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Background

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 histopathology 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.fevrier-sullivan@nih.gov

CPTAC - TCGA Cancer Proteome Studies

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.

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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 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.  

• Radiology Data Portal
• Pathology Data Portal  

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

CPTAC - TCGA Cancer Proteome Studies

There are 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 BreastAnalyzed" 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 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/  Moreover, the case specific Clinical Data that matches each of those TCIA archived image cases are attached here as XLS sheets.pdc.cancer.gov/pdc/browse.  

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:

1. A marker paper has been published on that tumor type; or
2. It has been 12 months since the authors’ DICOM data for 100 cases of a given tumor type have been published on TCIA; or
3. 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.