Thyroid Carcinoma (TCGA, PanCancer Atlas 2018)

Overview

The TCGA Thyroid Carcinoma PanCancer Atlas 2018 cohort is the thyroid arm of the TCGA PanCancer Atlas, available in cBioPortal as thca_tcga_pan_can_atlas_2018. It covers thyroid carcinoma samples with uniformly reprocessed somatic mutation calls (MC3 pipeline), copy-number, and RNA-seq expression. Thyroid carcinoma is notable for having the lowest aneuploidy score and the highest rate of druggable kinase fusions in the pan-cancer landscape.

Composition

  • Cancer type: Thyroid Carcinoma (THCA), OncoTree code THCA.
  • Approximately 507 tumor samples.
  • Data modalities: WES, RNA-seq, SNP array.
  • Somatic mutations from MC3 ensemble pipeline.
  • Copy-number from Affymetrix SNP 6.0 / ABSOLUTE; thyroid carcinoma has near-diploid profiles in most papillary cases.

Assays / panels (linked)

Papers using this cohort

Notable findings derived from this cohort

  • THCA is dramatically enriched for kinase fusions: 35.6% of THCA samples carry kinase fusions (Fisher p < 2.2e-16 vs. pan-cancer background), with 94.0% being 3′-kinase fusions that borrow a stronger upstream promoter; the top recurrent 3′-kinase partners are RET, BRAF, NTRK1, NTRK3, and ALK PMID:29617662.
  • CCDC6-RET is the most recurrent fusion in THCA (4.2%); 33 THCA samples are flagged as harboring druggable fusions targeting RET per DEPO annotation; both RET and NTRK fusions occur as inframe 3′-kinase events with intact catalytic domains PMID:29617662.
  • THCA has among the lowest aneuploidy scores in the pan-cancer cohort (26% of samples with any arm-level event, mean score 0.87 — the lowest of all 33 TCGA disease types), consistent with the predominantly mutation/rearrangement-driven pathogenesis of papillary thyroid carcinoma PMID:29617662.
  • Median fusion burden in THCA is 0 (i.e., most samples have no detected fusions outside of the kinase-fusion-enriched subset), reflecting a bimodal distribution with a distinct fusion-positive subgroup driven by RET, NTRK, and BRAF rearrangements PMID:29617662.

Sources

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