title: Illumina human exome genotyping array clustering and quality control.
abstract: With the rise of high-throughput sequencing technology, traditional genotyping arrays are gradually being replaced by sequencing technology. Against this trend, Illumina has introduced an exome genotyping array that provides an alternative approach to sequencing, especially suited to large-scale genome-wide association studies (GWASs). The exome genotyping array targets the exome plus rare single-nucleotide polymorphisms (SNPs), a feature that makes it substantially more challenging to process than previous genotyping arrays that targeted common SNPs. Researchers have struggled to generate a reliable protocol for processing exome genotyping array data. The Vanderbilt Epidemiology Center, in cooperation with Vanderbilt Technologies for Advanced Genomics Analysis and Research Design (VANGARD), has developed a thorough exome chip-processing protocol. The protocol was developed during the processing of several large exome genotyping array-based studies, which included over 60,000 participants combined. The protocol described herein contains detailed clustering techniques and robust quality control procedures, and it can benefit future exome genotyping array-based GWASs.
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA.
authors.forename: Yan
authors.identifier: 0000000152523960
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: He
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA.
authors.forename: Shilin
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Wu
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA.
authors.forename: Xue
authors.initials: X
authors.lastname: Zhong
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA.
authors.forename: Quanhu
authors.identifier: 0000000189519295
authors.initials: Q
authors.lastname: Sheng
authors.affiliation: Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Samuels
authors.affiliation: Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Shyr
authors.affiliation: Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, USA.
authors.forename: Jirong
authors.initials: J
authors.lastname: Long
mesh_terms: D016000:Cluster Analysis; D059472:Exome; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D012984:Software