Background
NCI has announced resources for the Clinical Proteomic Tumor Analysis Consortium (CPTAC) (http://proteomics.cancer.gov/) aimed at integrating proteomic research with genomics to produce a more unified understanding of tumor biology. As the CPTAC available tissue donor resources begin to ramp up, a number of legacy TCGA genetic-focused cases -- CPTAC analyzed -- have diagnostic images already accessible on The Cancer Imaging Archive (TCIA).
CPTAC 3.0 Histopathology and Radiology Imaging
Histopathology Imaging
Histopathology imaging from approved CPTAC cases will be made available on TCIA. Currently TCIA hosts 265 images from 64 Subjects.
To access the histopathology imaging along with selected pathology report review data elements click here.
A tutorial walk-through of the histopatholgy review system is available here.
Radiology Imaging
TCIA is in the process of collection radiology clinical imaging from selected CPTAC tissue sources sites. The imaging data will be made available on TCIA as it is collected. For more information please contact: brenda.fevriersullivan@nih.gov
CPTAC - TCGA Cancer Proteome Studies
The NCI Cancer Imaging Program organized those CPTAC specific cases 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 from TCIA using the drop-down Tool-menu entry “shared lists” under the separate names of: "CPTAC Breast Analyzed" and "CPTAC OV Analyzed". The images of those grouped cases can be down-loaded by entering the afore-mentioned “shared lists” names on https://public.cancerimagingarchive.net/ncia/searchCustomList.jsf Their individual case-matched CPTAC Proteomic Analysis Data is down-loadable from: https://cptac-data-portal.georgetown.edu/cptacPublic/ Moreover, the case specific Clinical Data that matches each of those TCIA archived image cases are attached here as XLS sheets.
Image Downloads
Type "CPTAC Proteomic Breast TCIA TCGA cases" into the Image Search "Tools" drop-down menu item called "Shared List"
Type "CPTAC Proteomic Ovarian TCIA TCGA cases" into the Image Search "Tools" drop-down menu item called "Shared List"
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
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.