Oncotator

Overview

Oncotator is a cancer-focused variant annotation tool developed at the Broad Institute. It annotates somatic mutations with information from multiple cancer-specific databases including COSMIC, OncoKB, and UniProt, providing protein change information, functional impact predictions, and known oncogenicity classifications specifically tailored to somatic variant interpretation.

Used by

  • Applied alongside annovar for somatic variant annotation in ICGC PedBrain pilocytic astrocytoma WGS study (96 cases); annotated SNVs and indels discovered by genome-wide sequencing in the pediatric brain tumor cohort PMID:23817572
  • Used to annotate somatic variants from whole-exome sequencing of 45 BRAF V600 metastatic melanoma tumors (DeCOG cohort) aligned to hg19 via the Broad Picard/Firehose pipeline PMID:24265153.
  • Used for somatic variant annotation in the rhabdomyosarcoma genomic landscape study (147 tumor/normal pairs); applied alongside ANNOVAR to annotate mutation consequences, known cancer hotspots, and pathway membership; reference build hg19 PMID:24436047
  • Used to annotate somatic variants in 50 urothelial carcinoma tumors in the cisplatin-response WES study. PMID:25096233
  • Used to annotate somatic variants in 69 matched CRC trios with COSMIC v65 annotations as part of the MSK-IMPACT concordance study. PMID:25164765
  • Used to annotate somatic variants against dbSNP 134 and 1000 Genomes in the DFCI-ONCOPANEL-1 pipeline for 29 metastatic cSCC samples; identified high UV-signature mutation rate (~33 mut/Mb) and recurrent RAS/RTK/PI3K pathway activating mutations PMID:25589618
  • Oncotator used for variant annotation alongside Alamut in 243 HCC exomes to classify somatic mutations for driver discovery. PMID:25822088
  • Broad Institute Oncotator used to annotate somatic mutations identified by MuTect and VarScan in 109 microdissected PDA exomes. PMID:25855536
  • Oncotator used for somatic mutation annotation in colorectal cancer genomic analysis PMID:26343386
  • Oncotator used for functional annotation of somatic variants in 114 metastatic CRPC biopsies (whole-exome sequencing pipeline); variants annotated to identify non-silent SNVs and driver gene alterations PMID:26855148
  • Used for SNV/INDEL annotation in anti-PD-1-treated metastatic melanoma WES data (38 tumor/normal pairs) PMID:26997480
  • Used to annotate somatic variants identified by MuTect and SNVseeqer in 72 urothelial carcinoma tumours for functional classification. PMID:27749842
  • Oncotator used to annotate somatic mutations pooled from four sequencing centers (Broad, Washington University, UCSC, BCCA) in the TCGA esophageal/stomach study of 164 oesophageal carcinomas PMID:28052061.

Notes

  • Corpus-grown slug; not found in cBioPortal canonical gene panel ontology.
  • Now largely superseded by Funcotator in GATK4 workflows, but widely used in early TCGA-era analyses.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:24265153

This page was processed by crosslinker on 2026-05-14. - PMID:24436047

This page was processed by crosslinker on 2026-05-14. - PMID:25096233

This page was processed by crosslinker on 2026-05-14. - PMID:25164765

This page was processed by crosslinker on 2026-05-14. - PMID:25589618

This page was processed by crosslinker on 2026-05-14. - PMID:25822088

This page was processed by crosslinker on 2026-05-14. - PMID:25855536

This page was processed by crosslinker on 2026-05-14. - PMID:26343386

This page was processed by entity-page-writer on 2026-05-15. - PMID:26855148

This page was processed by entity-page-writer on 2026-05-15. - PMID:26997480

This page was processed by entity-page-writer on 2026-05-15. - PMID:27749842

This page was processed by entity-page-writer on 2026-05-15. - PMID:28052061

This page was processed by wiki-cli on 2026-05-14.