Inclusion of A priori information in genome-wide association analysis

Genetic Epidemiology

Volumn 33, Issue SUPPL. 1, 2009, Pages

  Tintle, Nathan ^a   Lantieri, Francesca ^b,c   Lebrec, Jérémie ^d   Sohns, Melanie ^e   Ballard, David ^f   Bickeböller, Heike ^e  

^a HOPE COLLEGE   (United States)

^b CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^c UNIVERSITY OF GENOA   (Italy)

^d LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^e UNIVERSITY MEDICAL CENTER GÖTTINGEN   (Germany)

^f YALE UNIVERSITY   (United States)

Author keywords

Candidate genes; Candidate regions; External information; Gene expression; Gene set analysis; Hierarchical Bayesian model; Pathway

Indexed keywords

CONFERENCE PAPER; FOLLOW UP; GENE EXPRESSION; GENE FREQUENCY; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOTYPE PHENOTYPE CORRELATION; HEART DISEASE; HUMAN; INTERMETHOD COMPARISON; LINKAGE ANALYSIS; LOGISTIC REGRESSION ANALYSIS; RHEUMATOID ARTHRITIS; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMATIC ERROR; VALIDATION PROCESS;

ARTHRITIS, RHEUMATOID; BAYES THEOREM; CARDIOVASCULAR DISEASES; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MOLECULAR EPIDEMIOLOGY; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 71249150319     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20476     Document Type: Conference Paper

References (33)

1. Allison DB, Cui X, Page GP, Sabripour M. 2006. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7:55-65. (Pubitemid 41828948)
2. Amos CI. 2007. Successful design and conduct of genome-wide association studies. Hum Mol Genet 16:R220-R225.
3. Ballard DH, Aporntewan C, Lee JY, Lee JS, Wu Z, Zhao H. 2009. A pathway analysis applied to Genetic Analysis Workshop 16 genome-wide rheumatoid arthritis data. BMC Proc 3:S91.
4. Becker KG, Barnes KC, Bright TJ, Wang SA. 2004. The genetic association database. Nat Genet 36:431-432.
5. Bossé Y, Bacot F, Montpetit A, Rung J, Qu HQ, Engert JC, Polychronakos C, Hudson TJ, Froguel P, Sladek R, Desrosiers M. 2009. Identification of susceptibility genes for complex diseases using pooling-based genome-wide association scans. Hum Genet 125:305-318.
6. Charlesworth JC, Peralta JM, Drigalenko E, Göring HHH, Almasy L, Dyer TD, Blangero J. 2009. Toward the identification of causal genes in complex diseases: A gene-centric joint test of significance combining genomic and transcriptomic data. BMC Proc 3:S92.
7. Chasman DI. 2008. On the utility of gene set methods in genomewide association studies of quantitative traits. Genet Epidemiol 32:658-668.
8. Chen GK, Witte JS. 2007. Enriching the analysis of genomewide association studies with hierarchical modeling. Am J Hum Genet 81:397-404. (Pubitemid 47236087)
9. Curtis D, Vine AE, Knight J. 2007. A pragmatic suggestion for dealing with results for candidate genes obtained from genome-wide association studies. BMC Genet 8:20. (Pubitemid 46831580)
10. Dinu I, Potter JD, Mueller T, Liu Q, Adewale AJ, Jhangri GS, Einecke G, Famulski KS, Halloran P, Yasui Y. 2007. Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics 8:242. (Pubitemid 47163143)
11. Efron B, Tibshirani R. 2007. On testing the significance of sets of genes. Ann Appl Stat 1:107-129.
12. Goeman JJ, Buhlmann P. 2007. Analyzing gene expression data in terms of gene sets: Methodological issues. Bioinformatics 23:980-987. (Pubitemid 47050585)
13. Göring HH, Curran JE, Johnson MP, Dyer TD, Charlesworth J, Cole SA, Jowett JB, Abraham LJ, Rainwater DL, Comuzzie AG, Mahaney MC, Almasy L, MacCluer JW, Kissebah AH, Collier GR, Moses EK, Blangero J. 2007. Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet 39:1208-1216. (Pubitemid 47482685)
14. Gregersen PK, Silver J, Winchester RJ. 1987. The shared epitope hypothesis. An approach to understanding the molecular genetics of susceptibility to rheumatoid arthritis. Arthritis Rheum 30:1205-1213.
15. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium. 2004. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258-D261. (Pubitemid 38081651)
16. Hinks A, Worthington J, Thomson W. 2006. The association of PTPN22 with rheumatoid arthritis and juvenile idiopathic arthritis. Rheumatology (Oxford) 45:365-368.
17. Lantieri F, Jhun MA, Park J, Park T, Devoto M. 2009. Comparative analysis of different approaches for dealing with candidate regions in the context of a genome-wide association study. BMC Proc 3:S93.
18. Lebrec JJ, Huizinga TWJ, Toes REM, Houwing-Duistermaat JJ, van Houwelingen HC. 2009a. Integration of gene ontogeny pathways with North American Rheumatoid Arthritis Consortium genome-wide association data via linear modeling. BMC Proc 3:S94.
19. Lebrec JJ, Nishchenko I, van der Wijk HJ, Huizinga TW, van Houwelingen HC. 2009b. A polygenic model for integration of linkage and pathway information. Genet Epidemiol 33:198-206.
20. Lewinger JP, Conti DV, Baurley JW, Triche TJ, Thomas DC. 2007. Hierarchical Bayes prioritization of marker associations from a genome-wide association scan for further investigation. Genet Epidemiol 31:871-882.
21. Li C, Li M, Lange EM, Watanabe RM. 2008. Prioritized subset analysis: Improving power in genome-wide association studies. Hum Hered 65:129-141. (Pubitemid 350253953)
22. Li J, Ji L. 2005. Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity 95:221-227. (Pubitemid 43093236)
23. Plenge RM, Seielstad M, Padyukov L, Lee AT, Remmers EF, Ding B, Liew A, Khalili H, Chandrasekaran A, Davies LR, Li W, Tan AK, Bonnard C, Ong RT, Thalamuthu A, Pettersson S, Liu C, Tian C, Chen WV, Carulli JP, Beckman EM, Altshuler D, Alfredsson L, Criswell LA, Amos CI, Seldin MF, Kastner DL, Klareskog L, Gregersen PK. 2007. TRAF1-C5 as a risk locus for rheumatoid arthritis - a genomewide study. N Engl J Med 357:1199-1209.
24. Raychaudhuri S, Remmers EF, Lee AT, Hackett R, Guiducci C, Burtt NP, Gianniny L, Korman BD, Padyukov L, Kurreeman FA, Chang M, Catanese JJ, Ding B, Wong S, van der Helm-van Mil AH, Neale BM, Coblyn J, Cui J, Tak PP, Wolbink GJ, Crusius JB, van der Horst-Bruinsma IE, Criswell LA, Amos CI, Seldin MF, Kastner DL, Ardlie KG, Alfredsson L, Costenbader KH, Altshuler D, Huizinga TW, Shadick NA, Weinblatt ME, de Vries N, Worthington J, Seielstad M, Toes RE, Karlson EW, Begovich AB, Klareskog L, Gregersen PK, Daly MJ, Plenge RM. 2008. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet 40:1216-1223.
25. Remmers EF, Plenge RM, Lee AT, Graham RR, Hom G, Behrens TW, de Bakker PI, Le JM, Lee HS, Batliwalla F, Li W, Masters SL, Booty MG, Carulli JP, Padyukov L, Alfredsson L, Klareskog L, Chen WV, Amos CI, Criswell LA, Seldin MF, Kastner DL, Gregersen PK. 2007. STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med 357:977-986.
26. Sohns M, Rosenberger A, Bickeböller H. 2009. Integration of a priori gene set information into genome-wide association studies. BMC Proc 3:S95.
27. 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. (Pubitemid 41528093)
28. The 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.
29. Tintle NL, Best AA, DeJongh M, Van Bruggen D, Heffron F, Porwollik S, Taylor RC. 2008. Gene set analyses for interpreting microarray experiments on prokaryotic organisms. BMC Bioinformatics 9:469.
30. Tintle NL, Borchers B, Brown M, Bekmetjev A. 2009. Comparing gene set analysis methods on single-nucleotide polymorphism data from Genetic Analysis Workshop 16. BMC Proc 3:S96.
31. Wacholder S, Chanock S, Garcia-Closas M, El Ghormli L, Rothman N. 2004. Assessing the probability that a positive report is false: an approach for molecular epidemiology studies. J Natl Cancer Inst 96:434-442. (Pubitemid 38443646)
32. Wang K, Li M, Bucan M. 2007. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 81:1278-1283. (Pubitemid 350211456)
33. Whitlock MC. 2005. Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach. J Evol Biol 18:1368-1373.