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 800+ cancer patients with diverse disease types including Endometrial, Renal, Lung Adenocarcinoma, Breast, Colon, Ovarian, and Head and Neck 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.

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, and head and neck cancers) or the CPTAC 2 Study (study accession phs000892 – ovarian, breast and colon cancers).

Cancer Types

Data Types and Access Levels

Data Type Data Format # of Cases and Files Estimated File Size Data Access Level
Clinical and Biospecimen TSV,
JSON
882 Cases N/A Open
WGS Aligned Reads BAM 531 Cases
1258 Files
126.63 TB Controlled
WXS Aligned Reads BAM 871 Cases
1972 Files
89.81 TB Controlled
WXS Raw Simple Somatic Mutations VCF 858 Cases
4303 Files (5 Callers)
4.4 GB Controlled
WXS Annotated Somatic Mutations VCF, MAF 858 Cases
8606 Files (5 Callers)
16.96 GB Controlled
WXS Aggregated Somatic Mutations MAF 858 Cases
861 Files
364.25 MB Controlled
WXS Masked Somatic Mutations MAF 858 Cases
861 Files
68.98 MB Controlled
RNA-Seq Aligned Reads BAM 880 Cases
3399 Files
18.33 TB Controlled
Gene Expression Quantification TXT 880 Cases
4532 Files (4 Quantification Types)
1.6 GB Open
Splice Junction Quantification TSV 880 Cases
1133 Files
3.44 GB Controlled
miRNA-Seq Aligned Reads BAM 877 Cases
1129 Files
311.29 GB Controlled
miRNA Expression Quantification TSV 877 Cases
1129 Files
56.94 MB Open
Isoform Expression Quantification TSV 877 Cases
1129 Files
845.17 MB Open