SNP mistyping in genotyping arrays-an important cause of spurious association in case-control studies

Genetic Epidemiology

Volumn 35, Issue 5, 2011, Pages 423-426

  Mitry, D ^a   Campbell, H ^a   Charteris, D G ^b   Fleck, B W ^a   Tenesa, A ^c   Dunlop, M G ^c   Hayward, C ^c   Wright, A F ^c   Vitart, V ^c  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b MOORFIELDS EYE HOSPITAL   (United Kingdom)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

False association; Genome wide association; Genotyping

Indexed keywords

ARTICLE; CASE CONTROL STUDY; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENOTYPE; HUMAN; QUALITY CONTROL; REPLICATION STUDY; SINGLE NUCLEOTIDE POLYMORPHISM;

BIAS (EPIDEMIOLOGY); CASE-CONTROL STUDIES; CLUSTER ANALYSIS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 79958113078     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20559     Document Type: Article

References (10)

1. Aulchenko YS, Ripke S, Isaacs A, Van Duijn CM. 2007. GenABEL: an R library for genome-wide association analysis. Bioinformatics. 23:1294-1296.
2. 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.
3. Clayton DG, Leung HT. 2007. An R package for analysis of whole-genome association studies. Hum Hered 64:45-51.
4. Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, Maier LM, Smink LJ, Lam AC, Ovington NR, Stevens HE, Nutland S, Howson JM, Faham M, Moorhead M, Jones HB, Falkowski M, Hardenbol P, Willis TD, Todd JA. 2005. Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 37:1243-1246.
5. Lasky-Su J, Lyon HN, Emilsson V, Heid IM, Molony C, Raby BA, Lazarus R, Klanderman B, Soto-Quiros ME, Avila L, Silverman EK, Thorleifsson G, Thorsteinsdottir U, Kronenberg F, Vollmert C, Illig T, Fox CS, Levy D, Laird N, Ding X, McQueen MB, Butler J, Ardlie K, Papoutsakis C, Dedoussis G, O'Donnell CJ, Wichmann HE, Celedón JC, Schadt E, Hirschhorn J, Weiss ST, Stefansson K, Lange C. 2008. On the replication of genetic associations: timing can be everything! Am J Hum Genet 82:849-858.
6. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hirschhorn JN. 2008. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9:356-369.
7. Plagnol V, Cooper JD, Todd JA, Clayton DG. 2007. A method to address differential bias in genotyping in large-scale association studies. PLoS Genet 3:e74.
8. Pluzhnikov A, Below JE, Konkashbaev A, Tikhomirov A, Kistner-Griffin E, Roe CA, Nicolae DL, Cox NJ. 2010. Spoiling the whole bunch: quality control aimed at preserving the integrity of high-throughput genotyping. Am J Hum Genet 87:123-128.
9. 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.
10. Tenesa A, Farrington SM, Prendergast JG, Porteous ME, Walker M, Haq N, Barnetson RA, Theodoratou E, Cetnarskyj R, Cartwright N, Semple C, Clark AJ, Reid FJ, Smith LA, Kavoussanakis K, Koessler T, Pharoah PD, Buch S, Schafmayer C, Tepel J, Schreiber S, Völzke H, Schmidt CO, Hampe J, Chang-Claude J, Hoffmeister M, Brenner H, Wilkening S, Canzian F, Capella G, Moreno V, Deary IJ, Starr JM, Tomlinson IP, Kemp Z, Howarth K, Carvajal-Carmona L, Webb E, Broderick P, Vijayakrishnan J, Houlston RS, Rennert G, Ballinger D, Rozek L, Gruber SB, Matsuda K, Kidokoro T, Nakamura Y, Zanke BW, Greenwood CM, Rangrej J, Kustra R, Montpetit A, Hudson TJ, Gallinger S, Campbell H, Dunlop MG. 2008. Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat Genet 40:631-637.