biostudies-literature00560Roy DMLouis Gerstner FoundationSontag FoundationNIH MSTPMSKCC Brain Tumor CenterThe Geoffrey Beene FoundationNCI NIH HHSNational Institutes of HealthHHMI Medical Research Fellows ProgramCanadian Institutes of Health ResearchNIGMS NIH HHS737-750https://www.ebi.ac.uk/biostudies/studies/S-EPMC4864611biostudies-literatureUnknown29(5)The identification of driver loci underlying arm-level somatic copy number alterations (SCNAs) in cancer has remained challenging and incomplete. Here, we assess the relative impact and present a detailed landscape of arm-level SCNAs in 10,985 patient samples across 33 cancer types from The Cancer Genome Atlas (TCGA). Furthermore, using chromosome 9p loss in lower grade glioma (LGG) as a model, we employ a unique multi-tiered genomic dissection strategy using 540 patients from three independent LGG datasets to identify genetic loci that govern tumor aggressiveness and poor survival. This comprehensive approach uncovered several 9p loss-specific prognostic markers, validated existing ones, and redefined the impact of CDKN2A loss in LGG.Cancer cellIntegrated Genomics for Pinpointing Survival Loci within Arm-Level Somatic Copy Number Alterations.PMC4864611T32 GM007739P30 CA008748RO1-CA154767A1R01 CA154767T32GM007739RO1 CA177828R01 CA177828Huse JTGao JChan TARoy DMWalsh LADesrichard AWu WLee WBose P56falseIntegrated Genomics for Pinpointing Survival Loci within Arm-Level Somatic Copy Number Alterations.The identification of driver loci underlying arm-level somatic copy number alterations (SCNAs) in cancer has remained challenging and incomplete. Here, we assess the relative impact and present a detailed landscape of arm-level SCNAs in 10,985 patient samples across 33 cancer types from The Cancer Genome Atlas (TCGA). Furthermore, using chromosome 9p loss in lower grade glioma (LGG) as a model, we employ a unique multi-tiered genomic dissection strategy using 540 patients from three independent LGG datasets to identify genetic loci that govern tumor aggressiveness and poor survival. This comprehensive approach uncovered several 9p loss-specific prognostic markers, validated existing ones, and redefined the impact of CDKN2A loss in LGG.2016-01-01T00:00:00Z2016 May2024-10-18T20:04:09.272Z2019-03-27T02:13:32ZS-EPMC48646112716574510.1016/j.ccell.2016.03.025