Genome-wide association scans for secondary traits using case-control samples

Genetic Epidemiology

Volumn 33, Issue 8, 2009, Pages 717-728

  Monsees, Genevieve M ^a   Tamimi, Rulla M ^a,b   Kraft, Peter ^a  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Ascertainment bias; Biomarker; Case control; Directed acyclic graph; Efficiency; Genome wide association studies; Inverse probability weighting

Indexed keywords

FIBROBLAST GROWTH FACTOR RECEPTOR 2;

ARTICLE; BREAST CANCER; DISEASE MARKER; GENETIC ASSOCIATION; GENETIC TRAIT; GENOME ANALYSIS; GENOTYPE; HUMAN; MAMMOGRAPHY; NULL HYPOTHESIS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REGRESSION ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMATIC ERROR; TYPE I ERROR; VALIDATION PROCESS;

ALLELES; BREAST NEOPLASMS; CASE-CONTROL STUDIES; COHORT STUDIES; COMPUTER SIMULATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MAMMOGRAPHY; MODELS, STATISTICAL; PROBABILITY; RECEPTOR, FIBROBLAST GROWTH FACTOR, TYPE 2; REGRESSION ANALYSIS; REPRODUCIBILITY OF RESULTS; RISK;

EID: 70449575858     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20424     Document Type: Article

References (26)

1. Amos CI, Wu X, Broderick P, Gorlov IP, Gu J, Eisen T, Dong Q, Zhang Q, Gu X, Vijayakrishnan J, Sullivan K, Matakidou A, Wang Y, Mills G, Doheny K, Tsai YY, Chen WV, Shete S, Spitz MR, Houlston RS. 2008. Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat Genet 40:616-622. (Pubitemid 351601203)
2. Chanock SJ, Hunter DJ. 2008. Genomics: when the smoke clears. Nature 452:537-538.
3. Chanock SJ, Manolio T, Boehnke M, Boerwinkle E, Hunter DJ, Thomas G, Hirschhorn JN, Abecasis G, Altshuler D, Bailey-Wilson JE, Brooks LD, Cardon LR, Daly M, Donnelly P, Fraumeni Jr JF, Freimer NB, Gerhard DS, Gunter C, Guttmacher AE, Guyer MS, Harris EL, Hoh J, Hoover R, Kong CA, Merikangas KR, Morton CC, Palmer LJ, Phimister EG, Rice JP, Roberts J, Rotimi C, Tucker MA, Vogan KJ, Wacholder S, Wijsman EM, Winn DM, Collins FS. 2007. Replicating genotype-phenotype associations. Nature 447:655-660.
4. Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, BallingerDG, Struewing JP, Morrison J, FieldH, Luben R, WarehamN, Ahmed S, Healey CS, Bowman R; SEARCH collaborators, Meyer KB, Haiman CA, Kolonel LK, Henderson BE, Le Marchand L, Brennan P, Sangrajrang S, Gaborieau V, Odefrey F, Shen CY, Wu PE, Wang HC, Eccles D, Evans DG, Peto J, Fletcher O, Johnson N, Seal S, StrattonMR, Rahman N, Chenevix-Trench G, Bojesen SE, Nordestgaard BG, Axelsson CK, Garcia-Closas M, Brinton L, Chanock S, Lissowska J, Peplonska B,NevanlinnaH, FagerholmR, EerolaH, Kang D, Yoo KY, Noh DY, Ahn SH, Hunter DJ, Hankinson SE, Cox DG, Hall P, Wedren S, Liu J, Low YL, Bogdanova N, Schürmann P, Dörk T, Tollenaar RA, Jacobi CE, Devilee P, Klijn JG, Sigurdson AJ, Doody MM, Alexander BH, Zhang J, Cox A, Brock IW, MacPherson G, Reed MW, Couch FJ, Goode EL, Olson JE, Meijers-Heijboer H, van den Ouweland A, Uitterlinden A, Rivadeneira F, Milne RL, Ribas G, Gonzalez-Neira A, Benitez J, Hopper JL, McCredie M, Southey M, Giles GG, Schroen C, Justenhoven C, Brauch H, Hamann U, Ko YD, Spurdle AB, Beesley J, Chen X, kConFab; AOCS Management Group, Mannermaa A, Kosma VM, Kataja V, Hartikainen J, Day NE, Cox DR, Ponder BA. 2007. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447:1087-1093.
5. Eeles RA, Kote-Jarai Z, Giles GG, Olama AA, Guy M, Jugurnauth SK, Mulholland S, Leongamornlert DA, Edwards SM, Morrison J, Field HI, Southey MC, Severi G, Donovan JL, Hamdy FC, Dearnaley DP, Muir KR, Smith C, Bagnato M, Ardern-Jones AT, Hall AL, O'Brien LT, Gehr-Swain BN, Wilkinson RA, Cox A, Lewis S, Brown PM, Jhavar SG, Tymrakiewicz M, Lophatananon A, Bryant SL; UK Genetic Prostate Cancer Study Collaborators; British Association of Urological Surgeons' Section of Oncology; UK ProtecT Study Collaborators, Horwich A, Huddart RA, Khoo VS, Parker CC, Woodhouse CJ, Thompson A, Christmas T, Ogden C, Fisher C, Jamieson C, Cooper CS, English DR, Hopper JL, Neal DE, Easton DF. 2008. Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 40:316-321.
6. Greenland S, Pearl J, Robins JM. 1999. Causal diagrams for epidemiologic research. Epidemiology 10:37-48.
7. Hung RJ, McKay JD, Gaborieau V, Boffetta P, Hashibe M, Zaridze D, Mukeria A, Szeszenia-Dabrowska N, Lissowska J, Rudnai P, Fabianova E, Mates D, Bencko V, Foretova L, Janout V, Chen C, Goodman G, Field JK, Liloglou T, Xinarianos G, Cassidy A, McLaughlin J, Liu G, Narod S, Krokan HE, Skorpen F, Elvestad MB, Hveem K, Vatten L, Linseisen J, Clavel-Chapelon F, Vineis P, Bueno-de-Mesquita HB, Lund E, Martinez C, Bingham S, Rasmuson T, Hainaut P, Riboli E, Ahrens W, Benhamou S, Lagiou P, Trichopoulos D, Holcátová I, Merletti F, Kjaerheim K, Agudo A, Macfarlane G, Talamini R, Simonato L, Lowry R, Conway DI, Znaor A, Healy C, Zelenika D, Boland A, Delepine M, Foglio M, Lechner D, Matsuda F, Blanche H, Gut I, Heath S, Lathrop M, Brennan P. 2008. A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature 452:633-637.
8. Hunter DJ, Kraft P. 2007. Drinking from the fire hose-statistical issues in genomewide association studies. N Engl J Med 357:436-439. (Pubitemid 47204871)
9. Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, Wacholder S, Wang Z, Welch R, Hutchinson A, Wang J, Yu K, Chatterjee N, Orr N, Willett WC, Colditz GA, Ziegler RG, Berg CD, Buys SS, McCarty CA, Feigelson HS, Calle EE, Thun MJ, Hayes RB, Tucker M, Gerhard DS, Fraumeni Jr JF, Hoover RN, Thomas G, Chanock SJ. 2007. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 39:870-874. (Pubitemid 47014500)
10. Kraft P. 2007. Analyses of genome-wide association scans for additional outcomes. Epidemiology 18:838. (Pubitemid 350295187)
11. Kraft P, Yen YC, Stram DO, Morrison J, Gauderman WJ. 2007. Exploiting gene-environment interaction to detect genetic associations. Hum Hered 63:111-119. (Pubitemid 46272239)
12. Langholz B, Rothman N, Wacholder S, Thomas DC. 1999. Cohort studies for characterizing measured genes. J Natl Cancer Inst Monogr 26:39-42.
13. Lauritzen S, Dawid A, Larsen B, Leimer H. 1990. Independence properties of directed Markov fields. Networks 20:491-505.
14. Lettre G, Jackson AU, Gieger C, Schumacher FR, Berndt SI, Sanna S, Eyheramendy S, Voight BF, Butler JL, Guiducci C, Illig T, Hackett R, Heid IM, Jacobs KB, Lyssenko V, Uda M; Diabetes Genetics Initiative; FUSION; KORA; Prostate, Lung Colorectal and Ovarian Cancer Screening Trial; Nurses' Health Study; SardiNIA, Boehnke M, Chanock SJ, Groop LC, Hu FB, Isomaa B, Kraft P, Peltonen L, Salomaa V, Schlessinger D, Hunter DJ, Hayes RB, Abecasis GR, Wichmann HE, Mohlke KL, Hirschhorn JN. 2008. Identification of ten loci associated with height highlights new biological pathways in human growth. Nat Genet 40:584-591. (Pubitemid 351601214)
15. Loos RJ, Lindgren CM, Li S, Wheeler E, Zhao JH, Prokopenko I, Inouye M, Freathy RM, Attwood AP, Beckmann JS, Berndt SI; Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial, Jacobs KB, Chanock SJ, Hayes RB, Bergmann S, Bennett AJ, Bingham SA, Bochud M, Brown M, Cauchi S, Connell JM, Cooper C, Smith GD, Day I, Dina C, De S, Dermitzakis ET, Doney AS, Elliott KS, Elliott P, Evans DM, Sadaf Farooqi I, Froguel P, Ghori J, Groves CJ, Gwilliam R, Hadley D, Hall AS, Hattersley AT, Hebebrand J, Heid IM; KORA, Lamina C, Gieger C, Illig T, Meitinger T, Wichmann HE, Herrera B, Hinney A, Hunt SE, Jarvelin MR, Johnson T, Jolley JD, Karpe F, Keniry A, Khaw KT, Luben RN, Mangino M, Marchini J, McArdle WL, McGinnis R, Meyre D, Munroe PB, Morris AD, Ness AR, Neville MJ, Nica AC, Ong KK, O'Rahilly S, Owen KR, Palmer CN, Papadakis K, Potter S, Pouta A, Qi L; Nurses' Health Study, Randall JC, Rayner NW, Ring SM, Sandhu MS, Scherag A, Sims MA, Song K, Soranzo N, Speliotes EK; Diabetes Genetics Initiative, Syddall HE, Teichmann SA, Timpson NJ, Tobias JH, Uda M; SardiNIA Study, Vogel CI, Wallace C, Waterworth DM, Weedon MN; Wellcome Trust Case Control Consortium, Willer CJ; FUSION, Wraight, Yuan X, Zeggini E, Hirschhorn JN, Strachan DP, Ouwehand WH, Caulfield MJ, Samani NJ, Frayling TM, Vollenweider P, Waeber G, Mooser V, Deloukas P, McCarthy MI, Wareham NJ, Barroso I, Jacobs KB, Chanock SJ, Hayes RB, Lamina C, Gieger C, Illig T, Meitinger T, Wichmann HE, Kraft P, Hankinson SE, Hunter DJ, Hu FB, Lyon HN, Voight BF, Ridderstrale M, Groop L, Scheet P, Sanna S, Abecasis GR, Albai G, Nagaraja R, Schlessinger D, Jackson AU, Tuomilehto J, Collins FS, Boehnke M, Mohlke KL. 2008. Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat Genet 40:768-775. (Pubitemid 351748863)
16. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559-575. (Pubitemid 47330214)
17. Reilly M, Pepe MS. 1995. Amean score method formissing and auxiliary covariate data in regression models. Biometrika 82:299-314.
18. Richardson DB, Rzehak P, Klenk J, Weiland SK. 2007. Analyses of case-control data for additional outcomes. Epidemiology 18:441-445. (Pubitemid 46955309)
19. Robins JM. 1995. Semiparametric efficiency in multivariate regression models with missing data. J Am Stat Assoc 90:122-129.
20. Robins JM, Rotnitzky A, Zhao L. 1995. Analysis of semiparametric regression models for repeated outcomes in the presence of missing data. J Am Stat Assoc 90:106-121.
21. Robins JM, Smoller JW, Lunetta KL. 2001. On the validity of the TDT test in the presence of comorbidity and ascertainment bias. Genet Epidemiol 21:326-336.
22. Sanna S, Jackson AU, Nagaraja R, Willer CJ, Chen WM, Bonnycastle LL, Shen H, Timpson N, Lettre G, Usala G, Chines PS, Stringham HM, Scott LJ, Dei M, Lai S, Albai G, Crisponi L, Naitza S, Doheny KF, Pugh EW, Ben-Shlomo Y, Ebrahim S, Lawlor DA, Bergman RN, Watanabe RM, Uda M, Tuomilehto J, Coresh J, Hirschhorn JN, Shuldiner AR, Schlessinger D, Collins FS, Davey Smith G, Boerwinkle E, Cao A, Boehnke M, Abecasis GR, Mohlke KL. 2008. Common variants in the GDF5-UQCC region are associated with variation in human height. Nat Genet 40:198-203. (Pubitemid 351171401)
23. Siegmund KD, Whittemore AS, Thomas DC. 1999. Multistage sampling for disease family registries. J Natl Cancer Inst Monogr 26:43-48.
24. Thorgeirsson TE, Geller F, Sulem P, Rafnar T, Wiste A, Magnusson KP, Manolescu A, Thorleifsson G, Stefansson H, Ingason A, Stacey SN, Bergthorsson JT, Thorlacius S, Gudmundsson J, Jonsson T, Jakobsdottir M, Saemundsdottir J, Olafsdottir O, Gudmundsson LJ, Bjornsdottir G, Kristjansson K, Skuladottir H, Isaksson HJ, Gudbjartsson T, Jones GT, Mueller T, Gottsäter A, Flex A, Aben KK, de Vegt F, Mulders PF, Isla D, Vidal MJ, Asin L, Saez B, Murillo L, Blondal T, Kolbeinsson H, Stefansson JG, Hansdottir I, Runarsdottir V, Pola R, Lindblad B, van Rij AM, Dieplinger B, Haltmayer M, Mayordomo JI, Kiemeney LA, Matthiasson SE, Oskarsson H, Tyrfingsson T, Gudbjartsson DF, Gulcher JR, Jonsson S, Thorsteinsdottir U, Kong A, Stefansson K. 2008. A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. Nature 452:638-642.
25. Wacholder S. 1996. The case-control study as data missing by design: estimating risk differences. Epidemiology 7:144-150. (Pubitemid 26068046)
26. Weedon MN, Lettre G, Freathy RM, Lindgren CM, Voight BF, Perry JR, Elliott KS, Hackett R, Guiducci C, Shields B, Zeggini E, Lango H, Lyssenko V, Timpson NJ, Burtt NP, Rayner NW, Saxena R, Ardlie K, Tobias JH, Ness AR, Ring SM, Palmer CN, Morris AD, Peltonen L, Salomaa V; Diabetes Genetics Initiative; Wellcome Trust Case Control Consortium, Davey Smith G, Groop LC, Hattersley AT, McCarthy MI, Hirschhorn JN, Frayling TM. 2007. A common variant of HMGA2 is associated with adult and childhood height in the general population. Nat Genet 39:1245-1250. (Pubitemid 47485762)