitution of phenylalanine for valine in the APP protein. Screening of persons at risk for the APP Phe-717 mutation using a variation of the polymerase chain reaction identified nine positives among 34 tested. In addition, DNA from 145 FAD subjects were tested for the three known APP 717 mutations. Images

Zeldenrust, S R; Murrell, J; Farlow, M; Ghetti, B; Roses, A D; Benson, M D

1993-01-01

341

Oncogenic mutations in GNAQ occur early in uveal melanoma  

PubMed Central

Purpose Early/initiating oncogenic mutations have been identified for many cancers, but such mutations remain unidentified in uveal melanoma (UM). An extensive search for such mutations was undertaken, focusing on the RAF/MEK/ERK pathway, which is often the target of initiating mutations in other types of cancer. Methods DNA samples from primary UMs were analyzed for mutations in 24 potential oncogenes that affect the RAF/MEK/ERK pathway. For GNAQ, a stimulatory ?q G-protein subunit which was recently found to be mutated in uveal melanomas, re-sequencing was expanded to include 67 primary UMs and 22 peripheral blood samples. GNAQ status was analyzed for association with clinical, pathologic, chromosomal, immunohistochemical and transcriptional features. Results Activating mutations at codon 209 were identified in GNAQ in 33/67 (49%) primary UMs, including 2/9 (22%) iris melanomas and 31/58 (54%) posterior UMs. No mutations were found in the other 23 potential oncogenes. GNAQ mutations were not found in normal blood DNA samples. Consistent with GNAQ mutation being an early or initiating event, this mutation was not associated with any clinical, pathologic or molecular features associated with late tumor progression. Conclusions GNAQ mutations occur in about half of UMs, representing the most common known oncogenic mutation in this cancer. The presence of this mutation in tumors at all stages of malignant progression suggests that it is an early event in UM. Mutations in this G-protein provide new insights into UM pathogenesis and could lead to new therapeutic possibilities.

Onken, Michael D.; Worley, Lori A.; Long, Meghan D.; Duan, Shenghui; Council, M. Laurin; Bowcock, Anne M.; Harbour, J. William

2008-01-01

342

Spectrum of mutations in the Fanconi anaemia group G gene, FANCG\\/XRCC9  

Microsoft Academic Search

FANCG was the third Faconi anaemia gene identified and proved to be identical to the previously cloned XRCC9 gene. We present the pathogenic mutations and sequence variants we have so far identified in a panel of FA-G patients. Mutation screening was performed by PCR, single strand conformational polymorphism analysis and protein truncation tests. Altogether 18 mutations have been determined in

Ilja Demuth; Marcin Wlodarski; Alex J Tipping; Neil V Morgan; Johan P de Winter; Michaela Thiel; Sonja Gräsl; Detlev Schindler; Alan D D'Andrea; Cigdem Altay; Hülya Kayserili; Adriana Zatterale; Jürgen Kunze; Wolfram Ebell; Christopher G Mathew; Hans Joenje; Karl Sperling; Martin Digweed

2000-01-01

343

Identification of recurring tumor-specific somatic mutations in acute myeloid leukemia by transcriptome sequencing  

Microsoft Academic Search

Genetic lesions are crucial for cancer initiation. Recently, whole genome sequencing, using next generation technology, was used as a systematic approach to identify mutations in genomes of various types of tumors including melanoma, lung and breast cancer, as well as acute myeloid leukemia (AML). Here, we identify tumor-specific somatic mutations by sequencing transcriptionally active genes. Mutations were detected by comparing

P A Greif; S H Eck; N P Konstandin; A Benet-Pagès; B Ksienzyk; A Dufour; A T Vetter; H D Popp; B Lorenz-Depiereux; T Meitinger; S K Bohlander; T M Strom

2011-01-01

344

Hepatoblastoma and APC gene mutation in familial adenomatous polyposis.  

PubMed Central

BACKGROUND: Hepatoblastoma is a rare, rapidly progressive, usually fatal childhood malignancy, which if confined to the liver can be cured by radical surgical resection. An association between hepatoblastoma and familial adenomatous polyposis (FAP), which is due to germline mutation of the APC (adenomatous polyposis coli) gene, has been confirmed, but correlation with site of APC mutation has not been studied. AIM: To analyse the APC mutational spectrum in FAP families with hepatoblastoma as a possible basis to select kindreds for surveillance. PATIENTS: Eight patients with hepatoblastoma in seven FAP kindreds were compared with 97 families with identified APC gene mutation in a large Registry. METHODS: APC gene mutation was evaluated by RNase protection assay or in vitro synthesis protein assay. The chi 2 test and correlation were used for data analysis. RESULTS: APC gene mutation was identified in all seven FAP kindreds in which an at risk member developed hepatoblastoma. A male predominance was noted (six of eight), similar to literature cases (18 of 25, p < 0.01. Mutations were restricted to codons 141 to 1230, but no significant difference in site of mutation between pedigrees with and without hepatoblastoma was identified. CONCLUSIONS: Hepatoblastoma occurs primarily in boys in FAP kindreds and is associated with germline APC mutation in the 5' end of the gene. However, the site of APC mutation cannot be used to predict occurrence of this extracolonic cancer in FAP pedigrees.

Giardiello, F M; Petersen, G M; Brensinger, J D; Luce, M C; Cayouette, M C; Bacon, J; Booker, S V; Hamilton, S R

1996-01-01

345

Mutations in GNAL cause primary torsion dystonia.  

PubMed

Dystonia is a movement disorder characterized by repetitive twisting muscle contractions and postures. Its molecular pathophysiology is poorly understood, in part owing to limited knowledge of the genetic basis of the disorder. Only three genes for primary torsion dystonia (PTD), TOR1A (DYT1), THAP1 (DYT6) and CIZ1 (ref. 5), have been identified. Using exome sequencing in two families with PTD, we identified a new causative gene, GNAL, with a nonsense mutation encoding p.Ser293* resulting in a premature stop codon in one family and a missense mutation encoding p.Val137Met in the other. Screening of GNAL in 39 families with PTD identified 6 additional new mutations in this gene. Impaired function of several of the mutants was shown by bioluminescence resonance energy transfer (BRET) assays. PMID:23222958

Fuchs, Tania; Saunders-Pullman, Rachel; Masuho, Ikuo; Luciano, Marta San; Raymond, Deborah; Factor, Stewart; Lang, Anthony E; Liang, Tsao-Wei; Trosch, Richard M; White, Sierra; Ainehsazan, Edmond; Hervé, Denis; Sharma, Nutan; Ehrlich, Michelle E; Martemyanov, Kirill A; Bressman, Susan B; Ozelius, Laurie J

2012-12-09

346

Ankyrin gene mutations in japanese patients with hereditary spherocytosis.  

PubMed

We studied mutations of the ankyrin-1 (ANK-1) gene of genomic DNA from Japanese patients with hereditary spherocytosis (HS). Forty-nine patients from 46 unrelated families were included in this study. Of these patients, 19 cases from 16 unrelated families had HS of autosomal-dominant inheritance, and 30 patients had non-autosomal-dominant HS. Fifteen mutations of the ANK-1 gene pathognomonic for HS were identified: 4 nonsense mutations, 7 frameshift mutations, and 4 abnormal splicing mutations. These 15 mutations have not been previously reported. The frameshift mutations were found from exon 1 to exon 26, corresponding particularly to the band 3-binding domain of ankyrin. The nonsense mutations, on the contrary, were present mostly at the 3'-terminal side, especially in the spectrin-binding domain and the regulatory domain. The patients with ankyrin gene mutations tended to be more anemic with a higher level of reticulocytosis than those without these mutations. Fifteen silent mutations of the ANK-1 gene, most of which have previously been detected in HS patients in Western populations, were also found. The allele frequency of these silent mutations in the HS patients was nearly identical to that in normal subjects. There was no difference between the Japanese and Western populations in the allele frequency of these gene polymorphisms in healthy subjects or HS patients. PMID:11372755

Nakanishi, H; Kanzaki, A; Yawata, A; Yamada, O; Yawata, Y

2001-01-01

347

Epistatic and Synergistic Interactions Between Circadian Clock Mutations in Neurospora crassa  

Microsoft Academic Search

We identified a series of epistatic and synergistic interactions among the circadian clock mutations of Neurospora crassa that indicate possible physical interactions among the various clock components encoded by these genes. The period-6 (prd-6) mutation, a short-period temperature-sensitive clock mutation, is epistatic to both the prd-2 and prd-3 mutations. The prd-2 and prd-3 long-period mutations show a synergistic interaction in

Louis W. Morgan; Jerry F. Feldman

348

Prognosis Is Correlated with p53 Mutation Type for Soft Tissue Sarcoma Patients1  

Microsoft Academic Search

We investigatedthe prognosticvalue ofpS3 mutationtype for 145 soft tissue sarcoma patients. In a PCR-SSCP-sequencing analysis, 15 mute tions were identified: 10 nonframeshift (non-fs) and 5 frameshift (fs) mutations. Patients possessing non-fs mutations had a significantly poorer prognosisthan patients withoutp53 mutations(P 0.014), accordingto Cox's multivariateanalysis. In contrast,the survivalof five patients with fs mutations was not affected by their mutation type. Furthermore,

Helge Taubert; Axel Meye

1996-01-01

349

Rare nonconservative LRP6 mutations are associated with metabolic syndrome.  

PubMed

A rare mutation in LRP6 has been shown to underlie autosomal dominant coronary artery disease (CAD) and metabolic syndrome in an Iranian kindred. The prevalence and spectrum of LRP6 mutations in the disease population of the United States is not known. Two hundred white Americans with early onset familial CAD and metabolic syndrome and 2,000 healthy Northern European controls were screened for nonconservative mutations in LRP6. Three novel mutations were identified, which cosegregated with the metabolic traits in the kindreds of the affected subjects and none in the controls. All three mutations reside in the second propeller domain, which plays a critical role in ligand binding. Two of the mutations substituted highly conserved arginines in the second YWTD domain and the third substituted a conserved glycosylation site. The functional characterization of one of the variants showed that it impairs Wnt signaling and acts as a loss of function mutation. PMID:23703864

Singh, Rajvir; Smith, Emily; Fathzadeh, Mohsen; Liu, Wenzhong; Go, Gwang-Woong; Subrahmanyan, Lakshman; Faramarzi, Saeed; McKenna, William; Mani, Arya

2013-06-18

350

Rates of spontaneous mutations  

Microsoft Academic Search

ABSTRACT Rates of spontaneous,mutation,per genome,as measured,in the laboratory are remarkably,similar within broad groups of organisms but differ strikingly among groups. Mutation rates in RNA viruses, whose genomes contain ca. 10, bases or base pairs. Mutation,rates in higher,eukaryotes,are roughly,0.1?100 per genome,per,sexual generation,but are currently indistinguishable from,1\\/300 per cell division per effective genome,(which excludes,the fraction of the genome,in which,most mutations,are neutral). It

J. W Drake; B Charlesworth; D Charlesworth; J. F Crow

1998-01-01

351

Wilson Disease Mutation Pattern with Genotype-Phenotype Correlations from Western India: Confirmation of p.C271* as a Common Indian Mutation and Identification of 14 Novel Mutations.  

PubMed

Wilson disease (WD) is an autosomal recessive disorder resulting from mutations in the ATP7B gene, with over 600 mutations described. Identification of mutations has made genetic diagnosis of WD feasible in many countries. The heterogeneity of ATP7B mutants is, however, yet to be identified in the Indian population. We analyzed the mutational pattern of WD in a large region of Western India. We studied patients (n = 52) for ATP7B gene mutations in a cohort of families with WD and also in first-degree relatives (n = 126). All 21 exon-intron boundaries of the WD gene were amplified and directly sequenced. We identified 36 different disease-causing mutations (31 exonic and five intronic splice site variants). Fourteen novel mutations were identified. Exons 2, 8, 13, 14, and 18 accounted for the majority of mutations (86.4%). A previously recognized mutation, p.C271*, and the novel mutation p.E122fs, were the most common mutations with allelic frequencies of 20.2% and 10.6%, respectively. Frequent homozygous mutations (58.9%) and disease severity assessments allowed analysis of genotype-phenotype correlations. Our study significantly adds to the emerging data from other parts of India suggesting that p.C271* may be the most frequent mutation across India, and may harbor a moderate to severely disabling phenotype with limited variability. PMID:23551039

Aggarwal, Annu; Chandhok, Gursimran; Todorov, Theodor; Parekh, Saloni; Tilve, Sharada; Zibert, Andree; Bhatt, Mohit; Schmidt, Hartmut H-J

2013-04-01

352

Rare mutations in non-small-cell lung cancer.  

PubMed

In the last decade, new insights in molecular biology have changed the therapeutic landscape of non-small-cell lung cancer. Since 2004, when activating mutations of the EGFR were firstly identified, several genetic aberrations have been discovered, mainly in adenocarcinoma. EGFR mutations are a relatively frequent event in non-small-cell lung cancer, generally consisting of exon 19 deletion or exon 21 substitution. In adenocarcinoma, additional rare mutations are detectable in the EGFR gene, as well as in other genes, including ALK, ROS1, RET, HER2 and BRAF. Recent studies in squamous cell carcinoma identified TP53 as the most frequent mutation, followed by additional more rare mutations, including PI3KCA, PTEN, DDR2 and FGFR. The aim of the present review is to analyze the potential prognostic and predictive role of rare mutations. PMID:23647298

D'Arcangelo, Manolo; D'Incecco, Armida; Cappuzzo, Federico

2013-05-01

353

Emerging patterns of somatic mutations in cancer.  

PubMed

Recent advances in technological tools for massively parallel, high-throughput sequencing of DNA have enabled the comprehensive characterization of somatic mutations in a large number of tumour samples. In this Review, we describe recent cancer genomic studies that have assembled emerging views of the landscapes of somatic mutations through deep-sequencing analyses of the coding exomes and whole genomes in various cancer types. We discuss the comparative genomics of different cancers, including mutation rates and spectra, as well as the roles of environmental insults that influence these processes. We highlight the developing statistical approaches that are used to identify significantly mutated genes, and discuss the emerging biological and clinical insights from such analyses, as well as the future challenges of translating these genomic data into clinical impacts. PMID:24022702

Watson, Ian R; Takahashi, Koichi; Futreal, P Andrew; Chin, Lynda

2013-09-11

354

Mutation analysis of Australasian Gaucher disease patients  

SciTech Connect

We have previously reported phenotype and genotype analyses in 28 Australasian Gaucher patients who were screened for several of the common Gaucher mutations: N370S, L444P, 84GG, and R463C. Horowitz and Zimran have reported that the complex alleles recNciI and recTL, which contain several point mutations including L444P, are relatively common, especially in non-Jewish Gaucher patients. Zimran and Horowitz have also stated that these recombinant alleles could easily be missed by laboratories testing only for the common Gaucher point mutations. Failure to correctly identify these mutations would influence any attempt to correlate genotype with phenotype. We have therefore retested our Gaucher patients for recNciI (L444P, A456P, and V46OV) and recTL (D409H, L444P, A456P, and V46OV) by PCR amplification, followed by hybridization with allele-specific oligonucleotides. 4 refs.

Nelson, P.V.; Carey, W.F.; Morris, C.P.; Lewis, B.D. [Women`s and Children`s Hospital, North Adelaide, South Australia (Australia)

1995-09-25

355

Cerebral Cavernous Malformations: Somatic Mutations in Vascular Endothelial Cells  

PubMed Central

OBJECTIVE Germline mutations in three genes have been found in familial cases of cerebral cavernous malformations (CCM). We previously discovered somatic and germline truncating mutations in the KRIT1 gene supporting the “two-hit” mechanism of CCM lesion formation in a single lesion. The purpose of this study was to screen for somatic, nonheritable, mutations in three more lesions from different patients and identify the cell type(s) in which somatic mutations occur. METHODS Somatic mutations were sought in DNA from three surgically excised, fresh-frozen CCM lesions by cloning and screening PCR products generated from KRIT1 or PDCD10 coding regions. Laser capture microdissection (LCM) was used to isolated endothelial and nonendothelial cells in order to determine if somatic mutations were found in endothelial cells. RESULTS A CCM lesion harbored somatic and germline KRIT1 mutations on different chromosomes and are therefore biallelic. Both mutations are predicted to truncate the protein. The KRIT1 somatic mutations (novel c.1800delG mutation and previously identified 34 nucleotide deletion) in CCMs from two different patients were only found in the vascular endothelial cells lining caverns. No obvious somatic mutations were identified in the two other lesions; however, the results were inconclusive possibly due to the technical limitations or the fact that these specimens had a small proportion of vascular endothelial cells lining pristine caverns. CONCLUSION The “two-hit” mechanism occurs in vascular endothelial cells lining CCM caverns from two patients with somatic and Hispanic-American KRIT1 germline mutations. Methods for somatic mutation detection should focus on vascular endothelial cells lining pristine caverns.

Gault, Judith; Awad, Issam A.; Recksiek, Peter; Shenkar, Robert; Breeze, Robert; Handler, Michael; Kleinschmidt-DeMasters, Bette Kay

2009-01-01

356

Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders  

PubMed Central

Abstract Background Mitochondrial DNA (mtDNA) diseases are rare disorders whose prevalence is estimated around 1 in 5000. Patients are usually tested only for deletions and for common mutations of mtDNA which account for 5–40% of cases, depending on the study. However, the prevalence of rare mtDNA mutations is not known. Methods We analysed the whole mtDNA in a cohort of 743 patients suspected of manifesting a mitochondrial disease, after excluding deletions and common mutations. Both heteroplasmic and homoplasmic variants were identified using two complementary strategies (Surveyor and MitoChip). Multiple correspondence analyses followed by hierarchical ascendant cluster process were used to explore relationships between clinical spectrum, age at onset and localisation of mutations. Results 7.4% of deleterious mutations and 22.4% of novel putative mutations were identified. Pathogenic heteroplasmic mutations were more frequent than homoplasmic mutations (4.6% vs 2.8%). Patients carrying deleterious mutations showed symptoms before 16?years of age in 67% of cases. Early onset disease (<1?year) was significantly associated with mutations in protein coding genes (mainly in complex I) while late onset disorders (>16?years) were associated with mutations in tRNA genes. MTND5 and MTND6 genes were identified as ‘hotspots’ of mutations, with Leigh syndrome accounting for the large majority of associated phenotypes. Conclusions Rare mitochondrial DNA mutations probably account for more than 7.4% of patients with respiratory chain deficiency. This study shows that a comprehensive analysis of mtDNA is essential, and should include young children, for an accurate diagnosis that is now accessible with the development of next generation sequencing technology.

Bannwarth, Sylvie; Procaccio, Vincent; Lebre, Anne Sophie; Jardel, Claude; Chaussenot, Annabelle; Hoarau, Claire; Maoulida, Hassani; Charrier, Nathanael; Gai, Xiaowu; Xie, Hongbo M; Ferre, Marc; Fragaki, Konstantina; Hardy, Gaelle; Mousson de Camaret, Benedicte; Marlin, Sandrine; Dhaenens, Claire Marie; Slama, Abdelhamid; Rocher, Christophe; Paul Bonnefont, Jean; Rotig, Agnes; Aoutil, Nadia; Gilleron, Mylene; Desquiret-Dumas, Valerie; Reynier, Pascal; Ceresuela, Jennifer; Jonard, Laurence; Devos, Aurore; Espil-Taris, Caroline; Martinez, Delphine; Gaignard, Pauline; Le Quan Sang, Kim-Hanh; Amati-Bonneau, Patrizia; Falk, Marni J; Florentz, Catherine; Chabrol, Brigitte; Durand-Zaleski, Isabelle; Paquis-Flucklinger, Veronique

2013-01-01

357

Adaptive mutation: implications for evolution  

Microsoft Academic Search

Summary Adaptive mutation is defined as a process that, during nonlethal selections, produces mutations that relieve the selective pressure whether or not other, nonselected mutations are also produced. Examples of adaptive mutation or related phenomena have been reported in bacteria and yeast but not yet outside of microorganisms. A decade of research on adaptive mutation has revealed mechanisms that may

Patricia L. Foster

2000-01-01

358

Mutation 2000: Uniting the Orthogonal  

Microsoft Academic Search

Mutation testing is a powerful, but computationally expensive,technique for unit testing software. This expensehas prevented mutation from becoming widelyused in practical situations, but recent engineering advanceshave given us techniques and algorithms for signicantly reducing the cost of mutation testing. Thesetechniques include a new algorithmic execution techniquecalled schema-based mutation, an approximationtechnique called weak mutation, a reduction techniquecalled selective...

A. Jefferson Offutt; Roland H. Untch

2000-01-01

359

Human somatic mutation assays as biomarkers of carcinogenesis  

SciTech Connect

This paper describes four assays that detect somatic gene mutations in humans: the hypoxanthine-guanine phosphoribosyl transferase assay, the glycophorin A assay, the HLA-A assay, and the sickle cell hemoglobin assay. Somatic gene mutations can be considered a biomarker of carcinogenesis, and assays for somatic mutation may assist epidemiologists in studies that attempt to identify factors associated with increased risks of cancer. Practical aspects of the use of these assays are discussed.

Compton, P.J.E.; Smith, M.T. (Univ. of California, Berkeley (United States)); Hooper, K. (California Dept. of Health Services, Berkeley (United States))

1991-08-01

360

The spectrum of Familial Mediterranean Fever (FMF) mutations  

Microsoft Academic Search

Familial Mediterranean Fever (FMF) is the prototype of a group of inherited inflammatory disorders. The gene (MEFV) responsible for this disease, comprises 10 exons and 781 codons. Twenty-nine mutations, most located in the last exon, have been identified so far. It is unclear whether all are true disease-causing mutations. Five founder mutations, V726A, M694V, M694I, M680I and E148Q account for

Isabelle Touitou

2001-01-01

361

KIT Gene Mutations and Copy Number in Melanoma Subtypes  

Microsoft Academic Search

Purpose:We recently identified a KIT exon11mutation in an anorectal melanoma of ap atient who had an excellent response to treatment with imatinib.To determine the frequency of KIT mutations across melanoma subtypes, we surveyed a large series of tumors. Experimental Design: One hundred eighty-nine melanomas were screened for mutations in KIT exons 11, 13, and 17. KIT copy number was assessed

Carol Beadling; F. Stephen Hodi; Claudia Le; Andrea Warrick; Janice Patterson; Ajia Town; Amy Harlow; Frank Cruz; Sharl Azar; Brian P. Rubin; Susan Muller; Rob West; Michael C. Heinrich; Christopher L. Corless

2008-01-01

362

Mutations of the HFE gene among Turkish hereditary hemochromatosis patients  

Microsoft Academic Search

Since the discovery of the HFE gene, C282Y and H63D mutations have been reported as significantly correlated with clinically manifested hereditary hemochromatosis (HH). As the other genes involved in iron metabolism have been described, non-HFE cases of HH have been identified. Since in the general Turkish population, the C282Y mutation is not found and the H63D mutation is of high

Halis Simsek; Yasemin H. Balaban; Engin Yilmaz; Hale Sumer; Yahya Buyukasik; Cem Cengiz; Osman Ozcebe; Gulsen Hascelik; Gonca Tatar

2005-01-01

363

PALB2 mutations in familial breast and pancreatic cancer  

Microsoft Academic Search

PALB2 (Partner And Localizer of BRCA2) binds to and co-localizes with BRCA2 in DNA repair. Germline mutations in PALB2 have been identified in approximately 1–2% of familial breast cancer and 3–4% of familial pancreatic cancer cases. The goal\\u000a of this study was to evaluate the prevalence of PALB2 mutations in women with breast cancer without BRCA1\\/2 mutations who also had

Erin W. Hofstatter; Susan M. Domchek; Alexander Miron; Judy Garber; Molin Wang; Kathryn Componeschi; Leigh Boghossian; Penelope L. Miron; Katherine L. Nathanson; Nadine Tung

2011-01-01

364

Renal Aplasia in Humans Is Associated with RET Mutations  

PubMed Central

In animal models, kidney formation is known to be controlled by the proteins RET, GDNF, and GFRA1; however, no human studies to date have shown an association between abnormal kidney development and mutation of these genes. We hypothesized that stillborn fetuses with congenital renal agenesis or severe dysplasia would possess mutations in RET, GDNF, or GFRA1. We assayed for mutations in these genes in 33 stillborn fetuses that had bilateral or unilateral renal agenesis (29 subjects) or severe congenital renal dysplasia (4 subjects). Mutations in RET were found in 7 of 19 fetuses with bilateral renal agenesis (37%) and 2 of 10 fetuses (20%) with unilateral agenesis. In two fetuses, there were two different RET mutations found, and a total of ten different sequence variations were identified. We also investigated whether these mutations affected RET activation; in each case, RET phosphorylation was either absent or constitutively activated. A GNDF mutation was identified in only one fetus with unilateral agenesis; this subject also had two RET mutations. No GFRA1 mutations were seen in any fetuses. These data suggest that in humans, mutations in RET and GDNF may contribute significantly to abnormal kidney development.

Skinner, Michael A.; Safford, Shawn D.; Reeves, Justin G.; Jackson, Margaret E.; Freemerman, Alex J.

2008-01-01

365

Mutating database queries  

Microsoft Academic Search

A set of mutation operators for SQL queries that retrieve information from a database is developed and tested against a set of queries drawn from the NIST SQL Conformance Test Suite. The mutation operators cover a wide spectrum of SQL features, including the handling of null values. Additional experiments are performed to explore whether the cost of executin g mutants

Javier Tuya; María José Suárez Cabal; Claudio De La Riva

2007-01-01

366

Mutational landscape and significance across 12 major cancer types.  

PubMed

The Cancer Genome Atlas (TCGA) has used the latest sequencing and analysis methods to identify somatic variants across thousands of tumours. Here we present data and analytical results for point mutations and small insertions/deletions from 3,281 tumours across 12 tumour types as part of the TCGA Pan-Cancer effort. We illustrate the distributions of mutation frequencies, types and contexts across tumour types, and establish their links to tissues of origin, environmental/carcinogen influences, and DNA repair defects. Using the integrated data sets, we identified 127 significantly mutated genes from well-known (for example, mitogen-activated protein kinase, phosphatidylinositol-3-OH kinase, Wnt/?-catenin and receptor tyrosine kinase signalling pathways, and cell cycle control) and emerging (for example, histone, histone modification, splicing, metabolism and proteolysis) cellular processes in cancer. The average number of mutations in these significantly mutated genes varies across tumour types; most tumours have two to six, indicating that the number of driver mutations required during oncogenesis is relatively small. Mutations in transcriptional factors/regulators show tissue specificity, whereas histone modifiers are often mutated across several cancer types. Clinical association analysis identifies genes having a significant effect on survival, and investigations of mutations with respect to clonal/subclonal architecture delineate their temporal orders during tumorigenesis. Taken together, these results lay the groundwork for developing new diagnostics and individualizing cancer treatment. PMID:24132290

Kandoth, Cyriac; McLellan, Michael D; Vandin, Fabio; Ye, Kai; Niu, Beifang; Lu, Charles; Xie, Mingchao; Zhang, Qunyuan; McMichael, Joshua F; Wyczalkowski, Matthew A; Leiserson, Mark D M; Miller, Christopher A; Welch, John S; Walter, Matthew J; Wendl, Michael C; Ley, Timothy J; Wilson, Richard K; Raphael, Benjamin J; Ding, Li

2013-10-17