Background
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NCI announced resources for the The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) (http://proteomics.cancer.gov/) aimed at integrating proteomic research with genomics so as to create a more unified understanding of tumor biology. As the CPTAC available tissue resources began to ramp up, a few legacy TCGA genetic-focused cases -- CPTAC analyzed -- were noted to have diagnostic images that are presently accessible on The Cancer Imaging Archive (TCIA). 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 Phase 3 Histopathology and Radiology Imaging
Histopathology Imaging
Find histopathology imaging matched with CPTAC Patient IDs or Specimen IDs here: https://cancerimagingarchive.net/datascope/cptac/simpleTable.html
You can query select pathology report details and view imaging from approved CPTAC cases here: https://cancerimagingarchive.net/datascope/cptac/.
A tutorial walk-through of the histopathology review system is available here.
Note: An improved histopathology imaging query system will be released Oct 1 2018
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 | Location |
Clear Cell Carcinoma | CT | 21 | Kidney | |
Cutaneous Melanoma | MR, CT, CR | 2 | Skin | |
Glioblastoma Multiforme | CT, MR | 27 | Brain | |
| CPTAC-HNSCC | Head and Neck Squamous Cell Carcinoma | CT, SC | 10 | Head-Neck |
Squamous Cell Carcinoma | CR, CT, DX, PT | 4 | Lung | |
Adenocarcinoma | CT, MR, PT, CR | 11 | Lung | |
Ductal Adenocarcinoma | CT, MR, DX, CR | 43 | Pancreas | |
Corpus Endometrial Carcinoma | CT, MR, PT, CR | 33 | Uterus |
CPTAC Phase 2 - TCGA Cancer Proteome Studies
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 The NCI Cancer Imaging Program is offering those specific cases, "shared list" downloadable as an opportunity for researchers to explore what such combined research resources might offer. They consist of 28 ovarian (TCGA-OV) and 14 breast (TCGA-BRCA) cases . Those imaging cases are easily downloadable as tumor specific groups from TCIA on the drop-down Tool-menu “shared lists” under the separate titles of: CPTAC BreastAnalyzed, and CPTAC OV Analyzed. Those image cases can be down-loaded by entering the afore-mentioned “shared lists” on https://public.cancerimagingarchive.net/ncia/searchCustomList.jsf Their case matched CPTAC Proteomic Analysis Data is down-loadable fromin TCIA which have corresponding CPTAC phase 2 proteomic analysis data. The Proteomic Analysis Data is available at: https://cptac-data-portal.georgetown.edu/cptacPublic/ The case specific Clinical Data that matches each of those TCIA archive image cases are attached here as XLS sheets.
CPTAC and TCGA Collections Publication Guidelines
TCIA publication guidelines, derived from the policy outlined by TCGA, must be followed in addition to the TCGA Data Portal publication policy: http://cancergenome.nih.gov/abouttcga/policies/publicationguidelines.
There are no limitations on publications containing analyses using TCGA-linked imaging data sets, if the data set meets one of the following three freedom-to-publish criteria:
- A marker paper has been published on that tumor type; or
- It has been 12 months since the authors’ DICOM data for 100 cases of a given tumor type have been published on TCIA; or
- The author receives specific approval from the TCGA ISS groups representing any relevant tumor types.
The specific status of each tumor data set is available on the Data Usage Policies and Restrictions page. Do not hesitate to contact help@cancerimagingarchive.net with any questions.
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Images and Clinical Data Downloads
These subsets of radiology images have been saved as Shared Lists using the following names:
- CPTAC Proteomic Breast TCIA TCGA cases
- CPTAC Proteomic Ovarian TCIA TCGA cases
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 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