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 900+ cancer patients with diverse disease types including Endometrial, Renal, Lung Adenocarcinoma and Squamous Cell Carcinoma, Breast, Colon, Ovarian, Brain, 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. 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, 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
990 Cases N/A Open
WGS Aligned Reads BAM 639 Cases
1539 Files
153.34 TB Controlled
WXS Aligned Reads BAM 979 Cases
2285 Files
101.37 TB Controlled
WXS Raw Simple Somatic Mutations VCF 966 Cases
4843 Files (5 Callers)
4.57 GB Controlled
WXS Annotated Somatic Mutations VCF, MAF 966 Cases
9686 Files (5 Callers)
18.13 GB Controlled
WXS Aggregated Somatic Mutations MAF 966 Cases
969 Files
401.24 MB Controlled
WXS Masked Somatic Mutations MAF 966 Cases
969 Files
78.03 MB Controlled
RNA-Seq Aligned Reads BAM 988 Cases
4011 Files
21.96 TB Controlled
Gene Expression Quantification TXT 988 Cases
5348 Files (4 Quantification Types)
1.9 GB Open
Splice Junction Quantification TSV 988 Cases
1337 Files
4.12 GB Controlled
miRNA-Seq Aligned Reads BAM 985 Cases
1332 Files
390.96 GB Controlled
miRNA Expression Quantification TSV 985 Cases
1332 Files
67.24 MB Open
Isoform Expression Quantification TSV 985 Cases
1332 Files
1.02 GB Open