{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HumanExome-12v1_A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00010000758"],"sample_count":["906"],"description":["EGA dataset EGAD00010000758"],"repository":["EGA"],"title":["Title not provided"],"pubmed_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."],"pubmed_title":["Search for new loci and low-frequency variants influencing glioma risk by exome-array analysis."],"pubmed_authors":["Kinnersley Ben B, Kamatani Yoichiro Y, Labussière Marianne M, Wang Yufei Y, Galan Pilar P, Mokhtari Karima K, Delattre Jean-Yves JY, Gousias Konstantinos K, Schramm Johannes J, Schoemaker Minouk J MJ, Swerdlow Anthony A, Fleming Sarah J SJ, Herms Stefan S, Heilmann Stefanie S, Nöthen Markus M MM, Simon Matthias M, Sanson Marc M, Lathrop Mark M, Houlston Richard S RS"],"additional_accession":[]},"is_claimable":false,"name":"Glioma_Exome_FRE_CASES - samples","description":"French glioma case germline genotypes using Illumina HumanExome-12v1_A array","dates":{"updated":"2017-07-26 15:39:26"},"accession":"EGAD00010000758","cross_references":{"TAXONOMY":["9606"],"pubmed":["26264438"],"EGA":["EGAC00001000345","EGAS00001001258"]}}