title: Quality Control for the Illumina HumanExome BeadChip.
abstract: The Illumina HumanExome BeadChip and other exome-based genotyping arrays offer inexpensive genotyping of some 240,000 mostly nonsynonymous coding variants across the human genome. The HumanExome chip, with its highly non-uniform distribution of markers and emphasis on rare coding variants, presents some unique challenges for quality control (QC) and data cleaning. Here, we describe QC procedures for HumanExome data, with examples of challenges specific to exome arrays from our experience cleaning a data set of ∼7,500 samples from the NEIGHBORHOOD Consortium. We focus on standard procedures for QC of genome-wide array data including genotype calling, sex verification, sample identity verification, relationship checking, and population structure that are complicated by the HumanExome panel's enrichment in rare, exonic variation. © 2016 by John Wiley & Sons, Inc.
authors.affiliation: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio.
authors.forename: Robert P
authors.initials: RP
authors.lastname: Igo
authors.affiliation: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio.
authors.forename: Jessica N
authors.initials: JN
authors.lastname: Cooke Bailey
authors.affiliation: Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland.
authors.forename: Jane
authors.initials: J
authors.lastname: Romm
authors.affiliation: Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio.|Institute of Computational Biology, Case Western Reserve University, Cleveland, Ohio.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: Haines
authors.affiliation: Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts.
authors.forename: Janey L
authors.initials: JL
authors.lastname: Wiggs
mesh_terms: D059472:Exome / Q000235:genetics*; D005260:Female; D015894:Genome, Human / Q000235:genetics*; D005838:Genotype; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011786:Quality Control; D012730:Sex Chromosomes / Q000235:genetics; D000073359:Exome Sequencing / Q000295:instrumentation* / Q000379:methods / Q000592:standards*
keywords: Illumina HumanExome BeadChip; NEIGHBORHOOD Consortium; exome arrays; genetic association studies; quality control