Dissecting Cellular Heterogeneity, Electronic Notebooks, and Next-Gen Cancer Models: August OCG e-Newsletter
, by OCG Staff
The latest edition of the Office of Cancer Genomics (OCG) e-Newsletter features single-cell RNA sequencing, applications of next-generation cancer models, the GenePattern Notebook, collecting uniform clinical data, and a perspective piece from OCG staff. OCG is a member office of the Center for Cancer Genomics.
Dissecting Cellular Heterogeneity using Single-cell RNA Sequencing
Anuja Sathe, M.B.B.S., Ph.D. and Hanlee P. Ji, M.D. from Stanford University
Single-cell RNA sequencing enables analysis of the transcriptomes of individual cells, provides information on cell-states, and allows a high-resolution characterization of heterogeneous tumor microenvironments. It can be used to discover therapeutic targets and enable mechanistic understanding of target inhibition, fostering translational applications.
Scientific Applications of Next-Generation Cancer Models
Cindy Kyi, Ph.D.
The Human Cancer Models Initiative (HCMI) is providing the scientific community with next-gen cancer models that more closely resemble primary tumors and are annotated with genomic and clinical data. The article provides examples of how next-gen models have been applied in research.
GenePattern Notebook: Integration of Electronic Notebooks with Bioinformatics Tools for Genomic Data Analysis
Michael Reich from the University of California, San Diego
The GenePattern Notebook is an electronic notebook that enables integrative genomic analyses. These analyses are displayed in a user-friendly form and allows scientists even without programming experience to share, collaborate, and publish the results.
Collecting Uniform Clinical Data for a Community Resource
Eva Tonsing-Carter, Ph.D.
HCMI’s clinical report forms (CRFs) standardize the clinical data collected from participating Tissue Source Sites (TSSs). The article discusses the process of developing cancer type-specific CRFs to ensure uniformity and compatibility for use at TSSs across the globe.
Leveraging a Genomics Background to Facilitate Molecular Characterization of HCMI Models
Lauren Hurd, Ph.D.
In this perspective article, Dr. Lauren Hurd, a new Scientific Program Manager for HCMI, discusses her background in genomics and its applications in her current role.