Next-Gen Technologies for Next-Gen Cancer Models, a PANACEA Database for Identifying Drug Off-Targets, and Updates to the CTD^2 and HCMI Programs: February OCG e-Newsletter
, by OCG Staff
The latest edition of the Office of Cancer Genomics (OCG) e-Newsletter features a new program which will develop technologies facilitating next-generation cancer model usage, new features and functions of the CTD2 Dashboard, updates to available models from HCMI and new features of the Searchable Catalog, and the CTD2 PANACEA DREAM Challenge. OCG is a member office of the Center for Cancer Genomics.
Next-Generation Technologies for Next-Generation Cancer Models
Cindy Kyi, Ph.D. and Eva-Tonsing-Carter, Ph.D.
The Next-Generation Technologies for Next-Generation Cancer Models Program (NGT) supports the development of technologies and tools that will facilitate and enhance research using organoids and other next-generation cancer models. Such tools include robust genome editing and screening protocols as well as computational methods for advanced data interpretation.
CTD² Dashboard: Content and Feature Updates
Kenneth Smith, Ph.D., Vlado Dancik, Ph.D., Zhou Ji, Ph.D., Aristidis Floratos, Ph.D., and Paul Clemons, Ph.D.
CTD2 Network researchers produce a large volume of observations gathered from multiple experimental and computational approaches. The CTD² Dashboard aims to help researchers navigate and understand these results. The Dashboard has recently been improved in presentation, annotation of experimental methods, search functionality, and linking to external data resources and web applications.
HCMI Program Updates and New Features of the Searchable Catalog
Eva Tonsing-Carter, Ph.D. and Cindy Kyi, Ph.D.
The Human Cancer Models Initiative (HCMI) has so far developed 148 cancer models from 18 primary sites, with quality-controlled clinical, biospecimen and molecular characterization data being added as they become available. The HCMI Searchable Catalog has been updated with new features for users to easily locate models of interest and their corresponding data at the Genomic Data Commons.
CTD² PANcancer Analysis of Chemical Entity Activity (PANACEA) DREAM Challenge
Eugene F. Douglass Jr., Ph.D., Bence Szalai, Ph.D., Robert J. Allaway, Ph.D., and Andrea Califano, Ph.D.
To better understand the off-target programs of cancer therapies, CTD2 researchers at Columbia University built PANACEA: a gene expression database for 21 cell lines treated with 400 FDA-approved cancer drugs. Additionally, a community DREAM Challenge using PANACEA data was hosted to identify machine learning methods to identify off-targets from 30 of the most common clinically-used targeted therapies.