Pathway-based analysis for genome-wide association studies using supervised principal components

Genetic Epidemiology

Volumn 34, Issue 7, 2010, Pages 716-724

  Chen, Xi ^a   Wang, Lily ^b   Hu, Bo ^c   Guo, Mingsheng ^a   Barnard, John ^c   Zhu, Xiaofeng ^d  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VANDERBILT UNIVERSITY   (United States)

^c LERNER RESEARCH INSTITUTE   (United States)

^d CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

Genome wide association; Pathway analysis; Principal component analysis; SNPs

Indexed keywords

ARTICLE; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; PRINCIPAL COMPONENT ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

COMPUTER SIMULATION; CROHN DISEASE; DATABASES, GENETIC; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MOLECULAR EPIDEMIOLOGY; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS;

EID: 77958611364     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20532     Document Type: Article

References (35)

1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29.
2. Bair E, Tibshirani R. 2004. Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol 2:511-522.
3. Bair E, Hastie T, Paul D, Tibshirani R. 2006. Prediction by supervised principal components. J Am Stat Assoc 101:119-137.
4. Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwilliam R, Tremelling M, Deloukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ. 2008. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 40:955-962.
5. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289-300.
6. Chasman DI. 2008. On the utility of gene set methods in genomewide association Studies of quantitative traits. Genet Epidemiol 32:658-668.
7. Chen X, Wang L, Smith JD, Zhang B. 2008. Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes. Bioinformatics 24:2474-2481.
8. 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.
9. Goeman JJ, Buhlmann P. 2007. Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23:980-987.
10. Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, Albrecht M, Mayr G, De La Vega FM, Briggs J, Gunther S, Prescott NJ, Onnie CM, Hasler R, Sipos B, Folsch UR, Lengauer T, Platzer M, Mathew CG, Krawczak M, Schreiber S. 2007. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 39:207-211.
11. Hoh J, Wille A, Ott J. 2001. Trimming, weighting, and grouping SNPs in human case-control association studies. Genome Res 11:2115-2119.
12. Holden M, Deng SW, Wojnowski L, Kulle B. 2008. GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics 24:2784-2785.
13. Holmans P, Green EK, Pahwa JS, Ferreira MAR, 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.
14. Kobayashi K, Inohara N, Hernandez LD, Galan JE, Nunez G, Janeway CA, Medzhitov R, Flavell RA. 2002. RICK/Rip2/CARDIAK mediates signalling for receptors of the innate and adaptive immune systems. Nature 416:194-199.
15. Leadbetter MR, Lindgren G, Rootzen H. 1982. Extremes and Related Properties of Random Sequences and Processes. New York: Springer.
16. Li C, Li MY. 2008. GWAsimulator: a rapid whole-genome simulation program. Bioinformatics 24:140-142.
17. 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 TFC, McCarroll SA, Visscher PM. 2009. Finding the missing heritability of complex diseases. Nature 461:747-753.
18. Mathew CG. 2008. New links to the pathogenesis of Crohn disease provided by genome-wide association scans. Nat Rev Genet 9:9-14.
19. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JPA, Hirschhorn JN. 2008. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9:356-369.
20. Neurath MF. 2007. IL23: a master regulator in Crohn disease. Nat Med 13:26-28.
21. Parkes M, Barrett JC, Prescott NJ, Tremelling M, Anderson CA, Fisher SA, Roberts RG, Nimmo ER, Cummings FR, Soars D, Drummond H, Lees CW, Khawaja SA, Bagnall R, Burke DA, Todhunter CE, Ahmad T, Onnie CM, McArdle W, Strachan D, Bethel G, Bryan C, Lewis CM, Deloukas P, Forbes A, Sanderson J, Jewell DP, Satsangi J, Mansfield JC, Cardon L, Mathew CG. 2007. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet 39:830-832.
22. Podolsky DK. 2002. Inflammatory bowel disease. N Engl J Med 347:417-429.
23. Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, Huett A, Green T, Kuballa P, Barmada MM, Datta LW, Shugart YY, Griffiths AM, Targan SR, Ippoliti AF, Bernard EJ, Mei L, Nicolae DL, Regueiro M, Schumm LP, Steinhart AH, Rotter JI, Duerr RH, Cho JH, Daly MJ, Brant SR. 2007. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet 39:596-604.
24. Schmid D, Munz C. 2007. Innate and adaptive immunity through autophagy. Immunity 27:11-21.
25. Schwarz DF, Hadicke O, Erdmann J, Ziegler A, Bayer D, Moller S. 2008. SNPtoGO: characterizing SNPs by enriched GO terms. Binformatics 24:146-148.
26. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. 2005. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545-15550.
27. Tomfohr J, Lu J, Kepler TB. 2005. Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics 6:225.
28. Wang K, Abbott D. 2008. A principal components regression approach to multilocus genetic association studies. Genet Epidemiol 32:108-118.
29. Wang K, Li MY, Bucan M. 2007. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 81:1278-1283.
30. Wang L, Zhang B, Wolfinger RD, Chen X. 2008. An integrated approach for the analysis of biological pathways using mixed models. PLoS Genet 4:e1000115.
31. Wang K, Zhang H, Kugathasan S, Annese V, Bradfield JR, Russell RK, Sleiman PMA, Imielinski M, Glessner J, Hou C, Wilson DC, Walters T, Kim C, Frackelton EC, Lionetti P, Barabino A, Van Limbergen J, Guthery S, Denson L, Piccoli D, Li M, Dubinsky M, Silverberg M, Griffiths A, Grant SFA, Satsangi J, Baldassano R, Hakonarson H. 2009. Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohn disease. Am J Hum Genet 84:399-405.
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. Wright FA, Huang HW, Guan XJ, Gamiel K, Jeffries C, Barry WT, de Villena FPM, Sullivan PF, Wilhelmsen KC, Zou F. 2007. Simulating association studies: a data-based resampling method for candidate regions or whole genome scans. Bioinformatics 23:2581-2588.
34. Xavier RJ, Podolsky DK. 2007. Unravelling the pathogenesis of inflammatory bowel disease. Nature 448:427-434.
35. Zhu XF, Zhang SL, Zhao HY, Cooper RS. 2002. Association mapping, using a mixture model for complex traits. Genet Epidemiol 23:181-196.