Thymic Epithelial Tumors — NCI 2014

Overview

The tet_nci_2014 dataset comprises 286 thymic epithelial tumor (TET) patients enrolled from four institutions: the National Cancer Institute (Bethesda), Pisa University Hospital, Padua University Hospital, and IRCCS Istituto Clinico Humanitas (Rozzano). It was generated by Petrini, Meltzer et al. (2014, Nature Genetics) and is the discovery cohort for the highly recurrent [[genes/GTF2I|GTF2I]] p.Leu404His hotspot mutation in TETs.

Composition

  • Cancer types: [[cancer_types/THYM|THYM]] (thymoma, WHO subtypes A, AB, B1, B2, B3) and [[cancer_types/THYC|THYC]] (thymic carcinoma).
  • 286 patients total; 270 tumors + 4 cell lines evaluated for GTF2I prevalence.
  • Survival data available for 204 patients (median follow-up 39.4 months, 95% CI 30.3–48.5).
  • Reference genome: hg19 / NCBI build 37.1.

Assays / panels (linked)

  • Whole-exome sequencing (tumor/normal pairs, n = 28)
  • Custom 197-gene targeted panel, MiSeq high-depth (n = 52; 26 overlapping with WES)
  • Array CGH — Agilent (n = 65)
  • RNA-seq — Illumina Genome Analyzer II / HiSeq2000 (n = 25)
  • GTF2I deep sequencing, n = 250; Sanger sequencing of GTF2I, n = 199

Papers using this cohort

  • PMID:24974848 — Petrini et al., Nature Genetics 2014. A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors.

Notable findings derived from this cohort

  • A single recurrent T>A missense mutation in [[genes/GTF2I|GTF2I]] (chr7:74146970; p.Leu404His in the β isoform) identified in 43.4% (119/270) of TETs overall; 82% of WHO type A and 74% of type AB thymomas; only 8% of thymic carcinomas PMID:24974848.
  • GTF2I-mutant patients had 96% 10-year disease-related survival vs 70% for wild-type (log-rank P < 0.001), establishing the mutation as a favorable prognostic biomarker PMID:24974848.
  • Thymic carcinomas had significantly higher mutation burden than thymomas (mean 43.5 vs 18.4 somatic mutations per sample, Mann-Whitney U P = 0.001) PMID:24974848.
  • Recurrent cancer-gene mutations in thymic carcinomas: [[genes/TP53|TP53]], [[genes/CYLD|CYLD]], [[genes/CDKN2A|CDKN2A]], [[genes/BAP1|BAP1]], [[genes/PBRM1|PBRM1]] PMID:24974848.
  • Copy-number aberrations enriched in aggressive histotypes; frequent arm-level gains at 1q (55%) and losses at 6q (29%), 6p (26%), 3p (22%); focal [[genes/BCL2|BCL2]] amplification correlated with elevated BCL2 mRNA PMID:24974848.
  • GEO accessions: GSE55852 (aCGH) and GSE57892 (NGS) PMID:24974848.

Sources

  • cBioPortal studyId: tet_nci_2014
  • Petrini I et al. A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors. Nat Genet. 2014. PMID:24974848.

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