1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061–1073
PubMed
Article
Google Scholar
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491:56–65
PubMed
Article
Google Scholar
Amberger J, Bocchini CA, Scott AF, Hamosh A (2009) McKusick’s Online mendelian inheritance in man (OMIM). Nucleic Acids Res 37:D793–D796
CAS
PubMed Central
PubMed
Article
Google Scholar
Andreasen C, Refsgaard L, Nielsen JB, Sajadieh A, Winkel BG, Tfelt-Hansen J, Haunsø S, Holst AG, Svendsen JH, Olesen MS (2013) Mutations in genes encoding cardiac ion channels previously associated with sudden infant death syndrome (SIDS) are present with high frequency in new exome data. Can J Cardiol 29(9):1104–1109
PubMed
Article
Google Scholar
Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, Langley RJ, Zhang L, Lee CC, Schilkey FD, Sheth V, Woodward JE, Peckham HE, Schroth GP, Kim RW, Kingsmore SF (2011) Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 3:65ra4
CAS
PubMed Central
PubMed
Article
Google Scholar
Calvo SE, Compton AG, Hershman SG, Lim SC, Lieber DS, Tucker EJ, Laskowski A, Garone C, Liu S, Jaffe DB, Christodoulou J, Fletcher JM, Bruno DL, Goldblatt J, Dimauro S, Thorburn DR, Mootha VK (2012) Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med 4:118ra10
PubMed Central
PubMed
Article
Google Scholar
Carter H, Douville C, Stenson PD, Cooper DN, Karchin R (2013) Identifying Mendelian disease genes with the Variant Effect Scoring Tool. BMC Genomics 14(Suppl 3):S3
PubMed Central
PubMed
Article
Google Scholar
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP (2012) Predicting the functional effect of amino acid substitutions and indels. PLoS ONE 2012:e46688
Article
Google Scholar
Cirulli ET, Goldstein DB (2007) In vitro assays fail to predict in vivo effects of regulatory polymorphisms. Hum Mol Genet 16:1931–1939
CAS
PubMed
Article
Google Scholar
Cooper DN, Chen JM, Ball EV, Howells K, Mort M, Phillips AD, Chuzhanova N, Krawczak M, Kehrer-Sawatzki H, Stenson PD (2010) Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum Mutat 31:631–655
CAS
PubMed
Article
Google Scholar
Cooper DN, Bacolla A, Férec C, Vasquez KM, Kehrer-Sawatzki H, Chen JM (2011) On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. Hum Mutat 32:1075–1099
CAS
PubMed Central
PubMed
Article
Google Scholar
Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H (2013) Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 132:1077–1130
CAS
PubMed Central
PubMed
Article
Google Scholar
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158
CAS
PubMed
Article
Google Scholar
Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Gutierrez Arcelus M, Sekowska M, Gagnebin M, Nisbett J, Deloukas P, Dermitzakis ET, Antonarakis SE (2009) Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325:1246–1250
CAS
PubMed Central
PubMed
Article
Google Scholar
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R (2013) CRAVAT: cancer-related analysis of VAriants Toolkit. Bioinformatics 29:647–648
CAS
PubMed
Article
Google Scholar
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJ, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Zadissa A, Searle SM (2013) ENSEMBL 2013. Nucleic Acids Res 41:D48–D55
CAS
PubMed Central
PubMed
Article
Google Scholar
Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, Teague JW, Campbell PJ, Stratton MR, Futreal PA (2011) COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39(Database issue):D945–D950
CAS
PubMed Central
PubMed
Article
Google Scholar
Gonsalves SG, Ng D, Johnston JJ, Teer JK, NISC Comparative Sequencing Program, Stenson PD, Cooper DN, Mullikin JC, Biesecker LG (2013) Using exome data for opportunistic screening of malignant hyperthermia susceptibility. Anesthesiology 6(4):337–346
Google Scholar
Green RC, Berg JS, Berry GT, Biesecker LG, Dimmock DP, Evans JP, Grody WW, Hegde MR, Kalia S, Korf BR, Krantz I, McGuire AL, Miller DT, Murray MF, Nussbaum RL, Plon SE, Rehm HL, Jacob HJ (2012) Exploring concordance and discordance for return of incidental findings from clinical sequencing. Genet Med 14:405–410
CAS
PubMed Central
PubMed
Article
Google Scholar
Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, McGuire AL, Nussbaum RL, O’Daniel JM, Ormond KE, Rehm HL, Watson MS, Williams MS, Biesecker LG (2013) ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 15:565–574
CAS
PubMed Central
PubMed
Article
Google Scholar
Guo Y, Wei X, Das J, Grimson A, Lipkin SM, Clark AG, Yu H (2013) Dissecting disease inheritance modes in a three-dimensional network challenges the “guilt-by-association” principle. Am J Hum Genet 93:78–89
CAS
PubMed
Article
Google Scholar
Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, Mullikin JC, Biesecker LG (2012) Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Am J Hum Genet 91:97–108
CAS
PubMed Central
PubMed
Article
Google Scholar
Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS (2009) A highly annotated whole-genome sequence of a Korean individual. Nature 460:1011–1015
CAS
PubMed Central
PubMed
Google Scholar
Lazarin GA, Haque IS, Nazareth S, Iori K, Patterson AS, Jacobson JL, Marshall JR, Seltzer WK, Patrizio P, Evans EA, Srinivasan BS (2013) An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23,453 individuals. Genet Med 15:178–186
PubMed
Article
Google Scholar
Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P (2009) Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 25:2744–2750
CAS
PubMed
Article
Google Scholar
Lopes MC, Joyce C, Ritchie GR, John SL, Cunningham F, Asimit J, Zeggini E (2012) A combined functional annotation score for non-synonymous variants. Hum Hered 73:47–51
CAS
PubMed Central
PubMed
Article
Google Scholar
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science 335:823–828
CAS
PubMed Central
PubMed
Article
Google Scholar
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ (2013) The UCSC Genome Browser database: extensions and updates. Nucleic Acids Res 41(1):D64–D69
CAS
PubMed Central
PubMed
Article
Google Scholar
Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG (2013) Interpreting secondary cardiac disease variants in an exome cohort. Circ Cardiovasc Genet 6:337–346
PubMed
Article
Google Scholar
Nishiguchi KM, Rivolta C (2012) Genes associated with retinitis pigmentosa and allied diseases are frequently mutated in the general population. PLoS ONE 7:e41902
CAS
PubMed Central
PubMed
Article
Google Scholar
Patrinos GP, Cooper DN, van Mulligen E, Gkantouna V, Tzimas G, Tatum Z, Schultes E, Roos M, Mons B (2012) Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain. Hum Mutat 33:1503–1512
PubMed
Article
Google Scholar
Peterson TA, Doughty E, Kann MG (2013) Towards precision medicine: advances in computational approaches for analysis of human variants. J Mol Biol. doi:10.1016/j.jmb.2013.08.008
Pruitt KD, Tatusova T, Klimke W, Maglott DR (2009) NCBI reference sequences: current status, policy and new initiatives. Nucleic Acids Res 37:D32–D36
CAS
PubMed Central
PubMed
Article
Google Scholar
Rat Genome Sequencing Project Consortium (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493–521
Article
Google Scholar
Rhesus Macaque Genome Sequencing and Analysis Consortium (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222–234
Article
Google Scholar
Ruiz-Pesini E, Lott MT, Procaccio V, Poole JC, Brandon MC, Mishmar D, Yi C, Kreuziger J, Baldi P, Wallace DC (2007) An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res 35:D823–D828
CAS
PubMed Central
PubMed
Article
Google Scholar
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O’Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483:169–175
CAS
PubMed Central
PubMed
Article
Google Scholar
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308–311
CAS
PubMed Central
PubMed
Article
Google Scholar
Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR (2013) Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat 34:57–65
CAS
PubMed Central
PubMed
Article
Google Scholar
Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC (2012) SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res 40:W452–W457
CAS
PubMed Central
PubMed
Article
Google Scholar
Thorn CF, Klein TE, Altman RB (2010) Pharmacogenomics and bioinformatics: PharmGKB. Pharmacogenomics 11:501–505
CAS
PubMed Central
PubMed
Article
Google Scholar
Tong P, Prendergast JG, Lohan AJ, Farrington SM, Cronin S, Friel N, Bradley DG, Hardiman O, Evans A, Wilson JF, Loftus B (2010) Sequencing and analysis of an Irish human genome. Genome Biol 11:R91
PubMed Central
PubMed
Article
Google Scholar
Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H (2012) Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat Biotechnol 30:159–164
CAS
PubMed Central
PubMed
Article
Google Scholar
Webb AJ, Thorisson GA, Brookes AJ, GEN2PHEN Consortium (2011) An informatics project and online “Knowledge Centre” supporting modern genotype-to-phenotype research. Hum Mutat 32:543–550
CAS
PubMed
Article
Google Scholar
Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN, Tyler-Smith C, the 1000 Genomes Project Consortium (2012) Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am J Hum Genet 91:1022–1032
CAS
PubMed Central
PubMed
Article
Google Scholar
Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y, van Gool AJ, Du H, Chen J, Chen R, Zhang P, Huang Z, Thompson JR, Meng Y, Bai Y, Wang J, Zhuo M, Wang T, Huang Y, Wei L, Li J, Wang Z, Hu H, Yang P, Le L, Stenson PD, Li B, Liu X, Ball EV, An N, Huang Q, Zhang Y, Fan W, Zhang X, Li Y, Wang W, Katze MG, Su B, Nielsen R, Yang H, Wang J, Wang X, Wang J (2011) Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol 29:1019–1023
CAS
PubMed
Article
Google Scholar