Although genome-wide association studies have identified a number of susceptibility loci for adult glioma, little is still known regarding whether polymorphisms in the human leukocyte antigen (HLA) region contribute risk. HLA associations have previously been reported for a number of malignancies, with selected HLA polymorphisms investigated in a subset of glioma studies. However, no systematic analysis has been conducted to date, and no investigation into potential non-additive effects of such associations has been described. In this study, we conducted comprehensive genetic analyses of HLA variants in the major histocompatibility complex (MHC) region among 1,746 adult glioma patients and 2,312 controls from the GliomaScan Consortium. Genotype data were generated with the Illumina 660-Quad array, containing 1,822 SNP probes across the MHC region. We imputed HLA alleles using a reference panel of 5,225 individuals in the Type 1 Diabetes Genetics Consortium who underwent high-resolution HLA typing via next-generation sequencing. Subjects were of European-ancestry, and case-control comparisons were adjusted for population stratification using ancestry-informative principal components. Because alleles in different loci across the MHC region are linked, we created multi-locus haplotypes consisting of genes DRB1, DQA1, and DQB1. Although none of the haplotypes were associated with glioma in additive models, DRB1*15:01-DQA1*01:02-DQB1*06:02 showed an improvement in model fit after the inclusion of a non-additive term, which was significant after Bonferroni correction (P = 2.5x10-3). Furthermore, the interaction of DRB1*15:01-DQA1*01:02-DQB1*06:02 with haplotype DRB1*04:01-DQA1*03:01- DQB1*03:01 resulted in a 3.80-fold increase in the odds of glioma (P = 8.8x10-3). Our results indicate that the DRB1*15:01-DQA1*01:02-DQB1*06:02 haplotype contributes to the risk of glioma via a dominant effect, with heterozygosity conferring greater risk of glioma than expected from homozygote disease risk in an additive model.
Citation Format: Chenan Zhang, Kyle Walsh. Non-additive and interaction effects of HLA class 2 polymorphism contributing to risk of glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1320. doi:10.1158/1538-7445.AM2017-1320