This month, TIES makes The Cancer Genome Atlas (TCGA) part of its big data TIES Cancer Research Network (TCRN). With access to the publicly available clinical data (NLP annotated pathology reports, TCGA clinical data, and Whole Slide Images), TIES users can quickly subset the TCGA cases to find exactly the right cohort, putting the semantic features of the clinical text and images at their fingertips.
The Cancer Genome Atlas is the premier encyclopedia of molecular changes in cancer, presenting more than 11,000 cancer cases and over 22 different cancer subtypes. With more than 2.5 petabytes of high throughput sequencing data and dozens of datatypes, TCGA data can be a challenge for investigators to work with. Even working with the publically available clinical data can be a barrier. Enter TIES – and the TIES Cancer Network.
More information about the TCGA dataset can be found here: https://cancergenome.nih.gov/
What can you do with TCGA in TIES?
- Find cases based on the semantic features of the pathology report, even though the TCGA clinical data fields may not include this feature (e.g. DCIS or tumor-infiltrating lymphocytes)
- Find cases based on combinations of structured and unstructured data (e.g. cases of Glioblastoma with necrosis from text, restricted to patients who had no radiation)
- Search only within specific TCGA disease groups or across all groups
- View whole slide images from cases
- Look up cases by TCGA barcode ID
- Export TCGA barcodes and other data to excel, to help you quickly create the subset you need for analyzing TCGA sequencing data
See TIES in action with the TCGA Data in this 4 minute video clip: http://ties.dbmi.pitt.edu/tcga-data/
How do I access the TCGA data through TIES?
We are making the publicly available TCGA clinical data accessible to all users within the TIES Cancer Research Network (TCRN) and to outside users.
TCRN Users – If you currently access TIES through any TCRN institution (University of Pittsburgh, University of Pennsylvania, Roswell Park Cancer Institute, Augusta University, or Thomas Jefferson University) look for the new TCGA study in your study list when you log in to TIES next time or ask your TCRN administrator to add you.
Other Users – If your institution is not part of TCRN, we will provide access to the publically available data through a TIES demo account. You can request the account here: http://ties.dbmi.pitt.edu/ties-demo-account-request-form/
With all of this new data, what will you use TCGA and TIES to do? What analyses can you do now that you weren’t able to do before?