Quality control procedures for genome-wide association studies.

Stephen Turner; Loren L. Armstrong; Yuki Bradford; Christopher S. Carlson; Dana C. Crawford; Andrew T. Crenshaw; Mariza de Andrade; Kimberly F. Doheny; Jonathan L. Haines; Geoffrey Hayes; Gail Jarvik; Lan Jiang; Iftikhar J. Kullo; Rongling Li; Hua Ling; Teri A. Manolio; Martha Matsumoto; Catherine A. McCarty; Andrew N. McDavid; Daniel B. Mirel; Justin E. Paschall; Elizabeth W. Pugh; Luke V. Rasmussen; Russell A. Wilke; Rebecca L. Zuvich; Marylyn D. Ritchie

doi:10.1002/0471142905.hg0119s68

Quality control procedures for genome-wide association studies.

Stephen Turner, Loren L. Armstrong, Yuki Bradford, Christopher S. Carlson, Dana C. Crawford, Andrew T. Crenshaw, Mariza de Andrade, Kimberly F. Doheny, Jonathan L. Haines, Geoffrey Hayes, Gail Jarvik, Lan Jiang, Iftikhar J. Kullo, Rongling Li, Hua Ling, Teri A. Manolio, Martha Matsumoto, Catherine A. McCarty, Andrew N. McDavid, Daniel B. MirelJustin E. Paschall, Elizabeth W. Pugh, Luke V. Rasmussen, Russell A. Wilke, Rebecca L. Zuvich, Marylyn D. Ritchie

Administration (DMED)

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256 Scopus citations

Abstract

Genome-wide association studies (GWAS) are being conducted at an unprecedented rate in population-based cohorts and have increased our understanding of the pathophysiology of complex disease. Regardless of context, the practical utility of this information will ultimately depend upon the quality of the original data. Quality control (QC) procedures for GWAS are computationally intensive, operationally challenging, and constantly evolving. Here we enumerate some of the challenges in QC of GWAS data and describe the approaches that the electronic MEdical Records and Genomics (eMERGE) network is using for quality assurance in GWAS data, thereby minimizing potential bias and error in GWAS results. We discuss common issues associated with QC of GWAS data, including data file formats, software packages for data manipulation and analysis, sex chromosome anomalies, sample identity, sample relatedness, population substructure, batch effects, and marker quality. We propose best practices and discuss areas of ongoing and future research.

Original language	English (US)
Article number	1.19
Journal	Current Protocols in Human Genetics
Volume	Chapter 1
Issue number	SUPPL.68
DOIs	https://doi.org/10.1002/0471142905.hg0119s68
State	Published - Jan 1 2011

Keywords

Biobanks
Electronic medical records
eMERGE
Genome-wide association studies
GWAS quality control
QC

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Turner, S., Armstrong, L. L., Bradford, Y., Carlson, C. S., Crawford, D. C., Crenshaw, A. T., de Andrade, M., Doheny, K. F., Haines, J. L., Hayes, G., Jarvik, G., Jiang, L., Kullo, I. J., Li, R., Ling, H., Manolio, T. A., Matsumoto, M., McCarty, C. A., McDavid, A. N., ... Ritchie, M. D. (2011). Quality control procedures for genome-wide association studies. Current Protocols in Human Genetics, Chapter 1(SUPPL.68), Article 1.19. https://doi.org/10.1002/0471142905.hg0119s68

Turner, S, Armstrong, LL, Bradford, Y, Carlson, CS, Crawford, DC, Crenshaw, AT, de Andrade, M, Doheny, KF, Haines, JL, Hayes, G, Jarvik, G, Jiang, L, Kullo, IJ, Li, R, Ling, H, Manolio, TA, Matsumoto, M, McCarty, CA, McDavid, AN, Mirel, DB, Paschall, JE, Pugh, EW, Rasmussen, LV, Wilke, RA, Zuvich, RL & Ritchie, MD 2011, 'Quality control procedures for genome-wide association studies.', Current Protocols in Human Genetics, vol. Chapter 1, no. SUPPL.68, 1.19. https://doi.org/10.1002/0471142905.hg0119s68

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Quality control procedures for genome-wide association studies.

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Keywords

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