Genotyping was performed in triplicate as part of two custom 384-plex multiplex oligo pools for analysis of SNP assays using the Illumina BeadXpress system following the manufacturer’s instructions (Illumina, Inc., San Diego, CA). Illumina’s internal controls, including allele-specific extension, PCR uniformity, gender genotype, gap extension efficiency, annealing specificity, and hybridization, were used to assure data quality and fidelity.
Purified DNA was plated by the NIEHS Molecular Genetics Core Facility and processed through several activation and ligation steps followed by PCR with universal primers and subsequent hybridization to Illumina genotyping beads. After hybridization and washing, plates were scanned on the BeadXpress® reader. Raw data were normalized across samples using Illumina's BeadStudio software suite®, and SNP genotype calls were made using genotyping cluster files generated by BeadStudio. Seven samples with a call rate below 50% were excluded from the analysis. Genotyping duplicate reproducibility was 99.76%, with a call rate of 95.8%. Chi-square analysis was used to calculate p values (0.05 level) for comparisons of genotype frequencies between different ethnic groups in this exploratory study. MAFs were calculated by race and ethnicity and were compared to the Genome Aggregation Database (gnomAD) of the Broad Institute populations [36 (link)].
Purified DNA was plated by the NIEHS Molecular Genetics Core Facility and processed through several activation and ligation steps followed by PCR with universal primers and subsequent hybridization to Illumina genotyping beads. After hybridization and washing, plates were scanned on the BeadXpress® reader. Raw data were normalized across samples using Illumina's BeadStudio software suite®, and SNP genotype calls were made using genotyping cluster files generated by BeadStudio. Seven samples with a call rate below 50% were excluded from the analysis. Genotyping duplicate reproducibility was 99.76%, with a call rate of 95.8%. Chi-square analysis was used to calculate p values (0.05 level) for comparisons of genotype frequencies between different ethnic groups in this exploratory study. MAFs were calculated by race and ethnicity and were compared to the Genome Aggregation Database (gnomAD) of the Broad Institute populations [36 (link)].