Table 1.

The component datasets of the SCC GWAS

Sample sizeGenotype
DatasetTotalSCC cases/controlsPlatformNumber of imputed SNPsa
Discovery set
 Harvard GWAS5,509424/5,085Affymetrics 6.01,777,244b
 RS-I5,892258/5,634Affymetrics 6.02,356,032c
 RS-II2,14963/2,086Affymetrics 6.01,956,891d
All (meta-analysis)13,550745/12,8052,392,512
Replication set
 Skin cancer study1,082531/551TaqMan OpenArray59e
  • aImputated on the basis of the genotyped SNPs and haplotype information in the HapMap phase II data build 35 (CEU).

  • bFiltered by imputation r2 > 0.95 and MAF > 0.01.

  • cFiltered by imputation r2 > 0.3 and MAF > 0.02.

  • dFiltered by imputation r2 > 0.3 and MAF > 0.08.

  • e64 SNPs were selected for replication but five of them failed in genotyping.