title: Quality control procedures for genome-wide association studies.
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.
authors.affiliation: Center for Human Genetics Research, Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, USA.
authors.forename: Stephen
authors.initials: S
authors.lastname: Turner
authors.forename: Loren L
authors.initials: LL
authors.lastname: Armstrong
authors.forename: Yuki
authors.initials: Y
authors.lastname: Bradford
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Carlson
authors.forename: Dana C
authors.initials: DC
authors.lastname: Crawford
authors.forename: Andrew T
authors.initials: AT
authors.lastname: Crenshaw
authors.forename: Mariza
authors.initials: M
authors.lastname: de Andrade
authors.forename: Kimberly F
authors.initials: KF
authors.lastname: Doheny
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: Haines
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Hayes
authors.forename: Gail
authors.initials: G
authors.lastname: Jarvik
authors.forename: Lan
authors.initials: L
authors.lastname: Jiang
authors.forename: Iftikhar J
authors.initials: IJ
authors.lastname: Kullo
authors.forename: Rongling
authors.initials: R
authors.lastname: Li
authors.forename: Hua
authors.initials: H
authors.lastname: Ling
authors.forename: Teri A
authors.initials: TA
authors.lastname: Manolio
authors.forename: Martha
authors.initials: M
authors.lastname: Matsumoto
authors.forename: Catherine A
authors.initials: CA
authors.lastname: McCarty
authors.forename: Andrew N
authors.initials: AN
authors.lastname: McDavid
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Mirel
authors.forename: Justin E
authors.initials: JE
authors.lastname: Paschall
authors.forename: Elizabeth W
authors.initials: EW
authors.lastname: Pugh
authors.forename: Luke V
authors.initials: LV
authors.lastname: Rasmussen
authors.forename: Russell A
authors.initials: RA
authors.lastname: Wilke
authors.forename: Rebecca L
authors.initials: RL
authors.lastname: Zuvich
authors.forename: Marylyn D
authors.initials: MD
authors.lastname: Ritchie
mesh_terms: D057286:Electronic Health Records; D055106:Genome-Wide Association Study / Q000379:methods / Q000592:standards*; D023281:Genomics; D005838:Genotype; D006801:Humans; D010641:Phenotype; D011786:Quality Control; D012984:Software