Genome-wide association study identifies five susceptibility loci for glioma

Abstract

To identify risk variants for glioma, we conducted a meta-analysis of two genome-wide association studies by genotyping 550K tagging SNPs in a total of 1,878 cases and 3,670 controls, with validation in three additional independent series totaling 2,545 cases and 2,953 controls. We identified five risk loci for glioma at 5p15.33 (rs2736100, TERT; P = 1.50 x 10(-17)), 8q24.21 (rs4295627, CCDC26; P = 2.34 x 10(-18)), 9p21.3 (rs4977756, CDKN2A-CDKN2B; P = 7.24 x 10(-15)), 20q13.33 (rs6010620, RTEL1; P = 2.52 x 10(-12)) and 11q23.3 (rs498872, PHLDB1; P = 1.07 x 10(-8)). These data show that common low-penetrance susceptibility alleles contribute to the risk of developing glioma and provide insight into disease causation of this primary brain tumor.

Figure 1

Subjects and single-SNP exclusion schema for genome-wide association studies.

Figure 2

LD structure and association results for the five confirmed glioma-associated regions. (a) 8q24.21. (b) 5p15.33. (c) 9p21.3. (d) 20q13.33. (e) 11q23.3. Chromosomal positions and genes based on NCBI build 36 coordinates. Armitage trend test P values (as −log₁₀ values; left y axis) are shown for SNPs analyzed in the GWA studies in blue and for the combined analysis including the replication series in red. Recombination rates in HapMap CEU across the region are shown in black (right y axis). Also shown are the relative positions of genes mapping to each region of association. Exons of genes have been redrawn to show the relative positions in the gene, and therefore maps are not to physical scale.

Figure 3

Cumulative effects of glioma risk alleles. (a) Distribution of risk alleles in glioma cases (green bars) and controls (blue bars). (b) Plot of the increasing ORs for glioma with increasing number of risk alleles. The ORs are relative to the median number of four risk alleles; vertical bars correspond to 95% confidence intervals. Horizontal line marks the null value (OR = 1). The distribution of risk alleles follows a normal distribution in both case and controls, with a shift toward a higher number of risk alleles in cases.