Search Results - "Stenson, Peter D."

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies by Stenson, Peter D., Mort, Matthew, Ball, Edward V., Evans, Katy, Hayden, Matthew, Heywood, Sally, Hussain, Michelle, Phillips, Andrew D., Cooper, David N.

“…The Human Gene Mutation Database (HGMD ® ) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are…”
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The Human Gene Mutation Database (HGMD®): optimizing its use in a clinical diagnostic or research setting by Stenson, Peter D., Mort, Matthew, Ball, Edward V., Chapman, Molly, Evans, Katy, Azevedo, Luisa, Hayden, Matthew, Heywood, Sally, Millar, David S., Phillips, Andrew D., Cooper, David N.

“…The Human Gene Mutation Database (HGMD ® ) constitutes a comprehensive collection of published germline mutations in nuclear genes that are thought to…”
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M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity by Jagadeesh, Karthik A, Wenger, Aaron M, Berger, Mark J, Guturu, Harendra, Stenson, Peter D, Cooper, David N, Bernstein, Jonathan A, Bejerano, Gill

“…Gill Bejerano and colleagues present M-CAP, a classifier that estimates variant pathogenicity in clinical exome data sets. They show that M-CAP outperforms…”
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The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine by Stenson, Peter D., Mort, Matthew, Ball, Edward V., Shaw, Katy, Phillips, Andrew D., Cooper, David N.

“…The Human Gene Mutation Database (HGMD ® ) is a comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human…”
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Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models by Shihab, Hashem A., Gough, Julian, Cooper, David N., Stenson, Peter D., Barker, Gary L. A., Edwards, Keith J., Day, Ian N. M., Gaunt, Tom R.

“…ABSTRACT The rate at which nonsynonymous single nucleotide polymorphisms (nsSNPs) are being identified in the human genome is increasing dramatically owing to…”
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The mutation significance cutoff: gene-level thresholds for variant predictions by Itan, Yuval, Shang, Lei, Boisson, Bertrand, Ciancanelli, Michael J, Markle, Janet G, Martinez-Barricarte, Ruben, Scott, Eric, Shah, Ishaan, Stenson, Peter D, Gleeson, Joseph, Cooper, David N, Quintana-Murci, Lluis, Zhang, Shen-Ying, Abel, Laurent, Casanova, Jean-Laurent

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The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity by Grimm, Dominik G., Azencott, Chloé-Agathe, Aicheler, Fabian, Gieraths, Udo, MacArthur, Daniel G., Samocha, Kaitlin E., Cooper, David N., Stenson, Peter D., Daly, Mark J., Smoller, Jordan W., Duncan, Laramie E., Borgwardt, Karsten M.

“…ABSTRACT Prioritizing missense variants for further experimental investigation is a key challenge in current sequencing studies for exploring complex and…”
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Analysis of missense variants in the human genome reveals widespread gene-specific clustering and improves prediction of pathogenicity by Quinodoz, Mathieu, Peter, Virginie G., Cisarova, Katarina, Royer-Bertrand, Beryl, Stenson, Peter D., Cooper, David N., Unger, Sheila, Superti-Furga, Andrea, Rivolta, Carlo

“…We used a machine learning approach to analyze the within-gene distribution of missense variants observed in hereditary conditions and cancer. When applied to…”
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Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing by Xue, Yali, Chen, Yuan, Ayub, Qasim, Huang, Ni, Ball, Edward V., Mort, Matthew, Phillips, Andrew D., Shaw, Katy, Stenson, Peter D., Cooper, David N., Tyler-Smith, Chris

“…We have assessed the numbers of potentially deleterious variants in the genomes of apparently healthy humans by using (1) low-coverage whole-genome sequence…”
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The genetic structure of the Turkish population reveals high levels of variation and admixture by Kars, M. Ece, Başak, A. Nazlı, Onat, O. Emre, Bilguvar, Kaya, Choi, Jungmin, Itan, Yuval, Çağlar, Caner, Palvadeau, Robin, Casanova, Jean-Laurent, Cooper, David N., Stenson, Peter D., Yavuz, Alper, Buluş, Hakan, Günel, Murat, Friedman, Jeffrey M., Özçelik, Tayfun

“…The construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we…”
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The human gene damage index as a gene-level approach to prioritizing exome variants by Itan, Yuval, Shang, Lei, Boisson, Bertrand, Patin, Etienne, Bolze, Alexandre, Moncada-Vélez, Marcela, Scott, Eric, Ciancanelli, Michael J., Lafaille, Fabien G., Markle, Janet G., Martinez-Barricarte, Ruben, de Jong, Sarah Jill, Kong, Xiao-Fei, Nitschke, Patrick, Belkadi, Aziz, Bustamante, Jacinta, Puel, Anne, Boisson-Dupuis, Stéphanie, Stenson, Peter D., Gleeson, Joseph G., Cooper, David N., Quintana-Murci, Lluis, Claverie, Jean-Michel, Zhang, Shen-Ying, Abel, Laurent, Casanova, Jean-Laurent

“…The protein-coding exome of a patient with a monogenic disease contains about 20,000 variants, only one or two of which are disease causing. We found that 58%…”
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AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature by Birgmeier, Johannes, Haeussler, Maximilian, Deisseroth, Cole A, Steinberg, Ethan H, Jagadeesh, Karthik A, Ratner, Alexander J, Guturu, Harendra, Wenger, Aaron M, Diekhans, Mark E, Stenson, Peter D, Cooper, David N, Ré, Christopher, Beggs, Alan H, Bernstein, Jonathan A, Bejerano, Gill

“…The diagnosis of Mendelian disorders requires labor-intensive literature research. Trained clinicians can spend hours looking for the right publication(s)…”
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CRAVAT: cancer-related analysis of variants toolkit by Douville, Christopher, Carter, Hannah, Kim, Rick, Niknafs, Noushin, Diekhans, Mark, Stenson, Peter D, Cooper, David N, Ryan, Michael, Karchin, Rachel

“…Advances in sequencing technology have greatly reduced the costs incurred in collecting raw sequencing data. Academic laboratories and researchers therefore…”
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Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations by Fragoza, Robert, Das, Jishnu, Wierbowski, Shayne D., Liang, Jin, Tran, Tina N., Liang, Siqi, Beltran, Juan F., Rivera-Erick, Christen A., Ye, Kaixiong, Wang, Ting-Yi, Yao, Li, Mort, Matthew, Stenson, Peter D., Cooper, David N., Wei, Xiaomu, Keinan, Alon, Schimenti, John C., Clark, Andrew G., Yu, Haiyuan

“…Each human genome carries tens of thousands of coding variants. The extent to which this variation is functional and the mechanisms by which they exert their…”
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The Human Gene Mutation Database: 2008 update by Stenson, Peter D, Mort, Matthew, Ball, Edward V, Howells, Katy, Phillips, Andrew D, Thomas, Nick St, Cooper, David N

“…The Human Gene Mutation Database (HGMD((R))) is a comprehensive core collection of germline mutations in nuclear genes that underlie or are associated with…”
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Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques by Yan, Guangmei, Wang, Xiaoning, Wang, Jian, Zhang, Guojie, Fang, Xiaodong, Zhang, Yanfeng, Li, Cai, Ling, Fei, Cooper, David N, Li, Qiye, Li, Yan, van Gool, Alain J, Du, Hongli, Chen, Jiesi, Chen, Ronghua, Zhang, Pei, Huang, Zhiyong, Thompson, John R, Meng, Yuhuan, Bai, Yinqi, Wang, Jufang, Zhuo, Min, Wang, Tao, Huang, Ying, Wei, Liqiong, Li, Jianwen, Wang, Zhiwen, Hu, Haofu, Yang, Pengcheng, Le, Liang, Stenson, Peter D, Li, Bo, Liu, Xiaoming, Ball, Edward V, An, Na, Huang, Quanfei, Zhang, Yong, Fan, Wei, Zhang, Xiuqing, Li, Yingrui, Wang, Wen, Katze, Michael G, Su, Bing, Nielsen, Rasmus, Yang, Huanming, Wang, Jun

“…The nonhuman primates most commonly used in medical research are from the genus Macaca. To better understand the genetic differences between these animal…”
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X-CAP improves pathogenicity prediction of stopgain variants by Rastogi, Ruchir, Stenson, Peter D, Cooper, David N, Bejerano, Gill

“…Stopgain substitutions are the third-largest class of monogenic human disease mutations and often examined first in patient exomes. Existing computational…”
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The landscape of rare genetic variation associated with inflammatory bowel disease and Parkinson's disease comorbidity by Kars, Meltem Ece, Wu, Yiming, Stenson, Peter D, Cooper, David N, Burisch, Johan, Peter, Inga, Itan, Yuval

“…Inflammatory bowel disease (IBD) and Parkinson's disease (PD) are chronic disorders that have been suggested to share common pathophysiological processes…”
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Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set by Stein, David, Kars, Meltem Ece, Wu, Yiming, Bayrak, Çiğdem Sevim, Stenson, Peter D, Cooper, David N, Schlessinger, Avner, Itan, Yuval

“…Gain-of-function (GOF) variants give rise to increased/novel protein functions whereas loss-of-function (LOF) variants lead to diminished protein function…”
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Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics by Cooper, David N, Chen, Jian-Min, Ball, Edward V, Howells, Katy, Mort, Matthew, Phillips, Andrew D, Chuzhanova, Nadia, Krawczak, Michael, Kehrer-Sawatzki, Hildegard, Stenson, Peter D

“…The number of reported germline mutations in human nuclear genes, either underlying or associated with inherited disease, has now exceeded 100,000 in more than…”
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