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SNP mistyping in genotyping arrays—an important cause of spurious association in case‐control studies
Author(s) -
Mitry D.,
Campbell H.,
Charteris D.G.,
Fleck B.W.,
Tenesa A.,
Dunlop M.G.,
Hayward C.,
Wright A.F.,
Vitart V.
Publication year - 2011
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/gepi.20559
Subject(s) - spurious relationship , genotyping , genetic association , snp , genome wide association study , replication (statistics) , biology , genetics , genotype , snp genotyping , computational biology , population , single nucleotide polymorphism , computer science , medicine , gene , machine learning , environmental health , virology
Using genome‐wide association studies to identify genetic variants contributing to disease has been highly successful with many novel genetic predispositions identified and biological pathways revealed. Several pitfalls for spurious association or non‐replication have been highlighted: from population structure, automated genotype scoring for cases and controls, to age‐varying association. We describe an important yet unreported source of bias in case‐control studies due to variations in chip technology between different commercial array releases. As cases are commonly genotyped with newer arrays and freely available control resources are frequently used for comparison, there exists an important potential for false associations which are robust to standard quality control and replication design. Genet. Epidemiol . 2011. © 2011 Wiley‐Liss, Inc. 35:423‐426, 2011