{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HumanExome-12v1_A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00010000756"],"sample_count":["699"],"description":["EGA dataset EGAD00010000756"],"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"],"name_synonyms":["Glioma 1, Glioma NOS, whole exome, Glioma (except Nasal glioma, sfrp3, GLM, glial tumors, malignant, neuroglial tumor, obsolete_glioma, Mixed Glioma, Malignant Glioma, Neuroglial Tumor, fiz, fre, frp-3, tumour of the neuroglia, Tumor, Malignant, neoplasm of neuroglia, FZRB, hFIZ., xfrzb, [M]Glioma NOS (morphologic abnormality), frzb-pen, FRP-3, tumor of the neuroglia, SFRP3, fritz, [M]Gliomas (morphologic abnormality), fzrb, Gliomas, Mixed, Glial Cell Tumor, [M]Glioma NOS, FRZB-1, Mixed Gliomas, FRZB1, FRZB-PEN, Glial Tumor, NOS (except Nasal glioma, FRITZ, Neuroglial Neoplasm, glioma (morphologic abnormality), Neuroglial Neoplasms, Glioma NOS (morphologic abnormality), Frzb-1, os1, OS1, neuroglial tumour, Glial Cell, Malignant glioma, Exomes, Neoplasm of the Neuroglia, Tumor of Neuroglia, Glial Neoplasm, SRFP3, neuroglial neoplasm, tumor of neuroglia, Neoplasm of Neuroglia, srfp3, glial tumor, no ICD-O subtype, Tumor of the Neuroglia, frzb1, tumour of neuroglia, glial tumour, Glial Cell Tumors, not neoplastic), Gliomas (morphologic abnormality), Malignant Gliomas, Glioma, glial neoplasm, [M]Gliomas, malignant (morphologic abnormality), FRE, glioma, Tumors of Neuroglia, neoplasm of the neuroglia, Neoplasms of Neuroglia, Tumors"],"description_synonyms":["Glioma 1, Glioma NOS, Glioma (except Nasal glioma, Controlling, preventive therapy, GLM, glial tumors, malignant, neuroglial tumor, obsolete_glioma, Mixed Glioma, Malignant Glioma, Neuroglial Tumor, tumour of the neuroglia, Tumor, Malignant, neoplasm of neuroglia, prevention, [M]Glioma NOS (morphologic abnormality), microarray., Genogroup, tumor of the neuroglia, [M]Gliomas (morphologic abnormality), Gliomas, Mixed, Glial Cell Tumor, [M]Glioma NOS, Mixed Gliomas, prevention and control, Glial Tumor, NOS (except Nasal glioma, Neuroglial Neoplasm, glioma (morphologic abnormality), reference sample, Neuroglial Neoplasms, Glioma NOS (morphologic abnormality), prophylaxis, neuroglial tumour, Glial Cell, Malignant glioma, Neoplasm of the Neuroglia, Tumor of Neuroglia, Glial Neoplasm, neuroglial neoplasm, Genotypes, tumor of neuroglia, Neoplasm of Neuroglia, preventive measures, Genogroups, glial tumor, no ICD-O subtype, control, Tumor of the Neuroglia, tumour of neuroglia, glial tumour, Glial Cell Tumors, not neoplastic), Gliomas (morphologic abnormality), Malignant Gliomas, Glioma, glial neoplasm, [M]Gliomas, malignant (morphologic abnormality), glioma, Tumors of Neuroglia, neoplasm of the neuroglia, Neoplasms of Neuroglia, Controlled, Tumors"],"pubmed_title_synonyms":["Glioma 1, Glioma NOS, whole exome, Glioma (except Nasal glioma, cou, GLM, determination, glial tumors, malignant, frequency, neuroglial tumor, obsolete_glioma, Mixed Glioma, Malignant Glioma, Neuroglial Tumor, tumour of the neuroglia, Tumor, Tl3, Tl2, Malignant, neoplasm of neuroglia, Relative, Lr, [M]Glioma NOS (morphologic abnormality), tumor of the neuroglia, Relative Risks, [M]Gliomas (morphologic abnormality), Low, Gliomas, Mixed, Glial Cell Tumor, [M]Glioma NOS, Mixed Gliomas, outbreaks, Relative Risk, Glial Tumor, NOS (except Nasal glioma, me75, Neuroglial Neoplasm, glioma (morphologic abnormality), Risk, Neuroglial Neoplasms, Glioma NOS (morphologic abnormality), occurrence, neuroglial tumour, Glial Cell, Risks, prevalence, Malignant glioma, Exomes, Neoplasm of the Neuroglia, chemical analysis., Tumor of Neuroglia, Glial Neoplasm, surveillance, D17Mit170, morbidity, T1, endemics, neuroglial neoplasm, tumor of neuroglia, Neoplasm of Neuroglia, glial tumor, no ICD-O subtype, Tumor of the Neuroglia, tumour of neuroglia, glial tumour, Glial Cell Tumors, Bra, not neoplastic), Gliomas (morphologic abnormality), Malignant Gliomas, microarray, epidemics, Glioma, assay, glial neoplasm, [M]Gliomas, malignant (morphologic abnormality), glioma, Tumors of Neuroglia, neoplasm of the neuroglia, Neoplasms of Neuroglia, incidence, Tumors"],"pubmed_abstract_synonyms":["Glioma 1, Malignant tumor of lung, scale tissue, Breasts, Materials, GLM, determination, glial tumors, acetylglucosaminyltransferase-like protein, HO3, DmelCG30169, Mbp1, Lactiferous gland, malignant tumor of lung, Mixed Glioma, mNADP-IDH, protein, malignant neoplasm of the lung, tumour of the neuroglia, Tumor, Astrocytomas, glandula mammaria, Mutations, Relative, Odds Ratios, Personal, BcDNA:SD25109, [M]Glioma NOS (morphologic abnormality), diseases, Roles, Associations, tumor of the neuroglia, Familiar breast and Ovarian cancer syndrome, Concepts, [M]Gliomas (morphologic abnormality), diseases and disorders, BROVCA2, protein aggregate, myd, Risk Ratio, Pulmonary cancer, imprinted and ancient gene protein, Psychological, strong, Lung Cancer, me75, human disease, Occidental, FAD1, glioma (morphologic abnormality), like-acetylglucosaminyltransferase, Genomes, BRCC2, plant peltate hair, alveolar cell carcinoma, neuroglial tumour, Neoplasm of the Neuroglia, Mbp-1, D2HGA2, Lung Cancers, AW047063, Giant Cell Glioblastoma, IDPm, bA379J5.3, D17Mit170, PNCA2, T1, Astrocytoma, Social, resistance to, Malignant neoplasm of lung, CCA4, grade IV adult Astrocytic tumor, HARS2, Role Concepts, tumour of neuroglia, Gliomas (morphologic abnormality), Homo sapiens disease, Social Power, glioma, IDPM, neoplasm of the neuroglia, RAB163, FACD, somatic mutation, Hars2, Power, Tumors, mamma, hereditary breast ovarian cancer, Glioma (except Nasal glioma, Lung cancer, HARSL, wide/broad, gyltl1b-b, BRCA1, BRCA2, IDH, HARSR, frequency, Cancer of Lung, Ratios, obsolete_glioma, white, IDP, Malignant Glioma, Psychological Powers, Giant Cell, somatic, Tl3, Tl2, predicted, CG13583, CG13584, Role Concept, cancer of lung, European, MDDGA6, primary glioblastoma multiforme, mKIAA0609, Lobe of mammary gland, Relative Risks, Diseases, Role, Genetic Materials, Malignant lung tumor, malignant tumour of lung, Gliomas, Glial Cell Tumor, Harsl, XRCC11, KIAA0609, Genetic Material, acetylglucosaminyltransferase-like 1A, Caucasians, fg, Idh-2, Lung malignant tumors, malignant lung neoplasm, gyltl1b, Glioblastoma, Risk, spongioblastoma multiforme, adenocarcinoma of lung, DUEB, susceptibility to, mdc1d, Exomes, GBM, Tumor of Neuroglia, INSDC_feature:gene, whole genome, LARGE_HUMAN, surveillance, morbidity, brca2, Fancd1, AI256696, response to tyrosine kinase inhibitor in, MDC1D, disease, wide, enr, FAD, Grade IV Astrocytomas, Material, Tumor of the Neuroglia, glial tumour, AW045498, not neoplastic), microarray, White, Cistron, Glioma, glial neoplasm, Cancer of the Lung, lung neoplasm, malignant (morphologic abnormality), E430016J11Rik, Powers, Neoplasms of Neuroglia, Cancer of the lung, Glioma NOS, mammary region, Psychological Power, whole exome, other disease, Lung, GLM3, Zmat2, Professional Power, malignant lung tumor, Neoplasms, peltate hair, neuroglial tumor, lung cancer, number, Gene, Neuroglial Tumor, broad, Grade IV, protein-containing complex, Malignant, Ximpact, LARGE1, presence, autosomal dominant, CG30169, froggy, Gyltl1a, E430004F23, C20orf88, Caucasian, resilient, tough, Gene Products, disease or disorder, MAF, glioblastoma, Low, FANCD1, Pulmonary Cancer, Giant Cell Glioblastomas, Mixed Gliomas, Pulmonary, c-MAF, IDHM, study, malignant tumour of the lung, Cross-Product Ratio, Risk Ratios, Genetic, grade IV adult astrocytic tumor, Glioma NOS (morphologic abnormality), occurrence, MDDGB6, mammary part of chest, prevalence, LNCR, LARGE, Glial Neoplasm, Ratio, neuroglial neoplasm, non-neoplastic, c-maf, Odds, BPFD#36, Glioblastoma Multiforme, Maf2, glial tumor, IDH2, Lung Neoplasm, FANCB, malignant neoplasm of lung, DUE-B, FANCD, disorder, 2810401A20Rik, Grade IV Astrocytoma, [M]Gliomas, Tumors of Neuroglia, Hars2l, incidence, Cancer, grade IV adult astrocytic tumour, bA555E18.1, Cross-Product, Pulmonary Neoplasms, cou, pqn-68, protein complex, malignant, ICD-M, Proteins, disorders, medical condition, 0610006H08Rik, Cistrons, Brustdruese, impact-a, neoplasm of neuroglia, Cross-Product Ratios, hars2, Concept, adult glioblastoma multiforme, count in organism, Lr, native protein, Protein, chemical analysis, malignant lung tumour, Nonsmall cell lung cancer, Neoplasm, imprinted and ancient gene protein homolog, IMPACT, condition, Professional, Mixed, rare (European definition), [M]Glioma NOS, scales, outbreaks, Caucasoid, Cross Product Ratio, Relative Risk, Glial Tumor, cMaf, glioblastoma multiforme, NOS (except Nasal glioma, malignant tumor of the lung, Power (Psychology)., Neuroglial Neoplasm, scale, Neuroglial Neoplasms, AI593507, Pulmonary Neoplasm, Glial Cell, Risks, Malignant glioma, Lobe of breast, 30169, dmbrca2, Glioblastomas, Cancers, RGD1308426, A230108G15Rik, endemics, Protein Gene Products, tumor of neuroglia, Neoplasm of Neuroglia, Gene Proteins, PRLTS2, Relative Odds, Personal Power, nonsmall cell lung cancer, 4631412B19Rik, no ICD-O subtype, like-glycosyltransferase, Whites, cardinality, Glial Cell Tumors, Bra, Malignant Gliomas, protection against, epidemics, Pulmonary Cancers, assay, RWDD5, breast, glycosyltransferase-like protein LARGE1"],"additional_accession":[]},"is_claimable":false,"name":"Glioma_Exome_FRE_CONTROLS - samples","description":"French glioma control germline genotypes using Illumina HumanExome-12v1_A array","dates":{"updated":"2017-07-26 15:39:26"},"accession":"EGAD00010000756","cross_references":{"TAXONOMY":["9606"],"pubmed":["26264438"],"EGA":["EGAC00001000345","EGAS00001001258"]}}