The individuals were genotyped using the Illumina OmniExpress 700K chip, imputed to the 1000 genome imputation panel. After imputation we selected SNPs from the HapMap3 panel since this SNP set was optimized to capture common genetic variation,21 (link) which is required for the GREML analysis. For quality control, SNPs with a minor allele frequency less than 1%, a higher missing rate than 0.03 and that failed the Hardy-Weinberg equilibrium for a threshold of 10-6 were removed. The first 20 principal components are included as covariates to adjust for population stratification.22 (link)
Omniexpress 700k chip
Manufactured by Illumina
The OmniExpress 700K chip is a high-density genotyping array designed by Illumina. It provides comprehensive genome-wide coverage with over 700,000 markers, enabling efficient and cost-effective genetic analysis.
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Lab products found in correlation
4 protocols using omniexpress 700k chip
1
Genotyping and QC for GREML analysis
2
Genetic Variant Identification and Adjustment
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The individuals were genotyped using the Illumina OmniExpress 700 K chip, imputed to the 1000 genome imputation panel. After imputation we selected SNPs from the HapMap3 panel since this SNP set was optimized to capture common genetic variation,21 (link) which is required for the GREML analysis. For quality control, SNPs with a minor allele frequency <1%, a higher missing rate than 0.03 and that failed the Hardy-Weinberg equilibrium for a threshold of 10−6 were removed. The first 20 principal components are included as covariates to adjust for population stratification.22 (link)
3
Genotyping of TAS2R38 Receptor Gene
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Saliva samples were collected from all participants using the Oragene DNA collection kit and DNA was extracted (DNA Genotek, Ontario, Canada). Three polymorphisms in the TAS2R38 receptor gene (rs1726866, rs10246939 and rs713598) define the genotype. The first two were genotyped with the Omni Express 700k Illumina Chip. The third one was analysed using TaqMan probe-based assays (Applied Biosystems, Foster City, CA, USA).
4
Saliva-based Genotyping Protocol
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Saliva samples were collected from all enrolled subjects using the Oragene DNA collection kit, and DNA extraction was performed (DNA Genotek, Ontario, Canada). Genotyping was carried out using the Omni Express 700k Illumina Chip, including only samples and sites with call rate ≥0.99 (43,655 variants excluded), Hardy-Weinberg Equilibrium p-value ≥1*10–6 (3,153 variants excluded), and minor allele frequency (MAF) ≥ 0.01 (18 variants excluded). Imputation was performed using MINIMAC v4 (Howie et al., 2012 (link)) to Haplotype Reference Consortium imputation panel version r1.1 (McCarthy et al., 2016 (link)). All data were aligned to the human reference genome build 37 (GRCh37). After imputation, SNPs with Info Score <0.4 (13626943 variants excluded) and MAF <0.01 (40,203 variants excluded) were discarded from statistical analyses. A total of 7783479 SNPs were analysed.
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