Illumina human exome genotyping array clustering and quality control

Yan Guo, Jing He, Shilin Zhao, Hui Wu, Xue Zhong, Quanhu Sheng, David C. Samuels, Yu Shyr, Jirong Long

Research output: Contribution to journalArticlepeer-review

85 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)2643-2662
Number of pages20
JournalNature Protocols
Issue number11
Publication statusPublished - 2014 Nov 27

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)


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