Comparison of the performance of two commercial genome-wide association study genotyping platforms in Han Chinese samples

Jiang, L., Willner, D., Danoy, P., Xu, H., & Brown, M. A. (2013) Comparison of the performance of two commercial genome-wide association study genotyping platforms in Han Chinese samples. G3: Genes, Genomes, Genetics, 3(1), pp. 23-29.

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Most genome-wide association studies to date have been performed in populations of European descent, but there is increasing interest in expanding these studies to other populations. The performance of genotyping chips in Asian populations is not well established. Therefore, we sought to test the performance of widely used fixed-marker, genome-wide association studies chips in the Han Chinese population. Non-HapMap Chinese samples (n = 396) were genotyped using the Illumina OmniExpress and Affymetrix 6.0 platforms, whereas a subset also were genotyped using the Immunochip. Genotyped markers from the Affymetrix 6.0 and Illumina OmniExpress were used for full genome imputation based on the HapMap 2 JPT+CHB (Japanese from Tokyo, Japan and Chinese from Beijing, China) reference panel. The concordance between markers genotypes for the three platforms was very high whether directly genotyped or genotyped and imputed single nucleotide polymorphisms (SNPs; .99.8% for directly genotyped and .99.5% for genotyped and imputed SNPs, respectively) were compared. The OmniExpress chip data enabled more SNPs to be imputed, particularly SNPs with minor allele frequency .5%. The OmniExpress chip achieved better coverage of HapMap SNPs than the Affymetrix 6.0 chip (73.6% vs. 65.9%, respectively, for minor allele frequency .5%). The Affymetrix 6.0 and Illumina OmniExpress chip have similar genotyping accuracy and provide similar accuracy of imputed SNPs. The OmniExpress chip however provides better coverage of Asian HapMap SNPs, although its coverage of HapMap SNPs is moderate. © 2013 Jiang et al.

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ID Code: 89288
Item Type: Journal Article
Refereed: No
Additional Information: Cited By :5
Export Date: 21 September 2015
Correspondence Address: Xu, H.; Department of Rheumatology, Shanghai Changzheng Hospital, The Second Military Medical University, 200003 Shanghai, China; email:
Keywords: Affymetrix 6.0, Genetic, Illumina, Immunochip, OmniExpress, Polymorphisms, accuracy, article, gene frequency, genetic analysis, genetic association, genome, genotype, Han Chinese, haplotype map, heterozygote, homozygote, human, intermethod comparison, single nucleotide polymorphism
DOI: 10.1534/g3.112.004069
ISSN: 2160-1836
Divisions: Current > QUT Faculties and Divisions > Faculty of Health
Current > Institutes > Institute of Health and Biomedical Innovation
Deposited On: 20 Oct 2015 02:06
Last Modified: 25 Oct 2016 23:41

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