Search for new loci and low-frequency variants influencing glioma risk by exome-array analysis

Eur J Hum Genet. 2016 May;24(5):717-24. doi: 10.1038/ejhg.2015.170. Epub 2015 Aug 12.

Abstract

To identify protein-altering variants (PAVs) for glioma, we analysed Illumina HumanExome BeadChip exome-array data on 1882 glioma cases and 8079 controls from three independent European populations. In addition to single-variant tests we incorporated information on the predicted functional consequences of PAVs and analysed sets of genes with a higher likelihood of having a role in glioma on the basis of the profile of somatic mutations documented by large-scale sequencing initiatives. Globally there was a strong relationship between effect size and PAVs predicted to be damaging (P=2.29 × 10(-49)); however, these variants which are most likely to impact on risk, are rare (MAF<5%). Although no single variant showed an association which was statistically significant at the genome-wide threshold a number represented promising associations - BRCA2:c.9976A>T, p.(Lys3326Ter), which has been shown to influence breast and lung cancer risk (odds ratio (OR)=2.3, P=4.00 × 10(-4) for glioblastoma (GBM)) and IDH2:c.782G>A, p.(Arg261His) (OR=3.21, P=7.67 × 10(-3), for non-GBM). Additionally, gene burden tests revealed a statistically significant association for HARS2 and risk of GBM (P=2.20 × 10(-6)). Genome scans of low-frequency PAVs represent a complementary strategy to identify disease-causing variants compared with scans based on tagSNPs. Strategies to lessen the multiple testing burden by restricting analysis to PAVs with higher priors affords an opportunity to maximise study power.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acyl-tRNA Synthetases / genetics
  • BRCA2 Protein / genetics
  • Brain Neoplasms / genetics*
  • Case-Control Studies
  • Exome*
  • Female
  • Genetic Loci*
  • Genotyping Techniques / methods*
  • Glioma / genetics*
  • Humans
  • Isocitrate Dehydrogenase / genetics
  • Male
  • Middle Aged
  • Polymorphism, Single Nucleotide*

Substances

  • BRCA2 Protein
  • BRCA2 protein, human
  • IDH2 protein, human
  • Isocitrate Dehydrogenase
  • Amino Acyl-tRNA Synthetases
  • HARS2 protein, human