SNP genotyping
polyp, colorectal polyp
COLORECTAL POLYP
Genotyping was carried out using the Fluidigm microfluidic SNP genotyping system (Fluidigm), using custom-built SNP Type genotyping assays (Fluidigm) for 92 SNPs (Supplementary Table S1).A multiplexed preamplification PCR was carried out to increase the available template DNA and reduce allelic drop-out associated with low template concentration. DNA samples were run on 96.96 Dynamic Array IFCs (integrated fluidic circuits), which were primed and loaded using the IFC Controller HX (96.96 arrays), as per manufacturer's instructions. In total, 691 individual samples including 10 technical duplicates, 31 participant duplicate samples and 1 participant triplicate sample, were analyzed, representing 648 individual participant DNA samples.Genotyping PCR and measurement of endpoint fluorescent values were carried out using the Fluidigm BioMark HD system. Data were analyzed and genotyping calls made using Fluidigm SNP Genotype Analysis software.Fourteen SNPs failed quality control; one SNP was monoallelic, one SNP was repeatedly called differently in duplicate sample runs, and 12 SNPs had an absence of genotype call >5% (Supplementary Table S1).Therefore, genotype data for 78 SNPs were available for analysis inside the seAFOod trial database. Twelve SNPs did not satisfy Hardy–Weinberg equilibrium (This report is restricted to an analysis of the relationship between the 35 SNPs in genes controlling oxylipin synthesis and degradation (Data on the relationship between the SNPs in genes controlling PUFA metabolism (Supplementary Table S1) with blood and rectal mucosal levels of PUFAs measured in the seAFOod polyp prevention trial, as well as colorectal polyp risk, are the subject of a separate report.