SNP mistyping in genotyping arrays--an important cause of spurious association in case-control studies.
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.
Department of Public Health Sciences, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom. mitryd@gmail.com
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Mitry
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Campbell
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Charteris
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Fleck
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Tenesa
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Dunlop
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Hayward
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Wright
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Vitart
D015982:Bias; D016022:Case-Control Studies; D016000:Cluster Analysis; D055106:Genome-Wide Association Study / Q000706:statistics & numerical data*; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D020641:Polymorphism, Single Nucleotide