For studies 1 and 2, germline DNA was extracted from peripheral blood (QiAamp DNA Blood Kit; Qiagen, Valencia, CA, USA). In the discovery analysis, 27 potential functional single nucleotide polymorphisms (SNPs) were selected from 13 candidate genes with evidence of involvement in angiogenesis or in the metabolism, disposition, or mode of action of pazopanib (Xu et al, 2011 (link)). Genotyping was conducted using single-base chain extension assays modified by GlaxoSmithKline (Research Triangle Park, NC, USA), TaqMan SNP assays (Applied Biosystems, Foster City, CA, USA), GoldenGate and Infinium genotyping assays (Illumina, San Diego, CA, USA), the KASPar SNP genotyping system (LGC Genomics, Hoddesdon, UK), and Sanger sequencing. For study 3, DNA was isolated from peripheral blood with FlexiGene DNA kit (Qiagen) or from saliva with Oragene DNA self-collection kits (DNA Genotek, Ottawa, Canada), and genotyping was conducted using the KASPar SNP genotyping system (Garcia-Donas et al, 2011 (link)).
All genotypes were called following the assay manufacturers' guidelines. Genotyping quality was confirmed by call rate, manual examination of cluster plots, concordance with previously reported allele frequencies, and checks of Hardy–Weinberg proportions within self-reported non-Hispanic white patients and within self-reported East Asian patients.
All genotypes were called following the assay manufacturers' guidelines. Genotyping quality was confirmed by call rate, manual examination of cluster plots, concordance with previously reported allele frequencies, and checks of Hardy–Weinberg proportions within self-reported non-Hispanic white patients and within self-reported East Asian patients.