Single Nucleotide Polymorphism Selection and Genotyping

We selected 36 tagging single nucleotide polymorphisms (SNPs) in the VDR gene ± 20 kb by using the tagger algorithm implemented in Haploview, with a cutoff of r² = 0.8 and a minor allele frequency of ≥ 5% in Whites from the HapMap Project database, and we forced in one previously reported SNP related to prostate cancer risk (rs11574143).²⁰ Of 397 patients with pancreatic cancer, DNA was extracted from archived buffy coat samples with Qiagen QIAmp (Valencia, CA) and whole-genome amplified with GE Healthcare Genomiphi (Pittsburgh, PA). All genotyping was carried out at the Partners HealthCare Center for Personalized Genetic Medicine by using a custom-designed Illumina Golden Gate genotyping assay (San Diego, CA). Three tagging SNPs were not supported by the Golden Gate platform and so could not be genotyped. Three SNPs deviated from Hardy-Weinberg Equilibrium at P < .01 and were excluded. Replicate samples included for quality control (n = 44 sample groups) had mean genotype concordance of 97.8% across the 30 SNPs.