An efficient algorithm to perform multiple testing in epistasis screening

BMC Bioinformatics

Volumn 14, Issue , 2013, Pages

  Lishout, François Van ^a   Mahachie John, Jestinah M ^a   Gusareva, Elena S ^a   Urrea, Victor ^d   Cleynen, Isabelle ^c   Théâtre, Emilie ^a,b   Charloteaux, Benoît ^a   Calle, Malu Luz ^d   Wehenkel, Louis ^a   Steen, Kristel Van ^a  

^a UNIVERSITY OF LIÈGE   (Belgium)

^b UNIVERSITY OF LIÈGE   (Belgium)

^c UNIVERSITY OF LEUVEN   (Belgium)

^d UNIVERSITY OF VIC CENTRAL UNIVERSITY OF CATALONIA   (Spain)

Author keywords

Crohn's disease; Epistasis; GWA studies; maxT; MB MDR; Multiple testing

Indexed keywords

CROHN'S DISEASE; EPISTASIS; GWA STUDIES; MAXT; MB-MDR; MULTIPLE TESTING;

ALGORITHMS; DIAGNOSIS; DISEASES; MULTICORE PROGRAMMING; SOFTWARE TESTING; STATISTICAL TESTS;

GENES;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; CROHN DISEASE; EPISTASIS; GENETIC ASSOCIATION; GENETICS; HUMAN; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; CROHN DISEASE; EPISTASIS, GENETIC; GENETIC ASSOCIATION STUDIES; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84876681553     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-138     Document Type: Article

References (29)

1. Hardy J, Singleton A. Genome-wide association studies and human disease. N Engl J Med 2009, 360:1759-1768. 10.1056/NEJMra0808700, 3422859, 19369657.
2. Manolio TA, Collins FS, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH. Finding the missing heritability of complex diseases. Nature 2009, 461(7265):747-753. 10.1038/nature08494, 2831613, 19812666.
3. Visscher PM, Brown MA, McCarthy MI, Yang J. Five years of GWAS discovery. Am Soc Hum Genet 2012, 90:7-24.
4. Zuk O, Hechter E, Sunyaev SR, Lander ES. The mystery of missing heritability: genetic interactions create phantom heritability. Proc Natl Acad Sci 2012, 109(4):1193-1198. 10.1073/pnas.1119675109, 3268279, 22223662.
5. Van Steen K. Traveling the world of gene-gene interactions. Brief Bioinform 2011, 13:1-19.
6. Calle ML, Urrea V, Malats N, Van Steen K. MB-MDR: model-based multifactor dimensionality reduction for detecting interactions in high-dimensional genomic data. Tech. Rep. 24, Department of Systems Biology, Universitat de Vic, Vic,: Spain; 2008.
7. Calle ML, Urrea V, Vellalta G, Malats N, Van Steen K. Improving strategies for detecting genetic patterns of disease susceptibility in association studies. Stat Med 2008, 27:6532-6546. 10.1002/sim.3431, 18837071.
8. Cattaert T, Calle ML, Dudek SM, Mahachie John JM, Van Lishout F, Urrea V, Ritchie MD, Van Steen K. Model-based multifactor dimensionality reduction for detecting epistasis in case-control data in the presence of noise. Ann Hum Genet 2011, 75:78-89. 10.1111/j.1469-1809.2010.00604.x, 3059142, 21158747.
9. Mahachie John JM, Cattaert T, Van Lishout F, Gusareva E, Van Steen K. Lower-order effects adjustment in quantitative traits model-based multifactor dimensionality reduction. PLoS ONE 2012, 7(1):e29594. http://dx.doi.org/10.1371/journal.pone.0029594, 10.1371/journal.pone.0029594, 3252336, 22242176.
10. Calle ML, Urrea V, Malats N, Van Steen K. mbmdr: an R package for exploring gene-gene interactions associated with binary or quantitative traits. Bioinformatics 2010, 26(17):2198-2199. 10.1093/bioinformatics/btq352, 20595460.
11. Ge Y, Dudoit S, Speed TP. Resampling-based multiple testing for microarray data analysis. Tech. Rep. 633, Department of Statistics: University of California, Berkley; 2003.
12. Westfall PH, Young SS. Resampling-base Multiple Testing 1993, New York: Wiley.
13. Knuth D. The Art of Computer Programming, Volume 3: Sorting and Searching, Second Edition 1998, Addison-Wesley: Reading.
14. Cattaert T, Urrea V, Naj AC, De Lobel L, De Wit V, Fu M, Mahachie John JM, Shen H, Calle ML, Ritchie MD. FAM-MDR: A Flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals. PLoS ONE 2010, 5(4):e10304. http://dx.doi.org/10.1371/journal.pone.0010304, 10.1371/journal.pone.0010304, 2858665, 20421984.
15. Mahachie John JM, Van Lishout F, Van Steen K. Model-based multifactor dimensionality reduction to detect epistasis for quantitative traits in the presence of error-free and noisy data. Eur J Hum Genet 2011, 19(6):696-703. 10.1038/ejhg.2011.17, 3110049, 21407267.
16. Ritchie MD, Hahn LW, Moore JH. Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Genet Epidemil 2003, 24(2):150-157.
17. Libioulle C, Louis E, Hansoul S, Sandor C, Farnir F, Franchimont D, Vermeire S, Dewit O, de Vos M, Dixon A. Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet 2007, 3(4):e58. 10.1371/journal.pgen.0030058, 1853118, 17447842.
18. Barett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 2008, 40(8):955-962. 10.1038/ng.175, 2574810, 18587394.
19. Bush WL, Dudek SM, Ritchie MD. Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pacific Symposium on Biocomputing 2009, 368-379. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859610/pdf/nihms186228.pdf].
20. Raychaudhuri S, Plenge RM, Rossin E, Ng AC, Consortium IS, Purcell SM, Sklar P, Scolnick EM, Xavier RJ, Altshuler D. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet 2009, 5(9):1-15.
21. Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith G, Ahmad T, Lees CW, Balschun T, Lee J, Roberts R. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet 2010, 42(12):1118-1126. 10.1038/ng.717, 3299551, 21102463.
22. Kaser A, Zeissig S, Blumberg RS. Inflammatory bowel disease. Annu Rev Immunol 2010, 28:573-621. 10.1146/annurev-immunol-030409-101225, 20192811.
23. Dalal SR, Kwon HK. The role of MicroRNA in inflammatory bowel disease. Gastroenterol Hepatol 2010, 6:714-722.
24. Watkinson J, Anastassiou D. Synergy disequilibrium plots: graphical visualization of pairwise synergies and redundancies of SNPs with respect to a phenotype. Bioinformatics 2009, 25(11):1445-1446. 10.1093/bioinformatics/btp159, 2682510, 19297347.
25. Taylor KD, Targn SR, Mei L, Ippoliti AF, McGovern D, Mengesha E, King L, Rotter JI. IL23R Haplotypes provide a large population attributable risk for Crohn's disease. Inflamm Bowel Dis 2008, 14(9):1185-1191. 10.1002/ibd.20478, 2574614, 18470928.
26. Zhou X, Richon VM, Wang AH, Yang XJ, Rifkind RA, Marks PA. Histone deacetylase 4 associates with extracellular signal-regulated kinases 1 and 2, and its cellular localization is regulated by oncogenic Ras. Proc Natl Acad Sci USA 2000, 97:14329-14333. 10.1073/pnas.250494697, 18918, 11114188.
27. Sarin R, Wu X, Abraham C. Inflammatory disease protective R381Q IL23 receptor polymorphism results in decreased primary CD4+ and CD8+ human T-cell functional responses. Proc Natl Acad Sci USA 2011,
28. Sinnott-Armstrong NA, Greene CS, Cancare F, Moore JH. Accelerating epistasis analysis in human genetics with consumer graphics hardware. BMC Res Notes 2009, 2:149. 10.1186/1756-0500-2-149, 2732631, 19630950.
29. Wang Z, Wang Y, Tan KL, Wong L, Agrawal D. CEO: a cloud epistasis computing model in GWAS. International Conference on Bioinformatics & Biomedicine; Hong Kong 2010, [http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5706522].