On optimal gene-based analysis of genome scans

Genetic Epidemiology

Volumn 36, Issue 4, 2012, Pages 333-339

  Bacanu, Silviu Alin ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

GATES; Principal components; Sequencing; Simes; VEGAS

Indexed keywords

ADAPTIVE SUM; ARTICLE; CONTROLLED STUDY; GENE BASED ASSOCIATION TEST USING EXTENDED SIMES PROCEDURE; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC PROCEDURES; GENOME; GENOME SCAN; HUMAN; KERNEL METHOD; SIMES PROCEDURE; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; VERSATILE GENE BASED ASSOCIATION STUDY;

COMPUTER SIMULATION; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS; SCHIZOPHRENIA; SEQUENCE ANALYSIS, DNA;

EID: 84860346478     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21625     Document Type: Article

References (34)

1. Bacanu SA, Nelson MR, Ehm MG. 2008. Comparison of association methods for dense marker data. Genet Epidemiol 32:791-799.
2. Baranzini SE, Galwey NW, Wang J, Khankhanian P, Lindberg R, Pelletier D, Wu W, Uitdehaag BM, Kappos L, Polman CH, Matthews PM, Hauser SL, Gibson RA, Oksenberg JR, Barnes MR. 2009. Pathway and network-based analysis of genome-wide association studies in multiple sclerosis. Hum Mol Genet 18:2078-2090.
3. Basu S, Pan W, Shen X, Oetting WS. 2011. Multilocus association testing with penalized regression. Genet Epidemiol 35(8):755-765.
4. Chapman J, Whittaker J. 2008. Analysis of multiple SNPs in a candidate gene or region. Genet Epidemiol 32:560-566.
5. Cheverud JM. 2001. A simple correction for multiple comparisons in interval mapping genome scans. Heredity 87:52-58.
6. Dewan A, Liu M, Hartman S, Zhang SS, Liu DT, Zhao C, Tam PO, Chan WM, Lam DS, Snyder M, Barnstable C, Pang CP, Hoh J. 2006. HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 314:989-992.
7. Dudbridge F, Gusnanto A. 2008. Estimation of significance thresholds for genomewide association scans. Genet Epidemiol 32:227-234.
8. Elbers CC, van Eijk KR, Franke L, Mulder F, van der Schouw YT, Wijmenga C, Onland-Moret NC. 2009. Using genome-wide pathway analysis to unravel the etiology of complex diseases. Genet Epidemiol 33:419-431.
9. Gauderman WJ, Murcray C, Gilliland F, Conti DV. 2007. Testing association between disease and multiple SNPs in a candidate gene. Genet Epidemiol 31:383-395.
10. Han F, Pan W. 2010. A data-adaptive sum test for disease association with multiple common or rare variants. Hum Hered 70:42-54.
11. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106:9362-9367.
12. Holmans P, Green EK, Pahwa JS, Ferreira MA, Purcell SM, Sklar P, Owen MJ, O'Donovan MC, Craddock N. 2009. Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. Am J Hum Genet 85:13-24.
13. Huang H, Chanda P, Alonso A, Bader JS, Arking DE. 2011. Gene-based tests of association. PLoS Genet 7:e1002177
14. Kendler KS, Myers JM, O'Neill FA, Martin R, Murphy B, MacLean CJ, Walsh D, Straub RE. 2000. Clinical features of schizophrenia and linkage to chromosomes 5q, 6p, 8p, and 10p in the Irish Study of High-Density Schizophrenia Families. Am J Psychiatry 157:402-408.
15. Kwee LC, Liu D, Lin X, Ghosh D, Epstein MP. 2008. A powerful and flexible multilocus association test for quantitative traits. Am J Hum Genet 82:386-397.
16. Li B, Leal SM. 2008. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83:311-321.
17. Li M, Wang K, Grant SF, Hakonarson H, Li C. 2009. ATOM: a powerful gene-based association test by combining optimally weighted markers. Bioinformatics 25:497-503.
18. Li MX, Gui HS, Kwan JS, Sham PC. 2011. GATES: a rapid and powerful gene-based association test using extended Simes procedure. Am J Hum Genet 88:283-293.
19. Liu JZ, McRae AF, Nyholt DR, Medland SE, Wray NR, Brown KM, Hayward NK, Montgomery GW, Visscher PM, Martin NG, Macgregor S. 2010. A versatile gene-based test for genome-wide association studies. Am J Hum Genet 87:139-145.
20. 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 et al. 2009. Finding the missing heritability of complex diseases. Nature 461:747-753.
21. Moskvina V, Schmidt KM. 2008. On multiple-testing correction in genome-wide association studies. Genet Epidemiol 32:567-573.
22. Neale BM, Sham PC. 2004. The future of association studies: gene-based analysis and replication. Am J Hum Genet 75:353-362.
23. Perry JR, McCarthy MI, Hattersley AT, Zeggini E, Weedon MN, Frayling TM. 2009. Interrogating type 2 diabetes genome-wide association data using a biological pathway-based approach. Diabetes 58:1463-1467.
24. Ripke S, Sanders AR, Kendler KS, Levinson DF, Sklar P, Holmans PA, Lin DY, Duan J, Ophoff RA, Andreassen OA, Scolnick E, Cichon S, St Clair D, Corvin A, Gurling H, Werge T, Rujescu D, Blackwood DH, Pato CN, Malhotra AK, Purcell S, Dudbridge F, Neale BM, Rossin L, Visscher PM, Posthuma D, Ruderfer DM, Fanous A, Stefansson H, Steinberg S, Mowry BJ, Golimbet V, De Hert M, Jonsson EG, Bitter I, Pietilainen OP, Collier DA, Tosato S, Agartz I, Albus M, Alexander M, Amdur RL, Amin F, Bass N, Bergen SE, Black DW, Borglum AD, Brown MA, Bruggeman R, Buccola NG, Byerley WF, Cahn W, Cantor RM, Carr VJ, Catts SV, Choudhury K, Cloninger CR, Cormican P, Craddock N, Danoy PA, Datta S, de Haan L, Demontis D, Dikeos D, Djurovic S, Donnelly P, Donohoe G, Duong L, Dwyer S, Fink-Jensen A, Freedman R, Freimer NB, Friedl M, Georgieva L, Giegling I, Gill M, Glenthoj B, Godard S, Hamshere M, Hansen M, Hansen T, Hartmann AM, Henskens FA, Hougaard DM, Hultman CM, Ingason A, Jablensky AV, Jakobsen KD, Jay M, Jurgens G, Kahn RS, Keller MC, Kenis G, Kenny E, Kim Y, Kirov GK, Konnerth H, Konte B, Krabbendam L, Krasucki R, Lasseter VK, Laurent C, Lawrence J, Lencz T, Lerer FB, Liang KY, Lichtenstein P, Lieberman JA, Linszen DH, Lonnqvist J, Loughland CM, Maclean AW, Maher BS, Maier W, Mallet J, Malloy P, Mattheisen M, Mattingsdal M, McGhee KA, McGrath JJ, McIntosh A, McLean DE, McQuillin A, Melle I, Michie PT, Milanova V, Morris DW, Mors O, Mortensen PB, Moskvina V, Muglia P, Myin-Germeys I, Nertney DA, Nestadt G, Nielsen J, Nikolov I, Nordentoft M, Norton N, Nothen MM, O'Dushlaine CT, Olincy A, Olsen L, O'Neill FA, Orntoft TF, Owen MJ, Pantelis C, Papadimitriou G, Pato MT, Peltonen L, Petursson H, Pickard B, Pimm J, Pulver AE, Puri V, Quested D, Quinn EM, Rasmussen HB, Rethelyi JM, Ribble R, Rietschel M, Riley BP, Ruggeri M, Schall U, Schulze TG, Schwab SG, Scott RJ, Shi J, Sigurdsson E, Silverman JM, Spencer CC, Stefansson K, Strange A, Strengman E, Stroup TS, Suvisaari J, Terenius L, Thirumalai S, Thygesen JH, Timm S, Toncheva D, van den Oord E, van Os J, van Winkel R, Veldink J, Walsh D, Wang AG, Wiersma D, Wildenauer DB, Williams HJ, Williams NM, Wormley B, Zammit S, Sullivan PF, O'Donovan MC, Daly MJ, Gejman PV. 2011. Genome-wide association study identifies five new schizophrenia loci. Nat Genet 43:969-976.
25. Ruano D, Abecasis GR, Glaser B, Lips ES, Cornelisse LN, de Jong AP, Evans DM, Davey SG, Timpson NJ, Smit AB, Heutink P, Verhage M, Posthuma D. 2010. Functional gene group analysis reveals a role of synaptic heterotrimeric G proteins in cognitive ability. Am J Hum Genet 86:113-125.
26. Servin B, Stephens M. 2007. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet 3:e114
27. Slatkin M. 2009. Epigenetic inheritance and the missing heritability problem. Genetics 182:845-850
28. Suarez BK, Duan J, Sanders AR, Hinrichs AL, Jin CH, Hou C, Buccola NG, Hale N, Weilbaecher AN, Nertney DA, Olincy A, Green S, Schaffer AW, Smith CJ, Hannah DE et al. 2006. Genomewide linkage scan of 409 European-ancestry and African American families with schizophrenia: suggestive evidence of linkage at 8p23.3-p21.2 and 11p13.1-q14.1 in the combined sample. Am J Hum Genet 78:315-333.
29. Wang K, Abbott D. 2008. A principal components regression approach to multilocus genetic association studies. Genet Epidemiol 32:108-118.
30. Wang T, Elston RC. 2007. Improved power by use of a weighted score test for linkage disequilibrium mapping. Am J Hum Genet 80:353-360.
31. Wang K, Li M, Bucan M. 2007. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 81:1278-1283.
32. Wellcome Trust Case Control Consortium. 2007. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 447:661-678.
33. Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X. 2011. Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 89:82-93.
34. Zaykin DV, Zhivotovsky LA, Westfall PH, Weir BS. 2002. Truncated product method for combining P-values. Genet Epidemiol 22:170-185.