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

ABSTRACT: Affymetrix 6.0, Illumina OMNIExpress, and llumina Immunochip genotype data for Han Chinese population including rheumatoid arthritis cases and controls. Data is in PLINK binary format. Illumina genotype clustering was performed using Illuminaâ€™s BeadStudio software. SNPs were reclustered using the study samples, low quality subjects were removed, and a subset of clustering results were manually inspected and verified. All SNPs with GenCall scores less than 0.15 were excluded. For Affymetrix chips, clustering was performed using the program Birdseed version 2, as implemented using Affymetrix Genotyper Console v4.0, using the default quality control (QC) thresholds.

PROVIDER: EGAS00000000131 | EGA |

REPOSITORIES: EGA

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

Jiang Lei L Willner Dana D Danoy Patrick P Xu Huji H Brown Matthew A MA

G3 (Bethesda, Md.) 20130101 1

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 Affym ...[more]

PMID: 23316436

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