TCGA Lower-Grade Glioma

Overview

The TCGA Lower-Grade Glioma (LGG) cohort is a large, multi-institutional dataset assembled by The Cancer Genome Atlas program. It encompasses WHO grade II and grade III gliomas — a heterogeneous group that includes oligodendrogliomas, astrocytomas, and oligoastrocytomas. The cohort provides bulk genomic, transcriptomic, and clinical data across hundreds of samples, making it a widely used reference for validating findings derived from smaller or single-cell studies.

Composition

  • ~516 samples spanning WHO grade II–III gliomas (oligodendroglioma, astrocytoma, oligoastrocytoma); the oligodendroglioma subset (IDH-mutant, 1p/19q co-deleted) numbers approximately 69 samples used in validation analyses.
  • Cancer types (OncoTree): ODG and related lower-grade glioma subtypes.
  • Key molecular features captured: IDH1/IDH2 mutation status, 1p/19q co-deletion status, TERT promoter mutation, MGMT methylation, CpG island methylator phenotype (G-CIMP), copy-number alterations (GISTIC), somatic point mutations (WES), and bulk RNA expression (RNA-seq).
  • Reference genome: hg19.

Assays / panels (linked)

  • Bulk RNA-seq (gene expression profiles used for signature correlation analyses)
  • Whole-exome sequencing (somatic mutation and copy-number calling)

Papers using this cohort

  • PMID:27806376 — Tirosh et al. 2016, Nature: 69 bulk oligodendroglioma samples from TCGA LGG used as an external validation cohort for scRNA-seq-derived stem/progenitor and cell-cycle signatures.
  • PMID:28872634 — Bakas et al. 2017, Scientific Data: Expert-revised multi-parametric MRI segmentation labels and >700 radiomic features released for 108 TCGA-LGG cases (originating set n=199), enabling radiogenomic integration with lgg_tcga molecular data.
  • PMID:26824661 — Ceccarelli et al. 2016, Cell: TCGA pan-glioma integrated analysis using 516 LGG samples from this cohort merged with gbm_tcga into lgggbm_tcga_pub; identified six DNA-methylation subtypes and PA-like IDH-wildtype LGG.

Notable findings derived from this cohort

  • The scRNA-seq-derived stem/progenitor gene signature (defined in 6 primary oligodendrogliomas) correlates positively with the cell-cycle signature across the 69 TCGA LGG oligodendroglioma bulk samples, supporting the single-cell developmental hierarchy model in a larger independent cohort PMID:27806376.
  • Bakas et al. 2017 released expert-revised MRI segmentation labels (whole tumour, tumour core, non-enhancing tumour) for 108 TCGA-LGG cases via the TCIA tcia-tcga-lgg collection. LGG cases without apparent enhancing tumour were annotated as NET-only or NET+oedema, reflecting lower blood-brain-barrier disruption typical of low-grade glioma biology. These labels became the BraTS’17 reference standard and are paired with the molecular profiles in lgg_tcga for radiogenomic studies. PMID:28872634
  • Used as a component cohort (516 LGG samples, grades II–III) in the TCGA pan-glioma integrated analysis; merged with gbm_tcga into lgggbm_tcga_pub for a 1,122-patient study that redefined glioma classification by DNA-methylation subtype PMID:26824661

Sources

  • cBioPortal study: lgg_tcga — https://www.cbioportal.org/study/summary?id=lgg_tcga
  • TCGA LGG marker paper: Brat et al. 2015, NEJM (PMID 26061751).
  • PMID:26824661 — Ceccarelli et al. 2016, Cell, DOI 10.1016/j.cell.2015.12.028.

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