All samples except those in the OUH replication cohort were genotyped using Illumina HumanHap550 BeadChip or the Human610-Quad arrays. The 530,000 SNPs that are overlapped by these two platforms were included in the study. Samples in the OUH replication cohort were genotyped using the Affymetrix GeneChip 500 K Mapping Array Set.
Genechip 500 k mapping array set
Manufactured by Thermo Fisher Scientific
The GeneChip 500 K Mapping Array Set is a high-throughput genetic analysis platform designed for genome-wide association studies. It contains two arrays that enable the interrogation of approximately 500,000 single nucleotide polymorphisms (SNPs) across the human genome. The arrays are used for genotyping analysis to identify genetic variations associated with specific traits or diseases.
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Lab products found in correlation
3 protocols using genechip 500 k mapping array set
1
Genome-wide SNP Genotyping Protocol
2
Comparative GWAS Analysis of Bipolar Disorder
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The W-test is then applied to two real bipolar GWAS datasets. The first dataset is from the Wellcome Trust Case Control Consortium (WTCCC), comprising 2000 bipolar cases and 3000 controls of European Caucasians (21 (link)). The dataset includes 500 568 SNPs genotyped with GeneChip 500K Mapping Array Set (Affymetrix Chip). The second dataset is from the Genetic Association Information Network (GAIN) project (22 (link)). The GAIN data is composed of an American ancestry population with a bipolar phenotype, which contains 653 cases and 1767 controls. The data includes 906 600 SNPs genotyped with Affymetrix 6.0 platform. Quality control is performed: SNPs with high missing rates (>5%), MAF < 1%, and which depart from the Hardy–Weinberg equilibrium are excluded (23 (link)). After the quality control, the WTCCC dataset includes 414 682 SNPs and the GAIN data contains 729 304 SNPs.
3
Rheumatoid Arthritis Genotype Analysis
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Analyses using real data have also been performed. Rheumatoid arthritis (RA) genotype data on 1999 cases and 1504 controls have been obtained from WTCCC [44 (link)]. Genotypes from the Affymetrix GeneChip 500 K Mapping Array Set have been filtered using the usual quality controls tests on DNA quality (percentage of genotyped marker for any given individual above 90%), markers quality (percentage of genotyped individuals for any given marker above 90%), genotypes frequencies (markers with a p-value below a Bonferroni adjusted 5% threshold under the hypothesis of Hardy-Weinberg equilibrium in the controls cohort have been discarded). Missing genotypes for the GeneChip markers have been imputed using impute2 software [45 (link)]. This procedure led to 312583 SNP to be analyzed for the 2 cohorts. Zhang et al. [46 ] and [47 (link)] also used this dataset to infer potential interactions. These studies will therefore serve as a comparison for the results obtained with our approach.
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