Artifact due to differential error when cases and controls are imputed from different platforms

Human Genetics

Volumn 131, Issue 1, 2012, Pages 111-119

  Sinnott, Jennifer A ^a   Kraft, Peter ^a  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; ARTIFACT; CONTROLLED STUDY; GENETIC ASSOCIATION; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMATIC ERROR;

ALGORITHMS; ARTIFACTS; BREAST NEOPLASMS; CASE-CONTROL STUDIES; DIABETES MELLITUS, TYPE 2; DNA; FEMALE; GENE FREQUENCY; GENETIC MARKERS; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; ROC CURVE;

EID: 84856686798     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-011-1054-1     Document Type: Article

References (25)

1. B Alberts 2010 Editorial expression of concern Science 330 6006 912 10.1126/science.330.6006.912-b 21071647 10.1126/science.330.6006.912-b 1:CAS:528:DC%2BC3cXhsVyqtb%2FF
2. GW Beecham ER Martin JR Gilbert JL Haines MA Pericak-Vance 2010 APOE is not associated with alzheimer disease: a cautionary tale of genotype imputation Ann Hum Genet 74 3 189 94 10.1111/j.1469-1809.2010.00573.x 20529013 10.1111/j.1469-1809.2010.00573.x 1:CAS:528:DC%2BC3cXntVyms7k%3D
3. Carmichael M (2010) The little flaw in the longevity-gene study that could be a big problem. http://www.newsweek.com/2010/07/07/the-little-flaw-in- the-longevity-gene-study-that-could-be-a-big-problem.html
4. B Devlin K Roeder 1999 Genomic control for association studies Biometrics 55 4 997 1004 11315092 10.1111/j.0006-341X.1999.00997.x 1:STN:280: DC%2BD3M3itFSqtA%3D%3D
5. MD Fallin M Szymanski R Wang A Gherman SS Bassett D Avramopoulos 2010 Fine mapping of the chromosome 10q11-q21 linkage region in Alzheimer's disease cases and controls Neurogenetics 11 3 335 48 10.1007/s10048-010-0234-9 20182759 10.1007/s10048-010-0234-9 1:CAS:528:DC%2BC3cXns1ymsLk%3D
6. LA Ho EM Lange 2010 Using public control genotype data to increase power and decrease cost of case-control genetic association studies Hum Genet 128 6 597 608 10.1007/s00439-010-0880-x 20821337 10.1007/s00439-010-0880-x
7. G Hom RR Graham B Modrek KE Taylor W Ortmann S Garnier AT Lee SA Chung RC Ferreira PVK Pant DG Ballinger R Kosoy FY Demirci MI Kamboh AH Kao C Tian I Gunnarsson AA Bengtsson S Rantapaa-Dahlqvist M Petri S Manzi MF Seldin L Ronnblom AC Syvanen LA Criswell PK Gregersen TW Behrens 2008 Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N Engl J Med 358 9 900 909 10.1056/NEJMoa0707865 18204098 10.1056/NEJMoa0707865 1:CAS:528:DC%2BD1cXisF2hsLs%3D (Pubitemid 351397089)
8. Howie BN, Donnelly P, Marchini J (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5(6):e1000,529. doi: 10.1371/journal.pgen.1000529
9. DJ Hunter P Kraft KB Jacobs DG Cox M Yeager SE Hankinson S Wacholder Z Wang R Welch A Hutchinson J Wang K Yu N Chatterjee N Orr WC Willett GA Colditz RG Ziegler CD Berg SS Buys CA McCarty HS Feigelson EE Calle MJ Thun RB Hayes M Tucker DS Gerhard JFJ Fraumeni RN Hoover G Thomas SJ Chanock 2007 A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer Nat Genet 39 7 870 874 10.1038/ng2075 17529973 10.1038/ng2075 1:CAS:528:DC%2BD2sXmvFKlsLg%3D (Pubitemid 47014500)
10. Y Li C Willer S Sanna G Abecasis 2009 Genotype imputation Annu Rev Genomics Hum Genet 10 387 406 10.1146/annurev.genom.9.081307.164242 19715440 10.1146/annurev.genom.9.081307.164242 1:CAS:528:DC%2BD1MXht12qsrjP
11. Y Li CJ Willer J Ding P Scheet GR Abecasis 2010 MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes Genet Epidemiol 34 8 816 834 10.1002/gepi.20533 21058334 10.1002/gepi.20533
12. D Luca S Ringquist L Klei AB Lee C Gieger HE Wichmann S Schreiber M Krawczak Y Lu A Styche B Devlin K Roeder M Trucco 2008 On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants Am J Hum Genet 82 2 453 63 10.1016/j.ajhg.2007.11.003 18252225 10.1016/j.ajhg.2007.11.003 1:CAS:528:DC%2BD1cXit1Sisr0%3D
13. J Marchini B Howie 2010 Genotype imputation for genome-wide association studies Nat Rev Genet 11 7 499 511 10.1038/nrg2796 20517342 10.1038/nrg2796 1:CAS:528:DC%2BC3cXovVekurs%3D
14. MI McCarthy GR Abecasis LR Cardon DB Goldstein J Little JPA Ioannidis JN Hirschhorn 2008 Genome-wide association studies for complex traits: consensus, uncertainty and challenges Nat Rev Genet 9 5 356 369 10.1038/nrg2344 18398418 10.1038/nrg2344 1:CAS:528:DC%2BD1cXkvVOhs7Y%3D (Pubitemid 351556063)
15. V Moskvina N Craddock P Holmans MJ Owen MC O'Donovan 2006 Effects of differential genotyping error rate on the type I error probability of case-control studies Hum Hered 61 1 55 64 10.1159/000092553 16612103 10.1159/000092553 (Pubitemid 43804599)
16. N Patterson AL Price D Reich 2006 Population structure and eigenanalysis PLoS Genet 2 12 e190 10.1371/journal.pgen.0020190 17194218 10.1371/journal.pgen. 0020190 (Pubitemid 46045188)
17. AL Price NJ Patterson RM Plenge ME Weinblatt NA Shadick D Reich 2006 Principal components analysis corrects for stratification in genome-wide association studies Nat Genet 38 8 904 909 10.1038/ng1847 16862161 10.1038/ng1847 1:CAS:528:DC%2BD28XnsVCgsrg%3D (Pubitemid 44141658)
18. S Purcell B Neale K Todd-Brown L Thomas MAR Ferreira D Bender J Maller P Sklar PIW de Bakker MJ Daly PC Sham 2007 PLINK: a tool set for whole-genome association and population-based linkage analyses Am J Hum Genet 81 3 559 575 10.1086/519795 17701901 10.1086/519795 1:CAS:528:DC%2BD2sXhtVSqurrL (Pubitemid 47330214)
19. L Qi MC Cornelis P Kraft KJ Stanya WH Linda Kao JS Pankow J Dupuis JC Florez CS Fox G Pare Q Sun CJ Girman CC Laurie DB Mirel TA Manolio DI Chasman E Boerwinkle PM Ridker DJ Hunter JB Meigs CH Lee FB Hu RM van Dam 2010 Genetic variants at 2q24 are associated with susceptibility to type 2 diabetes Hum Mol Genet 19 13 2706 2715 10.1093/hmg/ddq156 20418489 10.1093/hmg/ddq156 1:CAS:528:DC%2BC3cXntlCquro%3D
20. R Development Core Team (2009) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, URL http://www.R-project.org, ISBN 3-900051-07-0
21. LJ Scott KL Mohlke LL Bonnycastle CJ Willer Y Li WL Duren MR Erdos HM Stringham PS Chines AU Jackson L Prokunina-Olsson CJ Ding AJ Swift N Narisu T Hu R Pruim R Xiao XY Li KN Conneely NL Riebow AG Sprau M Tong PP White KN Hetrick MW Barnhart CW Bark JL Goldstein L Watkins F Xiang J Saramies TA Buchanan RM Watanabe TT Valle L Kinnunen GR Abecasis EW Pugh KF Doheny RN Bergman J Tuomilehto FS Collins M Boehnke 2007 A genome-wide association study of type 2 diabetes in finns detects multiple susceptibility variants Science 316 5829 1341 1345 10.1126/science.1142382 17463248 10.1126/science.1142382 1:CAS:528:DC%2BD2sXmtVyitrY%3D (Pubitemid 46871655)
22. Sebastiani P, Solovieff N, Puca A, Hartley S, Melista E, Andersen S, Dworkis D, Wilk J, Myers R, Steinberg M, Montano M, Baldwin C, Perls T (2010) Genetic signatures of exceptional longevity in humans. Science doi: 10.1126/science.1190532
23. 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(7145):661-678. doi: 10.1038/nature05911 (Pubitemid 46889737)
24. M Wrensch RB Jenkins JS Chang RF Yeh Y Xiao PA Decker KV Ballman M Berger JC Buckner S Chang C Giannini C Halder TM Kollmeyer ML Kosel DH LaChance L McCoy BP O'Neill J Patoka AR Pico M Prados C Quesenberry T Rice AL Rynearson I Smirnov T Tihan J Wiemels P Yang JK Wiencke 2009 Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility Nat Genet 41 8 905 908 10.1038/ng.408 19578366 10.1038/ng.408 1:CAS:528:DC%2BD1MXotVClt7w%3D
25. JJ Zhuang K Zondervan F Nyberg C Harbron A Jawaid LR Cardon BJ Barratt AP Morris 2010 Optimizing the power of genome-wide association studies by using publicly available reference samples to expand the control group Genet Epidemiol 34 4 319 326 10.1002/gepi.20482 20088020 10.1002/gepi.20482