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. Data (genomics, proteomics, imaging), assays, and reagents are made available to the public as a Community Resource to accelerate cancer research and advance patient care. TCIA has partnered with CPTAC to host both the radiology and pathology imaging data generated by the project.

CPTAC Imaging Special Interest Group

You can join the CPTAC Imaging Special Interest Group to be notified of webinars & data releases, collaborate on common data wrangling tasks and seek out partners to explore research hypotheses!  Artifacts from previous webinars such as slide decks and video recordings can be found on the CPTAC SIG Webinars page.

On July 1, 2019 representatives from the CPTAC program presented to the Imaging SIG.  This included an overview of the program and tutorials about how to access the data in the various CPTAC websites:

CPTAC Imaging  Cohorts

CPTAC imaging data is being made available on a release schedule that is coordinated with the CPTAC program releases of proteomic and genomic data.  

Learn more about each cancer type by clicking on the collection names in the table below.  Data currently available is listed below. Clicking on the number of subjects will take you to these data portals with that particular cancer type pre-selected.  You can access the radiology and pathology data directly from the respective data portals.  

Collection

Cancer Type

Location

Radiology Modalities

Radiology Total

Pathology Total

CPTAC-AML

Acute Myeloid Leukemia

Marrow, Blood



88

CPTAC-CCRCC

Clear Cell Carcinoma

Kidney

CR, CT, DX, MR, SR

63

222

CPTAC-CM

Cutaneous Melanoma

Skin

CR, CT, MR, PT

13

92

CPTAC-GBM

Glioblastoma Multiforme

Brain

CR, CT, DX, MR, NM, SC

66

189
CPTAC-HNSCCHead and Neck Squamous Cell CarcinomaHead-NeckCT, SC, MR64112

CPTAC-LSCC

Squamous Cell Carcinoma

Lung

CR, CT, DX, NM, PT

39

212

CPTAC-LUAD

Adenocarcinoma

Lung

CT, MR, PT, CR, DX, NM

33

244
CPTAC-PDAPancreatic Ductal AdenocarcinomaPancreasCR, CT, DX, MR, PT, RF, US, XA98168
CPTAC-SARSarcomasVarious (11) locationsCT, MR, PT, SR2488

CPTAC-UCEC

Corpus Endometrial Carcinoma

Uterus

CT, MR, PT, CR, DX

74

250

Corresponding Genomic, Proteomic, and Clinical Data

The other data types will be hosted in separate tools and databases including:

  1. CPTAC Data Portal 
  2. Proteomic Data Commons 
  3. Genomic Data Commons 
  4. CPTAC Python/R notebooks are available at https://github.com/PayneLab/cptac and on Google Colab at https://cutt.ly/ekMMht7.

CPTAC 2 Cohorts

Collection Cancer TypeLocation Pathology (Subjects)

CPTAC-BRCA

Breast Invasive CarcinomaBreast134

CPTAC-COAD

Colon AdenocarcinomaColon106

CPTAC-OV

Ovarian Serous CystadenocarcinomaOvary102



CPTAC - TCGA Cancer Proteome Studies

There are 28 ovarian (TCGA-OV) and 14 breast (TCGA-BRCA) cases in TCIA which have corresponding CPTAC phase 2 proteomic analysis data.  The Proteomic Analysis Data is available at: https://pdc.cancer.gov/pdc/browse.  


Images and Clinical Data Downloads

These subsets of radiology images can be accessed using the following links:

The clinical data for these subjects can be found in these spreadsheets:

References

An early CPTAC publication which reports on a more comprehensive collection of cases from those TCGA tumor data collections (BRCA and OV) can be found at: “Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes”. Xu Z, et al., J Proteome Res. 2015 Jan 2;14(1):422-33. doi: 10.1021/pr500840w.

An excellent review of proteomic biomarkers is the publication: "Proteomics in cancer biomarkers discovery: challenges and applications."  Sallam RM1. Dis Markers. 2015;2015:321370. doi: 10.1155/2015/321370.

Also: Identification of protein biomarkers in human serum using iTRAQ and shotgun mass spectrometry  Methods Mol Biol. 2013;1061:291-307. doi: 10.1007/978-1-62703-589-7_18Koutroukides TA1













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