Only five SNPs showed a consistent significant association (P < 0.05). In another case-control population (507 cases and 215 controls), these SNPs were tested for association with HCC. However, only one SNP (rs17401966) was confirmed in this replication sample (P =

Bafilomycin A1 ic50 3.9 × 10−5). Again, this finding could be replicated in another independent case-control population (751 cases and 509 controls) as well as by evaluation of the rs17401966 transmission status in 159 family trios (cases and their unaffected parents) with HBV-related HCC, which allows a family-based association test robust against population stratification (transmission disequilibrium test) for the presence of genetic linkage between a marker locus and a disease susceptibility locus. The combined analysis of the three independent case-control populations (1962 cases and 1430 controls) from different Chinese regions as well as the combination of these and the genome-wide association data (2310 cases and 1789 controls) provided evidence for a highly significant association of rs17401966 at a genome-wide level (P = 5.1 × 10−15 and P = 3.4 × 10−19, respectively). HCC risk was significantly reduced in the presence of the mutant [G] allele of the

rs17401966 SNP (odds ratio = 0.61; confidence interval = 0.55-0.67). Risk-allele frequencies were 19.3% in patients with HCC (n = 2310), 27.7% in non-HCC controls (n = 1,789), selleck chemicals llc and 31.4% in non-HBV carriers (n = 185). Pairwise linkage disequilibrium analysis (measured by r2) revealed a linkage disequilibrium block of about 244 kilobases mapping to chromosome 1p36.22,

flanking rs17401966, and spanning the genes KIF1B (encodes a kinesin superfamily member involved in the transport of organelles and vesicles), PDG (protein involved in the pentose phosphate metabolism), and the 3′-end of UBE4B (encodes ubiquitin 上海皓元 conjugation factor E4 involved in multiubiquitin chain assembly). Multiple logistic regression analysis and haplotype analysis suggested that there might be a single susceptibility locus in this region, which was only attributable to rs17401966 (NM_015074.3: c.2537+518A>G), which is located in intron 24 of KIF1B. Regardless of the fact that the only common nonsynonymous SNP at this region (rs2297881) showed no disease association, it remains unclear whether rs17401966 is in linkage disequilibrium with a disease-causing mutation or whether the SNP itself has a direct influence on HCC development. The identified susceptibility locus on chromosome 1p36.22 lies in a region that has been identified to be commonly affected by chromosomal losses or gains in several malignancies such as colorectal cancer, breast cancer, neuroblastoma, and also in HCC.