New basal cell carcinoma susceptibility loci

In an ongoing screen for DNA sequence variants that confer risk of cutaneous basal cell carcinoma (BCC), we conduct a genome-wide association study (GWAS) of 24,988,228 SNPs and small indels detected through whole-genome sequencing of 2,636 Icelanders and imputed into 4,572 BCC patients and 266,358 controls. Here we show the discovery of four new BCC susceptibility loci: 2p24 MYCN (rs57244888C, OR=0.76, P=4.7 × 10(-12)), 2q33 CASP8-ALS2CR12 (rs13014235C, OR=1.15, P=1.5 × 10(-9)), 8q21 ZFHX4 (rs28727938G, OR=0.70, P=3.5 × 10(-12)) and 10p14 GATA3 (rs73635312A, OR=0.74, P=2.4 × 10(-16)). Fine mapping reveals that two variants correlated with rs73635312A occur in conserved binding sites for the GATA3 transcription factor. In addition, expression microarrays and RNA-seq show that rs13014235C and a related SNP rs700635C are associated with expression of CASP8 splice variants in which sequences from intron 8 are retained.