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Illumina human exome genotyping array clustering and quality control

Nature Protocols volume 9, pages 2643–2662 (2014)Cite this article

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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.

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Figure 1: Examples of low-quality clusters for the haploid genomes described in Steps 7–22.
Figure 2: Example clusters relevant to Steps 23–25.
Figure 3: General distribution of the basic quality control (QC) parameters.
Figure 4: Example clusters relevant to Steps 26 and 27.
Figure 5: Example clusters relevant to Steps 28–30.
Figure 6: Example clusters relevant to Step 34A.
Figure 7: Example clusters relevant to Steps 38 and 39 of the PROCEDURE.
Figure 8: Example clusters relevant to Steps 40–43.
Figure 9: Distribution of HWE and heterozygosity rates relevant to Steps 46–50.
Figure 10: Example clusters relevant to the PLINK-related Steps 53–56.
Figure 11: Example clusters relevant to the PLINK-related Steps 53–56.
Figure 12: Example clusters relevant to the PLINK-related Step 57.

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Acknowledgements

Development of this protocol is supported by Cancer Center Support Grant (CCSG) nos. (P30 CA068485) and R01CA158473. We thank M. Bjoring for editorial support.

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Authors and Affiliations

  1. Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee, USA

    Yan Guo, Shilin Zhao, Hui Wu, Xue Zhong, Quanhu Sheng & Yu Shyr

  2. Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, USA

    Jing He & Jirong Long

  3. Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA

    David C Samuels

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Contributions

Y.G. wrote the manuscript and designed the protocol with J.L.; S.Z., J.H., H.W., Q.S. and X.Z. contributed to script writing and generated the figures and tables; Y.S. and D.C.S. provided intellectual contributions to the overall design of the protocol.

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Correspondence to Yan Guo.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Example clusters relevant to the Step 34A of the Procedure.

Cartesian plot of the same two SNPs shown in Figure 6. The x-axis denotes normalized intensity value of A allele. The y-axis denotes normalized intensity value of B allele.

Supplementary information

Supplementary Figure 1

Example clusters relevant to the Step 34A of the Procedure. (PDF 965 kb)

Supplementary Table 1

Markers distributions of major SNP arrays. (XLSX 9 kb)

Supplementary Table 2

SNPs that do not match HG19 plus strand after perform Step 24 and 25. (XLSX 12 kb)

Supplementary Table 3

HAPMAP trio samples used in the example study. (XLSX 15 kb)

Supplementary Table 4

Supplementary script list. (XLSX 10 kb)

Supplementary Table 5

Resource files used in the protocol. (XLSX 9 kb)

Supplementary Table 6

AIMs on the exome chip. (XLSX 40 kb)

Supplementary Table 7

Identical and triallelic SNPs on the exome chip. (XLSX 57 kb)

Supplementary Table 8

SNPs with different alleles between the exome chip and the 1000 Genomes Project. (XLSX 21 kb)

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Guo, Y., He, J., Zhao, S. et al. Illumina human exome genotyping array clustering and quality control. Nat Protoc 9, 2643–2662 (2014). https://doi.org/10.1038/nprot.2014.174

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