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

D Mitry; H Campbell; D G Charteris; B W Fleck; A Tenesa; M G Dunlop; C Hayward; A F Wright; V Vitart

doi:10.1002/gepi.20559

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

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

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Pages (from-to)	423-6
Number of pages	4
Journal	Genetic Epidemiology
Volume	35
Issue number	5
DOIs	https://doi.org/10.1002/gepi.20559
Publication status	Published - 2011

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10.1002/gepi.20559

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abstract = "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.",

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AU - Fleck, B W

AU - Tenesa, A

AU - Dunlop, M G

AU - Hayward, C

AU - Wright, A F

AU - Vitart, V

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AB - 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.

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JO - Genetic Epidemiology

JF - Genetic Epidemiology

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ER -

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

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