Glioblastoma Multiforme (TCGA, PanCancer Atlas 2018)

Overview

The TCGA GBM PanCancer Atlas 2018 cohort is the glioblastoma multiforme arm of the TCGA PanCancer Atlas, curated under the canonical cBioPortal study ID gbm_tcga_pan_can_atlas_2018. It aggregates 617 GBM tumor samples with uniformly reprocessed somatic mutation calls (MC3 pipeline), copy-number segmentation (Affymetrix SNP 6.0 / ABSOLUTE), and RNA-seq expression. It is one of the 33 disease-type cohorts constituting the TCGA PanCancer Atlas released in 2018.

Composition

  • Cancer type: Glioblastoma Multiforme (GBM), OncoTree code GBM.
  • Approximately 617 tumor samples with matched normals.
  • Data modalities: whole-exome sequencing (WES), RNA-seq (Illumina), SNP array copy-number (Affymetrix SNP 6.0).
  • Somatic mutations from the MC3 ensemble pipeline (7 callers, open-access PASS MAF).
  • Arm-level and focal copy-number calls derived via ABSOLUTE and GISTIC 2.0.

Assays / panels (linked)

Papers using this cohort

  • PMID:29596782 — MC3 mutation calling (Ellrott et al., 2018)
  • PMID:29617662 — Pan-cancer fusion catalog (Gao et al., 2018)
  • PMID:29622463 — Pan-cancer aneuploidy landscape (Taylor et al., 2018)

Notable findings derived from this cohort

  • MC3 ensemble mutation calls (7 callers, 10,510 TCGA tumor/normal pairs, 33 cancer types) form the somatic-variant backbone of this PanCanAtlas cBioPortal study; GBM samples showed low median SNV burden consistent with non-tobacco/UV exposure PMID:29596782.
  • Pan-cancer RNA-seq fusion analysis (9,624 TCGA tumors) spanned GBM as one of 33 disease types, with the GBM fusion landscape anchored to this dataset; GBM showed a median of 1 fusion per sample consistent with the pan-cancer median PMID:29617662.
  • Pan-cancer aneuploidy analysis of 10,522 TCGA tumors found GBM to have the highest rate of any arm-level aneuploidy (99% of samples, mean aneuploidy score 8.2), clustering in a neural-lineage group with LGG characterized by chromosome 7 gain and chromosome 10 loss; IDH-wildtype GBM was specifically defined by this chr7-gain/chr10-loss pattern PMID:29622463.

Sources

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