HYST: A hybrid set-based test for genome-wide association studies, with application to protein-protein interaction-based association analysis

American Journal of Human Genetics

Volumn 91, Issue 3, 2012, Pages 478-488

  Li, Miao Xin ^a   Kwan, Johnny S H ^a   Sham, Pak C ^a,b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; COMPUTER SIMULATION; CROHN DISEASE; EFFECT SIZE; GENE; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; HUMAN; HYBRID SET BASED TEST; NON INSULIN DEPENDENT DIABETES MELLITUS; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; RHEUMATOID ARTHRITIS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE;

EID: 84866127370     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2012.08.004     Document Type: Article

References (47)

1. Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S., and Manolio, T.A. (2009). Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA 106, 9362-9367.
2. Eichler, E.E., Flint, J., Gibson, G., Kong, A., Leal, S.M., Moore, J.H., and Nadeau, J.H. (2010). Missing heritability and strategies for finding the underlying causes of complex disease. Nat. Rev. Genet. 11, 446-450.
3. Manolio, T.A., Collins, F.S., Cox, N.J., Goldstein, D.B., Hindorff, L.A., Hunter, D.J., McCarthy, M.I., Ramos, E.M., Cardon, L.R., Chakravarti, A., et al. (2009). Finding the missing heritability of complex diseases. Nature 461, 747-753.
4. Yang, J., Benyamin, B., McEvoy, B.P., Gordon, S., Henders, A.K., Nyholt, D.R., Madden, P.A., Heath, A.C., Martin, N.G., Montgomery, G.W., et al. (2010). Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42, 565-569.
5. Yang, J., Manolio, T.A., Pasquale, L.R., Boerwinkle, E., Caporaso, N., Cunningham, J.M., de Andrade, M., Feenstra, B., Feingold, E., Hayes, M.G., et al. (2011). Genome partitioning of genetic variation for complex traits using common SNPs. Nat. Genet. 43, 519-525.
6. Ghoussaini, M., Fletcher, O., Michailidou, K., Turnbull, C., Schmidt, M.K., Dicks, E., Dennis, J., Wang, Q., Humphreys, M.K., Luccarini, C., et al.; Netherlands Collaborative Group on Hereditary Breast and Ovarian Cancer (HEBON); Familial Breast Cancer Study (FBCS); Gene Environment Interaction of Breast Cancer in Germany (GENICA) Network; kConFab Investigators; Australian Ovarian Cancer Study Group. (2012). Genome-wide association analysis identifies three new breast cancer susceptibility loci. Nat. Genet. 44, 312-318.
7. Paternoster, L., Standl, M., Chen, C.M., Ramasamy, A., Bønnelykke, K., Duijts, L., Ferreira, M.A., Alves, A.C., Thyssen, J.P., Albrecht, E., et al.; Australian Asthma Genetics Consortium (AAGC); Genetics of Overweight Young Adults (GOYA) Consortium; EArly Genetics & Lifecourse Epidemiology (EAGLE) Consortium. (2012). Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatitis. Nat. Genet. 44, 187-192.
8. Curtis, D., Vine, A.E., and Knight, J. (2008). A simple method for assessing the strength of evidence for association at the level of the whole gene. Adv. Appl. Bioinform. Chem. 1, 115-120.
9. Dudbridge, F., and Koeleman, B.P. (2003). Rank truncated product of P-values, with application to genomewide association scans. Genet. Epidemiol. 25, 360-366. (Pubitemid 37486884)
10. Liu, J.Z., McRae, A.F., Nyholt, D.R., Medland, S.E.,Wray, N.R., Brown, K.M., Hayward, N.K., Montgomery, G.W., Visscher, P.M., Martin, N.G., and Macgregor, S.; AMFS Investigators. (2010). A versatile gene-based test for genome-wide association studies. Am. J. Hum. Genet. 87, 139-145.
11. Li, M.X., Gui, H.S., Kwan, J.S., and Sham, P.C. (2011). GATES: A rapid and powerful gene-based association test using extended Simes procedure. Am. J. Hum. Genet. 88, 283-293.
12. Moskvina, V., O'Dushlaine, C., Purcell, S., Craddock, N., Holmans, P., and O'Donovan, M.C. (2011). Evaluation of an approximation method for assessment of overall significance of multiple-dependent tests in a genomewide association study. Genet. Epidemiol. 35, 861-866.
13. Ge, H.,Walhout, A.J., and Vidal, M. (2003). Integrating 'omic' information: A bridge between genomics and systems biology. Trends Genet. 19, 551-560. (Pubitemid 37204914)
14. Bork, P., Jensen, L.J., von Mering, C., Ramani, A.K., Lee, I., and Marcotte, E.M. (2004). Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol. 14, 292-299. (Pubitemid 38749056)
15. Di Pietro, S.M., and Dell'Angelica, E.C. (2005). The cell biology of Hermansky-Pudlak syndrome: Recent advances. Traffic 6, 525-533. (Pubitemid 40872355)
16. Lim, J., Hao, T., Shaw, C., Patel, A.J., Szabó, G., Rual, J.F., Fisk, C.J., Li, N., Smolyar, A., Hill, D.E., et al. (2006). A proteinprotein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125, 801-814. (Pubitemid 43732348)
17. Jensen, M.K., Pers, T.H., Dworzynski, P., Girman, C.J., Brunak, S., and Rimm, E.B. (2011). Protein interaction-based genomewide analysis of incident coronary heart disease. Circ. Cardiovasc. Genet. 4, 549-556.
18. Rossin, E.J., Lage, K., Raychaudhuri, S., Xavier, R.J., Tatar, D., Benita, Y., Cotsapas, C., and Daly, M.J.; International Inflammatory Bowel Disease Genetics Constortium. (2011). Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet. 7, e1001273.
19. Barrenas, F., Chavali, S., Holme, P., Mobini, R., and Benson, M. (2009). Network properties of complex human disease genes identified through genome-wide association studies. PLoS ONE 4, e8090.
20. Neale, B.M., Kou, Y., Liu, L., Ma'ayan, A., Samocha, K.E., Sabo, A., Lin, C.F., Stevens, C.,Wang, L.S., Makarov, V., et al. (2012). Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 485, 242-245.
21. Jia, P., Zheng, S., Long, J., Zheng, W., and Zhao, Z. (2011). dmGWAS: Dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics 27, 95-102.
22. Akula, N., Baranova, A., Seto, D., Solka, J., Nalls, M.A., Singleton, A., Ferrucci, L., Tanaka, T., Bandinelli, S., Cho, Y.S., et al.; Bipolar Disorder Genome Study (BiGS) Consortium; Wellcome Trust Case-Control Consortium. (2011). A network-based approach to prioritize results from genomewide association studies. PLoS ONE 6, e24220.
23. Brown, M.B. (1975). A method for combining non-independent, one-sided tests of significance. Biometrics 31, 987-992.
24. Satterthwaite, F.E. (1946). An approximate distribution of estimates of variance components. Biometrics 2, 110-114.
25. Hou, C.D. (2005). A simple approximation for the distribution of the weighted combination of non-independent or independent probabilities. Stat. Probab. Lett. 73, 179-187.
26. Cochran, W.G. (1954). The combination of estimates from different experiments. Biometrics 10, 101-129.
27. Higgins, J.P., Thompson, S.G., Deeks, J.J., and Altman, D.G. (2003). Measuring inconsistency in meta-analyses. BMJ 327, 557-560. (Pubitemid 37088507)
28. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J., and Sham, P.C. (2007). PLINK: A tool set for wholegenome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575. (Pubitemid 47330214)
29. Wu, M.C., Kraft, P., Epstein, M.P., Taylor, D.M., Chanock, S.J., Hunter, D.J., and Lin, X. (2010). Powerful SNP-set analysis for case-control genome-wide association studies. Am. J. Hum. Genet. 86, 929-942.
30. Montana, G. (2005). HapSim: A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients. Bioinformatics 21, 4309-4311. (Pubitemid 41724314)
31. Jensen, L.J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M., et al. (2009). STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 37 (Database issue), D412-D416.
32. Barrett, J.C., Hansoul, S., Nicolae, D.L., Cho, J.H., Duerr, R.H., Rioux, J.D., Brant, S.R., Silverberg, M.S., Taylor, K.D., Barmada, M.M., et al.; NIDDK IBD Genetics Consortium; Belgian-French IBD Consortium; Wellcome Trust Case Control Consortium. (2008). Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat. Genet. 40, 955-962.
33. Stahl, E.A., Raychaudhuri, S., Remmers, E.F., Xie, G., Eyre, S., Thomson, B.P., Li, Y., Kurreeman, F.A.S., Zhernakova, A., Hinks, A., et al.; BIRAC Consortium; YEAR Consortium. (2010). Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat. Genet. 42, 508-514.
34. Zeggini, E., Scott, L.J., Saxena, R., Voight, B.F., Marchini, J.L., Hu, T., de Bakker, P.I.W., Abecasis, G.R., Almgren, P., Andersen, G., et al.; Wellcome Trust Case Control Consortium. (2008). Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat. Genet. 40, 638-645. (Pubitemid 351601209)
35. Devlin, B., and Roeder, K. (1999). Genomic control for association studies. Biometrics 55, 997-1004.
36. Kung, A.W., Xiao, S.M., Cherny, S., Li, G.H., Gao, Y., Tso, G., Lau, K.S., Luk, K.D., Liu, J.M., Cui, B., et al. (2010). Association of JAG1 with bone mineral density and osteoporotic fractures: A genome-wide association study and follow-up replication studies. Am. J. Hum. Genet. 86, 229-239.
37. Ferguson, L.R., Han, D.Y., Fraser, A.G., Huebner, C., Lam,W.J., Morgan, A.R., Duan, H., and Karunasinghe, N. (2010). Genetic factors in chronic inflammation: Single nucleotide polymorphisms in the STAT-JAK pathway, susceptibility to DNA damage and Crohn's disease in a New Zealand population. Mutat. Res. 690, 108-115.
38. Deleuran, M., Buhl, L., Ellingsen, T., Harada, A., Larsen, C.G., Matsushima, K., and Deleuran, B. (1996). Localization of monocyte chemotactic and activating factor (MCAF/MCP-1) in psoriasis. J. Dermatol. Sci. 13, 228-236. (Pubitemid 27062689)
39. Maharshak, N., Hart, G., Ron, E., Zelman, E., Sagiv, A., Arber, N., Brazowski, E., Margalit, R., Elinav, E., and Shachar, I. (2010). CCL2 (pM levels) as a therapeutic agent in Inflammatory Bowel Disease models in mice. Inflamm. Bowel Dis. 16, 1496-1504.
40. Zintzaras, E., and Lau, J. (2008). Trends in meta-analysis of genetic association studies. J. Hum. Genet. 53, 1-9.
41. Marchini, J., Howie, B., Myers, S., McVean, G., and Donnelly, P. (2007). A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39, 906-913. (Pubitemid 47014502)
42. Casals, F., Idaghdour, Y., Hussin, J., and Awadalla, P. (2012). Next-generation sequencing approaches for genetic mapping of complex diseases. J. Neuroimmunol. 248, 10-22.
43. Purcell, S., Daly, M.J., and Sham, P.C. (2007). WHAP: Haplotype-based association analysis. Bioinformatics 23, 255-256. (Pubitemid 46189621)
44. Wang, K., Li, M., and Bucan, M. (2007). Pathway-based approaches for analysis of genomewide association studies. Am. J. Hum. Genet. 81, 1278-1283. (Pubitemid 350211456)
45. Kanehisa, M., and Goto, S. (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30. (Pubitemid 30047706)
46. Heng, H.H. (2008). The gene-centric concept: A new liability? Bioessays 30, 196-197. (Pubitemid 351196955)
47. Wilkins, A.S. (2007). For the biotechnology industry, the penny drops (at last): Genes are not autonomous agents but function within networks!. Bioessays 29, 1179-1181. (Pubitemid 350221784)