Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM: Finding the missing heritability of complex diseases. Nature. 2009, 461: 747-753. 10.1038/nature08494.
Article
PubMed Central
CAS
PubMed
Google Scholar
Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD: Using BioBin to Explore Rare Variant Population Stratification. Pacific Symposium on Biocomputing. 2013
Google Scholar
Sanna S, Li B, Mulas A, Sidore C, Kang HM, Jackson AU, Piras MG, Usala G, Maninchedda G, Sassu A, Serra F, Palmas MA, Wood WH, Njølstad I, Laakso M, Hveem K, Tuomilehto J, Lakka TA, Rauramaa R, Boehnke M, Cucca F, Uda M, Schlessinger D, Nagaraja R, Abecasis GR: Fine mapping of five loci associated with low-density lipoprotein cholesterol detects variants that double the explained heritability. PLoS Genet. 2011, 7: e1002198-10.1371/journal.pgen.1002198.
Article
PubMed Central
CAS
PubMed
Google Scholar
Johansen CT, Wang J, Lanktree MB, Cao H, McIntyre AD, Ban MR, Martins RA, Kennedy BA, Hassell RG, Visser ME, Schwartz SM, Voight BF, Elosua R, Salomaa V, O'Donnell CJ, Dallinga-Thie GM, Anand SS, Yusuf S, Huff MW, Kathiresan S, Hegele RA: Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia. Nat Genet. 2010, 42: 684-687. 10.1038/ng.628.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V: A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol. 2010, 6: e1000954-10.1371/journal.pcbi.1000954.
Article
PubMed Central
PubMed
Google Scholar
Ionita-Laza I, Buxbaum JD, Laird NM, Lange C: A new testing strategy to identify rare variants with either risk or protective effect on disease. PLoS Genet. 2011, 7: e1001289-10.1371/journal.pgen.1001289.
Article
PubMed Central
CAS
PubMed
Google Scholar
Haack TB, Danhauser K, Haberberger B, Hoser J, Strecker V, Boehm D, Uziel G, Lamantea E, Invernizzi F, Poulton J, Rolinski B, Iuso A, Biskup S, Schmidt T, Mewes HW, Wittig I, Meitinger T, Zeviani M, Prokisch H: Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency. Nat Genet. 2010, 42: 1131-1134. 10.1038/ng.706.
Article
CAS
PubMed
Google Scholar
Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ, Shendure J: Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nature Genetics. 2010, 42: 790-793. 10.1038/ng.646.
Article
PubMed Central
CAS
PubMed
Google Scholar
Raychaudhuri S, Iartchouk O, Chin K, Tan PL, Tai AK, Ripke S, Gowrisankar S, Vemuri S, Montgomery K, Yu Y, Reynolds R, Zack DJ, Campochiaro B, Campochiaro P, Katsanis N, Daly MJ, Seddon JM: A rare penetrant mutation in CFH confers high risk of age-related macular degeneration. Nat Genet. 2011, 43: 1232-1236. 10.1038/ng.976.
Article
PubMed Central
CAS
PubMed
Google Scholar
Morgenthaler S, Thilly WG: A strategy to discover genes that carry multi- allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat Res. 2007, 615: 28-56. 10.1016/j.mrfmmm.2006.09.003.
Article
CAS
PubMed
Google Scholar
Li B, Leal SM: Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008, 83: 311-321. 10.1016/j.ajhg.2008.06.024.
Article
PubMed Central
CAS
PubMed
Google Scholar
Madsen BE, Browning SR: A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet. 2009, 5: e1000384-10.1371/journal.pgen.1000384.
Article
PubMed Central
PubMed
Google Scholar
Han F, Pan W: A data-adaptive sum test for disease association with multiple common or rare variants. Hum Hered. 2010, 70: 42-54. 10.1159/000288704.
Article
PubMed Central
PubMed
Google Scholar
Price AL, Kryukov GV, De Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR: Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet. 2010, 86: 832-838. 10.1016/j.ajhg.2010.04.005.
Article
PubMed Central
PubMed
Google Scholar
Hoffmann TJ, Marini NJ, Witte JS: Comprehensive approach to analyzing rare genetic variants. PLoS One. 2010, 5: e13584-10.1371/journal.pone.0013584.
Article
PubMed Central
PubMed
Google Scholar
Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X: Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet. 2011, 89: 82-93. 10.1016/j.ajhg.2011.05.029.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yandell M, Huff C, Hu H, Singleton M, Moore B, Xing J, Jorde LB, Reese MG: A probabilistic disease-gene finder for personal genomes. Genome Res. 2011, 21: 1529-1542. 10.1101/gr.123158.111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Province MA, Borecki IB: Gathering the gold dust: methods for assessing the aggregate impact of small effect genes in genomic scans. Pac Symp Biocomput. 2008, 190-200.
Google Scholar
Li B, Leal SM: Discovery of rare variants via sequencing: implications for the design of complex trait association studies. PLoS Genet. 2009, 5: e1000481-10.1371/journal.pgen.1000481.
Article
PubMed Central
PubMed
Google Scholar
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J: Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2010, 39: D38-D51.
Article
PubMed Central
PubMed
Google Scholar
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M: KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research. 2011, 40: D109-D114.
Article
PubMed Central
PubMed
Google Scholar
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L: Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Research. 2010, 39: D691-D697.
Article
PubMed Central
PubMed
Google Scholar
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter M-C, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek- Roggli P, Xenarios I, Apweiler R: The UniProt-GO Annotation database in 2011. Nucleic Acids Research. 2011, 40: D565-D570.
Article
PubMed Central
PubMed
Google Scholar
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD: The Pfam protein families database. Nucleic Acids Research. 2012, 40: D290-D301. 10.1093/nar/gkr1065.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GSS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HKC, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TSK, Lin J-X, Houtman JCD, Desiderio S, Renauld J-C, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A: NetPath: a public resource of curated signal transduction pathways. Genome Biol. 2010, 11: R3-10.1186/gb-2010-11-1-r3.
Article
PubMed Central
PubMed
Google Scholar
Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E, Castagnoli L, Cesareni G: MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 2012, 40: D857-861. 10.1093/nar/gkr930.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stark C, Breitkreutz B-J, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M: The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011, 39: D698-704. 10.1093/nar/gkq1116.
Article
PubMed Central
CAS
PubMed
Google Scholar
McDonagh EM, Whirl-Carrillo M, Garten Y, Altman RB, Klein TE: From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark Med. 2011, 5: 795-806. 10.2217/bmm.11.94.
Article
PubMed Central
CAS
PubMed
Google Scholar
Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJM, The Open Regulatory Annotation Consortium: ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research. 2007, 36: D107-D113. 10.1093/nar/gkm967.
Article
PubMed Central
PubMed
Google Scholar
Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ: The UCSC Genome Browser database: update 2011. Nucl Acids Res. 2010
Google Scholar
Core Team RD: R: A language and environment for statistical computing. ISBN 3900051070, URL. 2011, Vienna, Austria: R Foundation for Statistical Computing, [http://www.R-project.org]
Google Scholar
Li B, Wang G, Leal SM: SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits. Bioinformatics.
Peng B, Amos CI, Kimmel M: Forward-time simulations of human populations with complex diseases. PLoS Genet. 2007, 3: e47-10.1371/journal.pgen.0030047.
Article
PubMed Central
PubMed
Google Scholar
Kryukov GV, Shpunt A, Stamatoyannopoulos JA, Sunyaev SR: Power of deep, all-exon resequencing for discovery of human trait genes. Proc Natl Acad Sci USA. 2009, 106: 3871-3876. 10.1073/pnas.0812824106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nelson MR, Wegmann D, Ehm MG, Kessner D, Jean PS, Verzilli C, Shen J, Tang Z, Bacanu S-A, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall MD, Nangle K, Wang J, Abecasis G, Cardon LR, Zöllner S, Whittaker JC, Chissoe SL, Novembre J, Mooser V: An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People. Science. 2012, 337: 100-104. 10.1126/science.1217876.
Article
PubMed Central
CAS
PubMed
Google Scholar
Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA: A map of human genome variation from population-scale sequencing. Nature. 2010, 467: 1061-1073. 10.1038/nature09534.
Article
CAS
PubMed
Google Scholar
Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA: Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010, 327: 78-81. 10.1126/science.1181498.
Article
CAS
PubMed
Google Scholar
Ladouceur M, Dastani Z, Aulchenko YS, Greenwood CMT, Richards JB: The empirical power of rare variant association methods: results from sanger sequencing in 1,998 individuals. PLoS Genet. 2012, 8: e1002496-10.1371/journal.pgen.1002496.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ellegren H, Smith NG, Webster MT: Mutation rate variation in the mammalian genome. Curr Opin Genet Dev. 2003, 13: 562-568. 10.1016/j.gde.2003.10.008.
Article
CAS
PubMed
Google Scholar
Hodgkinson A, Eyre-Walker A: Variation in the mutation rate across mammalian genomes. Nature Reviews Genetics. 2011, 12: 756-766. 10.1038/nrg3098.
Article
CAS
PubMed
Google Scholar
Armistead J, Khatkar S, Meyer B, Mark BL, Patel N, Coghlan G, Lamont RE, Liu S, Wiechert J, Cattini PA, Koetter P, Wrogemann K, Greenberg CR, Entian K-D, Zelinski T, Triggs-Raine B: Mutation of a gene essential for ribosome biogenesis, EMG1, causes Bowen-Conradi syndrome. Am J Hum Genet. 2009, 84: 728-739. 10.1016/j.ajhg.2009.04.017.
Article
PubMed Central
CAS
PubMed
Google Scholar