DNA was extracted from samples using conventional methodologies and quantified using PicoGreen (Invitrogen, Carlsbad, USA). Phase 1 of the UK-GWA study was conducted using Illumina Human550 BeadChips according to the manufacturer's protocols (Illumina, San Diego, USA). Phase 2 genotyping was carried out using Illumina Infinium custom arrays according to the manufacturer's protocols. Selection of SNPs were based on a stepwise procedure (Supplementary Figure 1); the majority, 20,000, were chosen by a hypothesis-free (agnostic) strategy, simply on the basis of being most significantly associated with lung cancer risk in Phase 1. The remainder were selected on an alternative basis, briefly: 1,799 additional SNPs (annotated in dbSNP) were included in the 15q25.1, 6p21.33 and 5p15.33 regions, which had been previously reported to be associated with disease risk. 79 SNPs showing an association with lung cancer risk in previously reported GWA studies (IARC-GWA and Texas-GWA studies) at P<10−4, not captured by the 20,000 most significant SNPs in Phase 1 and fine mapping SNPs. 11,182 agnostic SNPS not included in the aforementioned criteria, based on being most significantly associated with lung cancer in a previously reported meta-analysis of Phase 1 and IARC-GWA and Texas-GWA studies(4).
