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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. |
CPTAC has been conducted in multiple phases. For their phase 3 prospective data collection activities TCIA has partnered with CPTAC to host both the radiology and pathology imaging data generated by the project. The other data types will be hosted in separate databases managed by the CPTAC program. TCIA will provide links to these resources as they become publicly available.
CPTAC
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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.
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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:
- Welcome (Bob Nordstrom)
- Clinical Proteomic Tumor Analysis Consortium (CPTAC) Project Overview (Chris Kinsinger, 15min)
- CPTAC radiology & pathology image data at TCIA – live demo (Justin Kirby, 15min)
- CPTAC Data Portal and the Proteomics Data Commons (R. Rajesh Thangudu, 30min)
- CPTAC genomic data at the Genomics Data Commons (Ana Robles, 15min)
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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 Tumor Annotations | Radiology Total Subjects | Pathology Total Subjects |
| Acute Myeloid Leukemia | Marrow, Blood | 88 |
Histopathology Imaging
Histopathology imaging and select pathology report details from approved CPTAC cases will be made available on TCIA at: https://cancerimagingarchive.net/datascope/cptac/.
A tutorial walk-through of the histopathology review system is available here.
Radiology Imaging
TCIA is also in the process of collecting radiology imaging from contracted CPTAC tissue sources sites. The imaging data will be made available on a quarterly release schedule. Data currently available includes:
Collection
Cancer Type
Modalities
Subjects
| Clear Cell Carcinoma | Kidney | CT |
21
, MR, RTSTRUCT | CPTAC-CCRCC-Tumor-Annotations | 65 | 222 |
| Cutaneous Melanoma | Skin | CT, MR, |
PT |
13 |
| 92 | |||
| Glioblastoma Multiforme | Brain | CT, MR |
66 |
| 178 | |||
| CPTAC-HNSCC | Head and Neck Squamous Cell Carcinoma | Head-Neck | CT |
| , MR, PT, RTSTRUCT | CPTAC-HNSCC-Tumor-Annotations | 122 | 112 |
| Squamous Cell Carcinoma |
Lung | CT |
, PT |
36 |
| 212 | |||
| Adenocarcinoma | Lung | CT, MR, PT |
25 |
| 244 | |||
| CPTAC-PDA | Pancreatic Ductal Adenocarcinoma | Pancreas | CT, MR |
43
| , PT, US | CPTAC-PDA-Tumor-Annotations | 108 | 168 | |||
| CPTAC-SAR | Sarcomas | Abdomen, Arm, Bladder, Chest, Head-Neck, Kidney, Leg, Retroperitoneum, Stomach, Uterus | CT, MR, PT | 24 | 88 |
| Corpus Endometrial Carcinoma | Uterus | CT, MR, PT, |
33
Uterus
CPTAC Phase 2 - TCGA Cancer Proteome Studies
US | CPTAC-UCEC-Tumor-Annotations | 85 | 250 |
Corresponding Genomic, Proteomic, and Clinical Data
The other data types will be hosted in separate tools and databases including:
- CPTAC Data Portal
- Proteomic Data Commons
- Genomic Data Commons
- 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 Type | Location | Pathology (Subjects) |
|---|---|---|---|
| Breast Invasive Carcinoma | Breast | 134 | |
| Colon Adenocarcinoma | Colon | 106 | |
| Ovarian Serous Cystadenocarcinoma | Ovary | 102 |
CPTAC - TCGA Cancer Proteome Studies
There are TCIA did not formally participate in CPTAC phase 2, but a small subset of the radiology imaging studies for this cohort are available due to overlap with NIH's Cancer Genome Atlas activity. Specifically 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://cptac-data-portal.georgetown.edu/cptacPublic/pdc.cancer.gov/pdc/browse.
Images and Clinical Data Downloads
These subsets of radiology images have been saved as Shared Lists can be accessed using the following nameslinks:
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_18. Koutroukides TA1