Natural and orthogonal model for estimating gene-gene interactions applied to cutaneous melanoma

Human Genetics

Volumn 133, Issue 5, 2014, Pages 559-574

  Xiao, Feifei ^a   Ma, Jianzhong ^b   Cai, Guoshuai ^c   Fang, Shenying ^c   Lee, Jeffrey E ^c   Wei, Qingyi ^c   Amos, Christopher I ^d  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF TEXAS   (United States)

^c UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^d DARTMOUTH MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CANCER RISK; CDKN2A GENE; CHROMOSOME 15Q; CHROMOSOME 16Q; CHROMOSOME 4; CHROMOSOME 5; CHROMOSOME 9P; CONTROLLED STUDY; CUTANEOUS MELANOMA; EPISTASIS; GENE INTERACTION; GENE LOCUS; GENETIC PREDISPOSITION; GENETIC RISK; GENETIC TRAIT; HERC2 GENE; HUMAN; MAJOR CLINICAL STUDY; MC1R GENE; ONCOGENE; PRIORITY JOURNAL; SIMULATION; STATISTICAL MODEL;

CHROMOSOME MAPPING; EPISTASIS, GENETIC; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MELANOMA; MODELS, GENETIC; SKIN NEOPLASMS;

EID: 84899644043     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-013-1392-2     Document Type: Article

References (28)

1. Alvarez-Castro JM, Carlborg O (2007) A unified model for functional and statistical epistasis and its application in quantitative trait Loci analysis. Genetics 176(2):1151-1167. doi: 10.1534/genetics.106.067348
2. Alvarez-Castro JM, Le Rouzic A, Carlborg O (2008) How to perform meaningful estimates of genetic effects. PLoS Genet 4(5):e1000062. doi: 10.1371/journal.pgen.1000062
3. Amos CI, Wang LE, Lee JE, Gershenwald JE, Chen WV, Fang S, Kosoy R, Zhang M, Qureshi AA, Vattathil S, Schacherer CW, Gardner JM, Wang Y, Bishop DT, Barrett JH, MacGregor S, Hayward NK, Martin NG, Duffy DL, Mann GJ, Cust A, Hopper J, Brown KM, Grimm EA, Xu Y, Han Y, Jing K, McHugh C, Laurie CC, Doheny KF, Pugh EW, Seldin MF, Han J, Wei Q (2011) Genome-wide association study identifies novel loci predisposing to cutaneous melanoma. Hum Mol Genet 20(24):5012-5023. doi: 10.1093/hmg/ddr415
4. Bishop DT, Demenais F, Iles MM, Harland M, Taylor JC, Corda E, Randerson-Moor J, Aitken JF, Avril MF, Azizi E, Bakker B, Bianchi-Scarra G, Bressac-de Paillerets B, Calista D, Cannon-Albright LA, Chin AWT, Debniak T, Galore-Haskel G, Ghiorzo P, Gut I, Hansson J, Hocevar M, Hoiom V, Hopper JL, Ingvar C, Kanetsky PA, Kefford RF, Landi MT, Lang J, Lubinski J, Mackie R, Malvehy J, Mann GJ, Martin NG, Montgomery GW, van Nieuwpoort FA, Novakovic S, Olsson H, Puig S, Weiss M, van Workum W, Zelenika D, Brown KM, Goldstein AM, Gillanders EM, Boland A, Galan P, Elder DE, Gruis NA, Hayward NK, Lathrop GM, Barrett JH, Bishop JA (2009) Genome-wide association study identifies three loci associated with melanoma risk. Nat Genet 41(8):920-925. doi: 10.1038/ng.411
5. Breen MS, Kemena C, Vlasov PK, Notredame C, Kondrashov FA (2012) Epistasis as the primary factor in molecular evolution. Nature. doi: 10.1038/nature11510
6. Capasso M, Diskin SJ, Totaro F, Longo L, De Mariano M, Russo R, Cimmino F, Hakonarson H, Tonini GP, Devoto M, Maris JM, Iolascon A (2013) Replication of GWAS-identified neuroblastoma risk loci strengthens the role of BARD1 and affirms the cumulative effect of genetic variations on disease susceptibility. Carcinogenesis 34(3):605-611. doi: 10.1093/carcin/bgs380
7. Chung Y, Lee SY, Elston RC, Park T (2007) Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions. Bioinformatics 23(1):71-76. doi: 10.1093/bioinformatics/btl557
8. Cordell HJ (2009) Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10(6):392-404. doi: 10.1038/nrg2579
9. Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews TD, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, Blaszczyk K, Bowes J, Brand OJ, Braund PS, Bredin F, Breen G, Brown MJ, Bruce IN, Bull J, Burren OS, Burton J, Byrnes J, Caesar S, Clee CM, Coffey AJ, Connell JM, Cooper JD, Dominiczak AF, Downes K, Drummond HE, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans DM, Evans G, Eyre S, Farmer A, Ferrier IN, Feuk L, Fitzgerald T, Flynn E, Forbes A, Forty L, Franklyn JA, Freathy RM, Gibbs P, Gilbert P, Gokumen O, Gordon-Smith K, Gray E, Green E, Groves CJ, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman GA, Hocking L, Howard E, Howard P, Howson JM, Hughes D, Hunt S, Isaacs JD, Jain M, Jewell DP, Johnson T, Jolley JD, Jones IR, Jones LA, Kirov G, Langford CF, Lango-Allen H, Lathrop GM, Lee J, Lee KL, Lees C, Lewis K, Lindgren CM, Maisuria-Armer M, Maller J, Mansfield J, Martin P, Massey DC, McArdle WL, McGuffin P, McLay KE, Mentzer A, Mimmack ML, Morgan AE, Morris AP, Mowat C, Myers S, Newman W, Nimmo ER, O'Donovan MC, Onipinla A, Onyiah I, Ovington NR, Owen MJ, Palin K, Parnell K, Pernet D, Perry JR, Phillips A, Pinto D, Prescott NJ, Prokopenko I, Quail MA, Rafelt S, Rayner NW, Redon R, Reid DM, Renwick, Ring SM, Robertson N, Russell E, St Clair D, Sambrook JG, Sanderson JD, Schuilenburg H, Scott CE, Scott R, Seal S, Shaw-Hawkins S, Shields BM, Simmonds MJ, Smyth DJ, Somaskantharajah E, Spanova K, Steer S, Stephens J, Stevens HE, Stone MA, Su Z, Symmons DP, Thompson JR, Thomson W, Travers ME, Turnbull C, Valsesia A, Walker M, Walker NM, Wallace C, Warren-Perry M, Watkins NA, Webster J, Weedon MN, Wilson AG, Woodburn M, Wordsworth BP, Young AH, Zeggini E, Carter NP, Frayling TM, Lee C, McVean G, Munroe PB, Palotie A, Sawcer SJ, Scherer SW, Strachan DP, Tyler-Smith C, Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Gough SC, Hall AS, Hattersley AT, Hill AV, Mathew CG, Pembrey M, Satsangi J, Stratton MR, Worthington J, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand W, Parkes M, Rahman N, Todd JA, Samani NJ, Donnelly P (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464(7289):713-720. doi: 10.1038/nature08979
10. Culverhouse R, Suarez BK, Lin J, Reich T (2002) A perspective on epistasis: limits of models displaying no main effect. Am J Hum Genet 70(2):461-471. doi: 10.1086/338759
11. Ehret GB, Munroe PB, Rice KM, Bochud M, Johnson AD, Chasman DI, Smith AV, Tobin MD, Verwoert GC, Hwang SJ, Pihur V, Vollenweider P, O'Reilly PF, Amin N, Bragg-Gresham JL, Teumer A, Glazer NL, Launer L, Zhao JH, Aulchenko Y, Heath S, Sober S, Parsa A, Luan J, Arora P, Dehghan A, Zhang F, Lucas G, Hicks AA, Jackson AU, Peden JF, Tanaka T, Wild SH, Rudan I, Igl W, Milaneschi Y, Parker AN, Fava C, Chambers JC, Fox ER, Kumari M, Go MJ, van der Harst P, Kao WH, Sjogren M, Vinay DG, Alexander M, Tabara Y, Shaw-Hawkins S, Whincup PH, Liu Y, Shi G, Kuusisto J, Tayo B, Seielstad M, Sim X, Nguyen KD, Lehtimaki T, Matullo G, Wu Y, Gaunt TR, Onland-Moret NC, Cooper MN, Platou CG, Org E, Hardy R, Dahgam S, Palmen J, Vitart V, Braund PS, Kuznetsova T, Uiterwaal CS, Adeyemo A, Palmas W, Campbell H, Ludwig B, Tomaszewski M, Tzoulaki I, Palmer ND, Aspelund T, Garcia M, Chang YP, O'Connell JR, Steinle NI, Grobbee DE, Arking DE, Kardia SL, Morrison AC, Hernandez D, Najjar S, McArdle WL, Hadley D, Brown MJ, Connell JM, Hingorani AD, Day IN, Lawlor DA, Beilby JP, Lawrence RW, Clarke R, Hopewell JC, Ongen H, Dreisbach AW, Li Y, Young JH, Bis JC, Kahonen M, Viikari J, Adair LS, Lee NR, Chen MH, Olden M, Pattaro C, Bolton JA, Kottgen A, Bergmann S, Mooser V, Chaturvedi N, Frayling TM, Islam M, Jafar TH, Erdmann J, Kulkarni SR, Bornstein SR, Grassler J, Groop L, Voight BF, Kettunen J, Howard P, Taylor A, Guarrera S, Ricceri F, Emilsson V, Plump A, Barroso I, Khaw KT, Weder AB, Hunt SC, Sun YV, Bergman RN, Collins FS, Bonnycastle LL, Scott LJ, Stringham HM, Peltonen L, Perola M, Vartiainen E, Brand SM, Staessen JA, Wang TJ, Burton PR, Soler Artigas M, Dong Y, Snieder H, Wang X, Zhu H, Lohman KK, Rudock ME, Heckbert SR, Smith NL, Wiggins KL, Doumatey A, Shriner D, Veldre G, Viigimaa M, Kinra S, Prabhakaran D, Tripathy V, Langefeld CD, Rosengren A, Thelle DS, Corsi AM, Singleton A, Forrester T, Hilton G, McKenzie CA, Salako T, Iwai N, Kita Y, Ogihara T, Ohkubo T, Okamura T, Ueshima H, Umemura S, Eyheramendy S, Meitinger T, Wichmann HE, Cho YS, Kim HL, Lee JY, Scott J, Sehmi JS, Zhang W, Hedblad B, Nilsson P, Smith GD, Wong A, Narisu N, Stancakova A, Raffel LJ, Yao J, Kathiresan S, O'Donnell CJ, Schwartz SM, Ikram MA, Longstreth WT Jr, Mosley TH, Seshadri S, Shrine NR, Wain LV, Morken MA, Swift AJ, Laitinen J, Prokopenko I, Zitting P, Cooper JA, Humphries SE, Danesh J, Rasheed A, Goel A, Hamsten A, Watkins H, Bakker SJ, van Gilst WH, Janipalli CS, Mani KR, Yajnik CS, Hofman A, Mattace-Raso FU, Oostra BA, Demirkan A, Isaacs A, Rivadeneira F, Lakatta EG, Orru M, Scuteri A, Ala-Korpela M, Kangas AJ, Lyytikainen LP, Soininen P, Tukiainen T, Wurtz P, Ong RT, Dorr M, Kroemer HK, Volker U, Volzke H, Galan P, Hercberg S, Lathrop M, Zelenika D, Deloukas P, Mangino M, Spector TD, Zhai G, Meschia JF, Nalls MA, Sharma P, Terzic J, Kumar MV, Denniff M, Zukowska-Szczechowska E, Wagenknecht LE, Fowkes FG, Charchar FJ, Schwarz PE, Hayward C, Guo X, Rotimi C, Bots ML, Brand E, Samani NJ, Polasek O, Talmud PJ, Nyberg F, Kuh D, Laan M, Hveem K, Palmer LJ, van der Schouw YT, Casas JP, Mohlke KL, Vineis P, Raitakari O, Ganesh SK, Wong TY, Tai ES, Cooper RS, Laakso M, Rao DC, Harris TB, Morris RW, Dominiczak AF, Kivimaki M, Marmot MG, Miki T, Saleheen D, Chandak GR, Coresh J, Navis G, Salomaa V, Han BG, Zhu X, Kooner JS, Melander O, Ridker PM, Bandinelli S, Gyllensten UB, Wright AF, Wilson JF, Ferrucci L, Farrall M, Tuomilehto J, Pramstaller PP, Elosua R, Soranzo N, Sijbrands EJ, Altshuler D, Loos RJ, Shuldiner AR, Gieger C, Meneton P, Uitterlinden AG, Wareham NJ, Gudnason V, Rotter JI, Rettig R, Uda M, Strachan DP, Witteman JC, Hartikainen AL, Beckmann JS, Boerwinkle E, Vasan RS, Boehnke M, Larson MG, Jarvelin MR, Psaty BM, Abecasis GR, Chakravarti A, Elliott P, van Duijn CM, Newton-Cheh C, Levy D, Caulfield MJ, Johnson T (2011) Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature 478(7367):103-109. doi: 10.1038/nature10405
12. Gayan J, Gonzalez-Perez A, Bermudo F, Saez ME, Royo JL, Quintas A, Galan JJ, Moron FJ, Ramirez-Lorca R, Real LM, Ruiz A (2008) A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis. BMC genomics 9:360. doi: 10.1186/1471-2164-9-360
13. Ghilardi N, Li J, Hongo JA, Yi S, Gurney A, de Sauvage FJ (2002) A novel type I cytokine receptor is expressed on monocytes, signals proliferation, and activates STAT-3 and STAT-5. J Biol Chem 277(19):16831-16836. doi: 10.1074/jbc.M201140200
14. Hahn LW, Ritchie MD, Moore JH (2003) Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 19(3):376-382
15. Kraft P, Yen YC, Stram DO, Morrison J, Gauderman WJ (2007) Exploiting gene-environment interaction to detect genetic associations. Hum Hered 63(2):111-119. doi: 10.1159/000099183
16. Ma J, Xiao F, Xiong M, Andrew AS, Brenner H, Duell EJ, Haugen A, Hoggart C, Hung RJ, Lazarus P, Liu C, Matsuo K, Mayordomo JI, Schwartz AG, Staratschek-Jox A, Wichmann E, Yang P, Amos CI (2012) Natural and orthogonal interaction framework for modeling gene-environment interactions with application to lung cancer. Hum Hered 73(4):185-194. doi: 10.1159/000339906
17. Moore JH (2003) The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered 56(1-3):73-82. doi: 73735
18. Nagel RL (2001) Pleiotropic and epistatic effects in sickle cell anemia. Curr Opin Hematol 8(2):105-110
19. Nagel RL (2005) Epistasis and the genetics of human diseases. CR Biol 328(7):606-615. doi: 10.1016/j.crvi.2005.05.003
20. Nobori T, Miura K, Wu DJ, Lois A, Takabayashi K, Carson DA (1994) Deletions of the cyclin-dependent kinase-4 inhibitor gene in multiple human cancers. Nature 368(6473):753-756. doi: 10.1038/368753a0
21. Rajapakse I, Perlman MD, Martin PJ, Hansen JA, Kooperberg C (2012) Multivariate detection of gene-gene interactions. Genet Epidemiol 36(6):622-630. doi: 10.1002/gepi.21656
22. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH (2001) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69(1):138-147. doi: 10.1086/321276
23. Siegel R, Naishadham D, Jemal A (2012) Cancer statistics, 2012. CA Cancer J Clin 62(1):10-29. doi: 10.3322/caac.20138
24. Sturm RA, Duffy DL, Zhao ZZ, Leite FP, Stark MS, Hayward NK, Martin NG, Montgomery GW (2008) A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. Am J Hum Genet 82(2):424-431. doi: 10.1016/j.ajhg.2007.11.005
25. Visser M, Kayser M, Palstra RJ (2012) HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter. Genome Res 22(3):446-455. doi: 10.1101/gr.128652.111
26. Wandstrat A, Wakeland E (2001) The genetics of complex autoimmune diseases: non-MHC susceptibility genes. Nat Immunol 2(9):802-809
27. Wilson EB (1902) Mendel's principles of heredity and the maturation of the germ-cells. Science 16(416):991-993. doi: 10.1126/science.16.416.991-b
28. Xiao F, Ma J, Amos CI (2013) A unified framework integrating parent-of-origin effects for association study. PLoS One 8(8):e72208. doi: 10.1371/journal.pone.0072208