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

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 Illumina’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.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00010000417 Illumina OMNIExpress 62
EGAD00010000419 Affymetrix_6.0 62
EGAD00010000421 Affymetrix_6.0 187
EGAD00010000423 Illumina OMNIExpress 213
EGAD00010000425 HanChinese_Immunochip 192
Publications Citations
Comparison of the performance of two commercial genome-wide association study genotyping platforms in Han Chinese samples.
G3 (Bethesda) 3: 2013 23-29
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