We derived the genotypes for rs7903146 leveraging the data derived from high throughput genome-wide SNP genotyping, using the Illumina Infinium™ II HumanHap550 or Human 610 BeadChip technology (Illumina, San Diego), at one of the three participating sites. Samples were drawn from genome wide datasets that yielded SNPs with call rates <95%, minor allele frequency <1%, missing rate per person <2% and Hardy-Weinberg equilibrium P < 10-5 in order to assess most accurately the role of rs7903146
Human 610 beadchip
Manufactured by Illumina
The Human 610-Quad BeadChip is a high-throughput microarray platform designed for genome-wide genotyping of human DNA samples. The chip features over 610,000 genetic markers, enabling comprehensive analysis of genetic variation across the human genome. The BeadChip utilizes Illumina's proprietary BeadArray technology to provide accurate and reliable genotyping data.
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Lab products found in correlation
2 protocols using human 610 beadchip
1
Genotyping rs7903146 from SNP arrays
2
Genome-wide SNP Genotyping and Imputation
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Genome-wide tagging SNPs were genotyped using Illumina Infinium HumanHapmap550 or Human610 BeadChip for all individuals. Genotypes were filtered using PLINK (version 1.07) [20 (link)] with the following quality control cut off values: individuals were excluded when the call rate was lower than 95 % and SNPs with a minor allele frequency (MAF) below 5 %; a missing rate per SNP above 5 %; or with a Hardy-Weinberg equilibrium (HWE) test p value of < 1e-6 were removed. Genotype data were used to estimate cryptic relatedness between individuals. No individuals were found to be closely related at a pihat threshold of 0.05. Multidimensional scaling (MDS) plot including HapMap (Phase 2 release 23) [21 (link)] populations revealed one individual with African ancestry, which was removed for subsequent analysis. See Additional file 2 : Figure S1 for the MDS plot including HapMap populations.
Imputation was performed with MaCH [22 (link)] and MiniMac [23 (link)] based on the European reference haplotype from the 1000 Genomes Phase1 v2.20101123 data [24 (link)]. Prior to imputation, genotyped SNPs were filtered to remove variants where the call rate was less than 95 %, the minor allele frequency was less than 1 %, and the HWE p value was of <1e-6. Post imputation, any variant where the imputation quality score was less than 0.3 (r2 from MiniMac) was excluded from analysis.
Imputation was performed with MaCH [22 (link)] and MiniMac [23 (link)] based on the European reference haplotype from the 1000 Genomes Phase1 v2.20101123 data [24 (link)]. Prior to imputation, genotyped SNPs were filtered to remove variants where the call rate was less than 95 %, the minor allele frequency was less than 1 %, and the HWE p value was of <1e-6. Post imputation, any variant where the imputation quality score was less than 0.3 (r2 from MiniMac) was excluded from analysis.
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