Abstract 64: Fine mapping and in silico analysis of the 8q24.21 region for glioma identifies a low-frequency risk variant insight into etiological basis of glioma

• Published in: Cancer epidemiology, biomarkers & prevention biomarkers & prevention, 2012-11, Vol.21 (11_Supplement), p.64-64
• Main Authors: Enciso-mora, Victor, Liu, Yanhong, Hosking, Fay, Houlston, Richard, Bondy, Melissa
• Format: Article
• Language: English
• ISSN: 1055-9965; 1538-7755
• DOI: 10.1158/1055-9965.GWAS-64

Glioma comprises ∼40% of all primary brain tumors and most are associated with a poor prognosis irrespective of clinical care, with the most common type of glioma, glioblastoma (GBM), having a median overall survival of only ˜15 months. A number of glioma subtypes defined in part by malignancy grade (e.g., pilocytic astrocytomas WHO grade 1, diffuse “low-grade” gliomas WHO grade 2, anaplastic gliomas WHO grade 3, and GBM WHO grade 4) can be distinguished. Accumulating data indicate that these subtypes have different molecular genetic profiles possibly resulting from different etiologic pathways, which might be shared by different tumor subtypes or be type specific. We have previously demonstrated using a genome-wide association study (GWAS) strategy that genetic variation at 5p15.33, 8q24.21, 9p21.3, 11q23.3 and 20q13.33 influences the risk of glioma. We have sought to fine-map the location of the functional basis of the 8q24.21 association using data from four different non-overlapping GWASs of glioma, comprising a total of 4,147 glioma cases and 7,435 controls. To improve marker density across the 800kb region of association, we imputed genotypes using data from the 1000 Genomes Project and Hapmap3 data sets and high-density (80×) sequencing data generated on 250 CEU individuals. This combination of high-density genotyping and imputation allowed a wide and deep examination of SNPs with minor allele frequency (MAF) > 0.01 in this region. Coupled with these studies we performed a bioinformatic analysis of the most strongly associated variant to provide insight into the functional basis for the association. The region contained a number of single nucleotide polymorphisms (SNPs) showing a clearly stronger association signal than the original tagSNP rs4295627, notably the low frequency SNP rs55705857 (MAF=0.05 in the European population) which was sufficient to capture the 8q24.21 association (P= 2.24 x10-38). This 8q24 association is primarily for low-grade glioma, stronger for 1p/19q deletion oligodendroglioma and is associated with IDH mutation glioma. Functional annotation showed rs55705857 maps to a highly-evolutionarily conserved sequence predicted to impact on OCT1 binding. Glioma incidence varies between countries and is much lower in individuals of African/Asian descent than European. It is possible that these differences reflect differences in genetic predisposition. In this regard it intriguing that the rs55705857 is monomorphic in Asians, and has