Previously, we utilized publicly available databases to identify 382 immunomodulatory genes and these loci were used to isolate candidate SNPs of interest for genotyping25 (link). Employing resources from the MuTHER project28 (link),29 (link), 50 SNPs with the most significant cis-ieQTL activity on probes in LCLs from these immunomodulatory loci were selected for genotyping. While skin and adipose tissue data are also available in the MuTHER project, the cis-ieQTLs have been assessed from the LCL expression data, as the scope of the study is focused on the host immune cell component involved in MPM development. The selection procedure was described in detail elsewhere25 (link).
Genomic DNA from all 977 cases was isolated from whole blood samples using a QiaAmp kit (Qiagen). All SNP genotyping was completed using the MassARRAY System (Agena Bioscience Inc.) according to the manufacturer’s protocol. To ensure high-quality genotyping, quality control filters were used to remove SNPs with call rate <90%, samples with call rates <90%, and SNPs with a significant departure from Hardy-Weinberg equilibrium (p < 1E-04) resulting in 41 ieQTLs for analysis. Additionally, rare SNPs (defined by minor allele frequency <0.05) were removed prior to logistic regression analysis.
Genomic DNA from all 977 cases was isolated from whole blood samples using a QiaAmp kit (Qiagen). All SNP genotyping was completed using the MassARRAY System (Agena Bioscience Inc.) according to the manufacturer’s protocol. To ensure high-quality genotyping, quality control filters were used to remove SNPs with call rate <90%, samples with call rates <90%, and SNPs with a significant departure from Hardy-Weinberg equilibrium (p < 1E-04) resulting in 41 ieQTLs for analysis. Additionally, rare SNPs (defined by minor allele frequency <0.05) were removed prior to logistic regression analysis.
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