Genotyping analyses of replications in cohorts 2–4 were conducted by using the Sequenom MassARRAY system, at the Key Laboratory of Dermatology at Anhui Medical University (Ministry of Education), Hefei, Anhui, China. Locus-specific PCR primers (Supplementary Table 15 ) were designed using MassARRAY assay Design 3.0 software, following the manufacturer's instructions (Sequenom)53 (link). Quality control was performed in each data set separately using PLINK 1.07. In each case–control replications (cohorts 2–4), we excluded SNPs with a call rate <90% in cases or controls, or deviation from HWE proportions (P≤1 × 10−4) in the controls.
To evaluate the quality of the genotype data for the validation analyses, 100 randomly selected samples from the GWAS stage were re-genotyped using the Sequenom system. The concordance rate between the genotypes from the Illumina HumanOmniZhongHua-8 v1.1 BeadChip and the Sequenom MassARRAY assay analyses was >99%. The cluster plots from the Illumina and Sequenom analyses were checked to confirm their good quality. After quality control, 146 SNPs were remained for NSCLP replication and 40 SNPs were left for further replications in cohort 3 and 4 analyses, respectively.
To evaluate the quality of the genotype data for the validation analyses, 100 randomly selected samples from the GWAS stage were re-genotyped using the Sequenom system. The concordance rate between the genotypes from the Illumina HumanOmniZhongHua-8 v1.1 BeadChip and the Sequenom MassARRAY assay analyses was >99%. The cluster plots from the Illumina and Sequenom analyses were checked to confirm their good quality. After quality control, 146 SNPs were remained for NSCLP replication and 40 SNPs were left for further replications in cohort 3 and 4 analyses, respectively.