We genotyped the BBJ samples by one of the following: [1 (link)] a combination of Illumina Infinium Omni Express and Human Exome, [2 ] Infinium Omni Express Exome v.1•0, [3 (link)] Infinium Omni Express Exome v.1•2.
Infinium omni express
Manufactured by Illumina
The Infinium Omni Express is a high-throughput genotyping array designed for genome-wide association studies (GWAS) and other large-scale genetic research. It provides comprehensive genome coverage with a dense set of single nucleotide polymorphisms (SNPs) across the human genome.
Automatically generated - may contain errors
Lab products found in correlation
Infinium omniexpressexome, by Illumina (2 mentions)
Infinium omniexpress 24, by Illumina (1 mentions)
Lightcycler 480 real time polymerase chain reaction system, by Roche (1 mentions)
Human mapping 500k array set, by Thermo Fisher Scientific (1 mentions)
50k human gene focused panel, by Thermo Fisher Scientific (1 mentions)
5 protocols using infinium omni express
1
BBJ Genotyping Methods Comparison
2
Evaluating 1KGP Imputation Reference Panels
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To evaluate 1KGP imputation reference panels, we first generated pseudo-microarray variant calls from GIAB benchmark variants of HG002 and HG005 in the benchmark regions by extracting the variant sites used by a popular commercial microarray kit (Illumina Infinium OmniExpress-24). We obtained the microarray sites from the CSV manifest file (GRCh38 version) on Illumina’s official website (infinium-omniexpress-24-v1-2-manifest-file-csv.zip">ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/productfiles/humanomniexpress-24/v1-2/infinium-omniexpress-24-v1-2-manifest-file-csv.zip ) and converted it to VCF format using Illumina’s GTCtoVCF tool (github.com/Illumina/GTCtoVCF).
Starting from GIAB v3.3.2 benchmark variants for HG002 and HG005, we removed all existing phasing information from the VCF, extracted the high-confidence variants in the microarray sites using bcftools v1.9, and added homozygous-reference genotypes to all microarray sites not present in GIAB VCFs. We phased the resulting pseudo-microarray variants with Eagle v2.4.1 using the reference panel to evaluate (DV-GLN-OPT or GATK-VQSR, see Results) and the hg38 genetic map file released with Eagle.
Finally, we imputed the phased pseudo-microarray variants with Beagle v5.0 (Browning et al., 2018 (link)) using the same reference panel used in the phasing step. A complete script for running Beagle can be found inSupplementary Note S6.
Starting from GIAB v3.3.2 benchmark variants for HG002 and HG005, we removed all existing phasing information from the VCF, extracted the high-confidence variants in the microarray sites using bcftools v1.9, and added homozygous-reference genotypes to all microarray sites not present in GIAB VCFs. We phased the resulting pseudo-microarray variants with Eagle v2.4.1 using the reference panel to evaluate (DV-GLN-OPT or GATK-VQSR, see Results) and the hg38 genetic map file released with Eagle.
Finally, we imputed the phased pseudo-microarray variants with Beagle v5.0 (Browning et al., 2018 (link)) using the same reference panel used in the phasing step. A complete script for running Beagle can be found in
3
Genotyping rs2149356 using TaqMan
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Taqman genotyping for rs2149356 was performed for the sample sets excepting ARIC, FHS, HPFS and NHS using a Lightcycler 480 Real-Time Polymerase Chain Reaction System (Roche Applied Science, Indianapolis, USA) in 384-well plates. The FHS cohort had been genotyped by the Affymetrix SNP 5 platform and a custom-designed gene-centric 50K SNP platform and rs2149356 genotype was imputed using MACH1 v1.0.15 with the HapMap CEU sample set as reference haplotypes. In the ARIC sample set rs2149356 had been genotyped on the Affymetrix SNP 6 platform. The HPFS and NHS sample sets were genotyped using the Illumina Infinium OmniExpress and genotypes were imputed using MACH (imputation quality Rsq = 0.989). This resulted in N = 10807 non-missing genotype calls (1.5% missing). There was no evidence for departure from Hardy Weinberg equilibrium in any of the sample sets presented in Tables 2 and 3 (PHWE>0.01).
4
Genetic Influences on Vascular Function
5
Genomic DNA Extraction and Genotyping
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Prior to oncological resection, genomic DNA was extracted from peripheral blood leukocytes. Genotyping was performed by collaborating partners at the Department of Human Genetics, University of Bonn, Germany. It was accomplished for all patients using Infinium OmniExpress, Infinium OmniExpressExome, and Infinium Omni2.5Exome BeadChips (by Illumina) according to the manufacturer’s protocol at the University of Bonn. The overlap of the SNP content was subjected to initial quality control performed with PLINK v1.90b6.6. Samples with genotype call rate less than 97%, discrepancies in sex, divergent ancestry from the CEU HapMap 2010 population, and related samples were excluded from further analysis.
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