GSE111688 BRCA1 and BRCA2 classification of ovarian cancer

Contributors : Philip C Schouten ; Daniel J Vis ; Ewald van Dijk ; Esther H Lips ; Esther Scheerman ; Carolien H van Deurzen ; Patricia C Ewing-Graham ; Agnes Jager ; Els M Berns ; Petra M Nederlof ; Lodewyk F Wessels ; Sabine C LinnSeries Type : Genome variation profiling by genome tiling arrayOrganism : Homo sapiensInactivating germline BRCA1 and BRCA2 mutations confer a defect in homologous recombination DNA repair which was found to leave traces in tumor DNA copy number aberration (CNA) profiles. In analogy to previously trained breast cancer CNA classifiers that predicted association with BRCA1 and BRCA2 mutated cancer and benefit of high dose double strand break inducing chemotherapy, we trained BRCA1 and BRCA2 classifiers on CNA profiles of 50 BRCA1 mutated, 10 BRCA2 mutated and 13 non-familial ovarian cancers and investigated whether tumor type and mutation type independent classifiers could be trained. The cross validated area under the curve of the receiver/operator characteristic curve of ovarian cancer BRCA1 and BRCA2 classifiers were 0.67 (95% CI: 0.55-0.78) and 0.91 (95% CI: 0.79-1). These classifiers identified the majority of the samples with germline and somatic BRCA1 and BRCA2 mutations and BRCA1 promoter hypermethylation in the Cancer Genome Atlas (TCGA) dataset. Combining tumor type or mutated gene did not yield higher AUCs than single gene classifiers, although the ovarian BRCA1+BRCA2 classifier identified most BRCA1 and -2 mutated cases, including tho...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Genome variation profiling by genome tiling array Homo sapiens Source Type: research