Clinical Proteomic Tumor Analysis Consortium (CPTAC)

Clinical Proteomic Tumor Analysis Consortium (CPTAC)

The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics.

Program Description

CPTAC is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of robust, quantitative, proteomic technologies and workflows. The overarching goal of CPTAC is to improve our ability to diagnose, treat and prevent cancer. To achieve this goal in a scientifically rigorous manner, the NCI launched CPTAC to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, and provide this data with accompanying assays and protocols to the public.

CPTAC has provided the Genomic Data Commons (GDC) with genomic data from a total of 1500+ cancer patients with diverse disease types including Endometrial, Renal, Lung Adenocarcinoma and Squamous Cell Carcinoma, Breast, Colon, Ovarian, Brain, Head and Neck, and Pancreatic cancers. The GDC harmonized DNA sequences from CPTAC whole genome sequencing (WGS), whole exomes sequencing (WXS), and RNA sequences with the GRCh38 reference genome using GDC DNA-Seq Analysis Pipelines and mRNA Analysis Pipelines, respectively. The CPTAC harmonized genomic data is available in the GDC Data Portal. CPTAC makes proteomic data that are processed through the CPTAC Common Data analysis Pipeline (CDAP) available in the CPTAC Data Portal. CPTAC proteomic data is also available in the Proteomic Data Commons (PDC).

Data Overview

The CPTAC genomic data can be found on the GDC Data Portal. To request access to protected CPTAC data, please apply to dbGaP for access to the CPTAC 3 Study (study accession phs001287 – endometrial, lung, kidney, brain, head and neck, and pancreatic cancers) or the CPTAC 2 Study (study accession phs000892 – ovarian, breast and colon cancers).

Cancer Types

Disease Type Primary Site
Adenomas and Adenocarcinomas Breast, Bronchus and lung, Colon, Kidney, Rectum, Uterus, NOS
Blood Derived Normal Breast
Cystic, Mucinous and Serous Neoplasms Breast, Other and unspecified female genital organs, Ovary, Retroperitoneum and peritoneum
Ductal and Lobular Neoplasms Breast, Pancreas
Gliomas Brain
Solid Tissue Normal Brain, Pancreas, Breast
Squamous Cell Neoplasms Breast, Bronchus and lung, Other and ill-defined sites

Proteomic and Associated Genomic Data

Data Types and Access Levels

Data Type Data Format # of Cases Data Access Level
Clinical and Biospecimen TSV,
1527 Open
WGS Aligned Reads BAM 1154 Controlled
WXS Aligned Reads BAM 1509 Controlled
WXS Raw Simple Somatic Mutations VCF 1496 Controlled
WXS Annotated Somatic Mutations VCF, MAF 1496 Controlled
WXS Aggregated Somatic Mutations MAF 1496 Controlled
WXS Masked Somatic Mutations MAF 1496 Open
Targeted Sequencing Aligned Reads BAM 72 Controlled
Targeted Sequencing Raw Simple Somatic Mutation VCF 72 Controlled
RNA-Seq Aligned Reads BAM 1523 Controlled
Gene Expression Quantification TXT 1523 Open
Splice Junction Quantification TSV 1523 Controlled
Transcript Fusion TSV, BEDPE 1523 Controlled
miRNA-Seq Aligned Reads BAM 1467 Controlled
miRNA Expression Quantification TSV 1467 Open
Isoform Expression Quantification TSV 1467 Open
Single Cell Analysis TSV, HDF5 22 Open
Methylation Arrays IDAT, TXT 1150 Open