Child pages
  • CPTAC Imaging Proteomics
Skip to end of metadata
Go to start of metadata

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 Phase 3 Histopathology and Radiology Imaging

Histopathology Imaging

You can query select pathology report details and view imaging from approved CPTAC cases here: CPTAC Pathology Portal.    

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

CPTAC-CCRCC

Clear Cell Carcinoma

CT

21

Kidney

CPTAC-CM

Cutaneous Melanoma

MR, CT, CR

2

Skin

CPTAC-GBM

Glioblastoma Multiforme

CT, MR

27

Brain

CPTAC-HNSCCHead and Neck Squamous Cell CarcinomaCT, SC10Head-Neck

CPTAC-LSCC

Squamous Cell Carcinoma

CR, CT, DX, PT

4

Lung

CPTAC-LUAD

Adenocarcinoma

CT, MR, PT, CR

11

Lung

CPTAC-PDA

Ductal Adenocarcinoma

CT, MR, DX, CR

43

Pancreas

CPTAC-UCEC

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 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/.  


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 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


 

  • No labels