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Background

Excerpt

NCI has 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 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. 

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

CPTAC imaging data will be made available on a quarterly release schedule.  Data currently available includes:

Collection

Cancer Type

Location

Radiology Modalities

Radiology (Subjects)

Pathology (Subjects)

CPTAC-CCRCC

Clear Cell Carcinoma

Kidney

CT

26

221

CPTAC-CM

Cutaneous Melanoma

Skin

MR, CT, CR

2

49

CPTAC-GBM

Glioblastoma Multiforme

Brain

CT, MR

32

109
CPTAC-HNSCCHead and Neck Squamous Cell CarcinomaHead-NeckCT, SC2263

CPTAC-LSCC

Squamous Cell Carcinoma

Lung

CR, CT, DX, PT

4

84

CPTAC-LUAD

Adenocarcinoma

Lung

CT, MR, PT, CR

12

164

CPTAC-PDA

Ductal Adenocarcinoma

Pancreas

CT, MR, DX, CR

45

77

CPTAC-UCEC

Corpus Endometrial Carcinoma

Uterus

CT, MR, PT, CR

35

178

...


A tutorial walk-through of the histopathology review system is is available here.

...

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 Phase 2 - 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 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 . 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..  


Images and Clinical Data Downloads

These subsets of radiology images have been saved as Shared Lists using the following names:

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"

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.

...

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.