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

Abstract

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.

Keywords: Affymetrix 6.0; Illumina OmniExpress; Immunochip; genetic polymorphisms.

Figure 1

Study sample size. The total number of individuals genotyped by each platform is indicated under the platform name. Sample sizes in overlap regions represent the number of study subjects genotyped by two or more platforms.

Figure 2

Concordance vs. MAF and R² for genotyping platforms. Each data point represents a genetic marker genotyped on one platform and imputed by the other. Concordance represents the proportion of subjects for which the directly obtained and imputed genotypes were the same, and MAF and R² were calculated using PLINK.