Analysis of SNPs and haplotypes in vitamin D pathway genes and renal cancer risk

Abstract

In the kidney vitamin D is converted to its active form. Since vitamin D exerts its activity through binding to the nuclear vitamin D receptor (VDR), most genetic studies have primarily focused on variation within this gene. Therefore, analysis of genetic variation in VDR and other vitamin D pathway genes may provide insight into the role of vitamin D in renal cell carcinoma (RCC) etiology. RCC cases (N = 777) and controls (N = 1,035) were genotyped to investigate the relationship between RCC risk and variation in eight target genes. Minimum-p-value permutation (Min-P) tests were used to identify genes associated with risk. A three single nucleotide polymorphism (SNP) sliding window was used to identify chromosomal regions with a False Discovery Rate of <10%, where subsequently, haplotype relative risks were computed in Haplostats. Min-P values showed that VDR (p-value = 0.02) and retinoid-X-receptor-alpha (RXRA) (p-value = 0.10) were associated with RCC risk. Within VDR, three haplotypes across two chromosomal regions of interest were identified. The first region, located within intron 2, contained two haplotypes that increased RCC risk by approximately 25%. The second region included a haplotype (rs2239179, rs12717991) across intron 4 that increased risk among participants with the TC (OR = 1.31, 95% CI = 1.09-1.57) haplotype compared to participants with the common haplotype, TT. Across RXRA, one haplotype located 3' of the coding sequence (rs748964, rs3118523), increased RCC risk 35% among individuals with the variant haplotype compared to those with the most common haplotype. This study comprehensively evaluated genetic variation across eight vitamin D pathway genes in relation to RCC risk. We found increased risk associated with VDR and RXRA. Replication studies are warranted to confirm these findings.

Figure 1. VDR HaploWalk and Haploview analysis.

Top: HaploWalk analysis identified two chromosomal regions of interest in the vitamin D receptor (VDR) gene that were significant at an FDR of 10%. Region one included SNPs 3′- rs4760648, rs2853564, rs2254210 -5′; region two included SNPs 3′- rs12717991, rs2239179 -5′. Bottom: Haploview analysis also identified two haplotype blocks within the same chromosomal regions of interest.

Figure 2. RXRA HaploWalk and Haploview analysis.

Top: HaploWalk analysis identified a single chromosomal region of interest in the retinoid-X-receptor-alpha (RXRA) gene that was significant at an FDR of 10%. This region included SNPs 5′- rs748964, rs3118523 -3′. Bottom: Haploview analysis also identified one haplotype block within the same chromosomal region of interest.