A unified framework for multi-locus association analysis of both common and rare variants

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Shriner, Daniel ^a   Vaughan, Laura K ^b  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GAK PROTEIN; MEMBRANE PROTEIN; UNCLASSIFIED DRUG;

ANALYTICAL ERROR; ARTICLE; CELL MIGRATION; COMPUTER SIMULATION; CONTROLLED STUDY; DATA ANALYSIS; GENE FREQUENCY; GENE FUNCTION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC RISK; GENOME ANALYSIS; HAPLOTYPE; HUMAN; MAJOR CLINICAL STUDY; MULTI LOCUS ASSOCIATION ANALYSIS; NEUROPATHOLOGY; PARKINSON DISEASE; RARE DISEASE; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; GENE LINKAGE DISEQUILIBRIUM; GENETIC PREDISPOSITION; GENETICS; GENOTYPE; METHODOLOGY; THEORETICAL MODEL;

COMPUTATIONAL BIOLOGY; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, THEORETICAL; PARKINSON DISEASE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 79251553463     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-89     Document Type: Article

References (26)

1. The Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447:661-678. 10.1038/nature05911, 2719288, 17554300, The Wellcome Trust Case Control Consortium.
2. Kwee LC, Liu D, Lin X, Ghosh D, Epstein MP. A powerful and flexible multilocus association test for quantitative traits. Am J Hum Genet 2008, 82:386-397. 10.1016/j.ajhg.2007.10.010, 2664991, 18252219.
3. 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, 2842185, 18691683.
4. 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, 2633048, 19214210.
5. Ardlie KG, Kruglyak L, Seielstad M. Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 2002, 3:299-309. 10.1038/nrg777, 11967554.
6. Mueller JC. Linkage disequilibrium for different scales and applications. Brief Bioinform 2004, 5:355-364. 10.1093/bib/5.4.355, 15606972.
7. Fung HC, Scholz S, Matarin M, Simón-Sánchez J, Hernandez D, Britton A, Gibbs JR, Langefeld C, Stiegert ML, Schymick J, Okun MS, Mandel RJ, Fernandez HH, Foote KD, Rodriguez RL, Peckham E, De Vrieze FW, Gwinn-Hardy K, Hardy JA, Singleton A. Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 2006, 5:911-916. 10.1016/S1474-4422(06)70578-6, 17052657.
8. Simón-Sánchez J, Scholz S, Matarin M, Fung HC, Hernandez D, Gibbs JR, Britton A, Hardy J, Singleton A. Genomewide SNP assay reveals mutations underlying Parkinson disease. Hum Mutat 2008, 29:315-322.
9. Pankratz N, Wilk JB, Latourelle JC, DeStefano AL, Halter C, Pugh EW, Doheny KF, Gusella JF, Nichols WC, Foroud T, Myers RH. Genomewide association study for susceptibility genes contributing to familial Parkinson disease. Hum Genet 2009, 124:593-605. 10.1007/s00439-008-0582-9, 2627511, 18985386.
10. Ruczinski I, Kooperberg C, LeBlanc M. Logic regression. J Comput Graph Stat 2003, 12:475-511.
11. R Development Core Team R: A language and environment for statistical computing, Version 2.10.1. 2009, R Foundation for Statistical Computing, R Development Core Team.
12. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81:559-575. 10.1086/519795, 1950838, 17701901.
13. Wu MC, Kraft P, Epstein MP, Taylor DM, Chanock SJ, Hunter DJ, Lin X. Powerful SNP-set analysis for case-control genome-wide association studies. Am J Hum Genet 2010, 86:929-942. 10.1016/j.ajhg.2010.05.002, 3032061, 20560208.
14. Devlin B, Roeder K. Genomic control for association studies. Biometrics 1999, 55:997-1004. 10.1111/j.0006-341X.1999.00997.x, 11315092.
15. Zheng G, Freidlin B, Li Z, Gastwirth JL. Genomic control for association studies under various genetic models. Biometrics 2005, 61:186-192. 10.1111/j.0006-341X.2005.t01-1-.x, 15737092.
16. Won S, Elston RC. The power of independent types of genetic information to detect association in a case-control study design. Genet Epidemiol 2008, 32:731-756. 10.1002/gepi.20341, 18481783.
17. Redden DT, Divers J, Vaughan LK, Tiwari HK, Beasley TM, Fernandez JR, Kimberly RP, Feng R, Padilla MA, Liu N, Miller MB, Allison DB. Regional admixture mapping and structured association testing: conceptual unification and an extensible general linear model. PLoS Genet 2006, 2:e137. 10.1371/journal.pgen.0020137, 1557785, 16934005.
18. Longmate JA. Complexity and power in case-control association studies. Am J Hum Genet 2001, 68:1229-1237. 10.1086/320106, 1226103, 11294658.
19. Pritchard JK, Cox NJ. The allelic architecture of human disease genes: common disease-common variant...or not?. Hum Mol Genet 2002, 11:2417-2423. 10.1093/hmg/11.20.2417, 12351577.
20. Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI. Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet 2008, 82:100-112. 10.1016/j.ajhg.2007.09.006, 2253956, 18179889.
21. Fearnhead NS, Wilding JL, Winney B, Tonks S, Bartlett S, Bicknell DC, Tomlinson IP, Mortensen NJ, Bodmer WF. Multiple rare variants in different genes account for multifactorial inherited susceptibility to colorectal adenomas. Proc Natl Acad Sci USA 2004, 101:15992-15997. 10.1073/pnas.0407187101, 528777, 15520370.
22. Cohen JC, Kiss RS, Pertsemlidis A, Marcel YL, McPherson R, Hobbs HH. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 2004, 305:869-872. 10.1126/science.1099870, 15297675.
23. Kooperberg C, Ruczinski I. Identifying interacting SNPs using Monte Carlo logic regression. Genet Epidemiol 2005, 28:157-170. 10.1002/gepi.20042, 15532037.
24. Suzuki T, Park H, Hollingsworth NM, Sternglanz R, Lennarz WJ. PNG1, a yeast gene encoding a highly conserved peptide:N-glycanase. J Cell Biol 2000, 149:1039-1052. 10.1083/jcb.149.5.1039, 2174826, 10831608.
25. Eisenberg E, Greene LE. Multiple roles of auxilin and Hsc70 in clathrin-mediated endocytosis. Traffic 2007, 8:640-646. 10.1111/j.1600-0854.2007.00568.x, 17488288.
26. Kao H-T, Porton B, Czernik AJ, Feng J, Yiu G, Häring M, Benfenati F, Greengard P. A third member of the synapsin gene family. Proc Natl Acad Sci USA 1998, 95:4667-4672. 10.1073/pnas.95.8.4667, 22548, 9539796.