TCGA in Action features profiles of The Cancer Genome Atlas (TCGA) researchers and case studies on how other researchers are using TCGA data to make or validate new discoveries.
CASE STUDY: A Researcher Mined TCGA Data to Study Her Own Ovarian Cancer
Faced the bleak prognosis associated with stage IIIC ovarian cancer, Shirley Pepke, Ph.D., used her computational biology background to study her own cancer in comparison to TCGA data. Pepke has now been in remission for a year. Image Credit: Gus Ruelas/USC
CASE STUDY: TCGA Data Leveraged for Developing FDA-Designated Breakthrough Therapy
Pharmaceutical company Loxo Oncology used TCGA data in the research that led them to develop FDA-designated Breakthrough Therapy LOXO-101, a promising new targeted therapy.
RESEARCHER PROFILE: Next Generation Mentoring
Dr. Hui Shen, Ph.D. is a cancer genomicist who was “born and raised in TCGA.” From the outset of her graduate education, she had the opportunity to work with multiple mentors spanning scientific fields and institutions. Her advice: “Definitely try out team science.”
RESEARCHER PROFILE: Compassion and Curiosity
William Kim, M.D., is motivated by two things: compassion and curiosity. Dr. Kim has taken these dual motivations and created a career in which he cares directly for patients and spearheads research that may lead to improved treatment options.
CASE STUDY: Filling in the Gaps in the Catalog of Cancer Genes
Dr. Gad Getz and his group at the Broad Institute of MIT and Harvard identifies 33 new cancer-causing genes and finds that the catalog of cancer genes is far from complete. Learn more about the current cancer genome landscape in this Case Study.
CASE STUDY: The Cancer Digital Slide Archive: A Web Platform for Accessing TCGA Data
Dr. David Gutman and Dr. Lee Cooper developed The Cancer Digital Slide Archive (CDSA), a web platform for accessing pathology slide images of TCGA samples. Find out how they did it and how to use the CDSA website in this Case Study.
CASE STUDY: Using Forensics to Untangle Batch Effects in TCGA Data
Rehan Akbani, Ph.D., and colleagues at the University of Texas MD Anderson Cancer Center developed a tool called MBatch to detect, diagnose, and correct batch effects in TCGA data. Read more about batch effects in this Case Study.
CASE STUDY: Reinvigorating GBM Research with Hope for Future Therapies
Dr. Antonio Iavarone and his research group at Columbia University have discovered the first recurrent gene fusion in glioblastoma. Find out how they did it and potential implications in this Case Study.
RESEARCHER PROFILE: Cancer Research by the Numbers
Biostatistician Dr. Jill Barnholtz-Sloan strives to make a difference in the field of cancer research while inspiring her students at the same time. Learn more about how she uses TCGA data in her career in this TCGA in Action Researcher Profile.
CASE STUDY: The New Genomic Bottleneck and How the Cloud Might Widen It
Computational biologist Dr. Ilya Shmulevich suggests that renting cloud computing power might widen the bottleneck for analyzing genomic data. Learn more about his experience with the Cloud in this TCGA in Action Case Study.
RESEARCHER PROFILE: The Business in Science
Dr. Raju Kucherlapati is an accomplished scientist and successful businessman. Learn more about how he fits these professions together in this TCGA in Action Researcher Profile.
CASE STUDY: From the Bedside to Bench and Back Again
Dr. Adam Bass talks about his bench to bedside and back again principle. Learn more about Dr. Bass and his philosophy in this TCGA in Action Case Study.
CASE STUDY: Using New Maps to Navigate Cancer Treatment
Drs.Scott Hwang and Chad Holder of Emory University discuss the development of VARSARI and The Cancer Imaging Program's TCGA Radiology Initiative. Learn more about their and Dr. Carl Jaffe's work in this TCGA In Action Case Study.
CASE STUDY: Using an Algorithm to Find “Driver” Mutations
Dr. Ben Raphael shares his experience developing HotNet and working with TCGA data. Learn more about Dr. Raphael and HotNet in this Case Study.
RESEARCHER PROFILE: How Phlebotomy and the Amish Paved the Way for this Leader in Cancer Genomics
Dr. Stacey Gabriel began her career in genetics while working on a rare disease in the Amish. Learn more about her experience witnessing the human element of genetics in this TCGA in Action Researcher Profile.
CASE STUDY: Screening Cancer Genomes for Essential Drivers
Associate Professor of Medicine at the Dana-Farber Cancer Institute, William Hahn, describes the method his lab has developed to tease apart the crucial driver mutations from passenger mutations in ovarian cancer. Learn more about his approach in this TCGA in Action Case Study.
RESEARCHER PROFILE: A Surgeon's Search for the Kidney Cancer Gene
Dr. Marston Linehan, NCI's Chief of Urologic Surgery, has spent the last several decades studying kidney cancer genes and treating kidney cancer patients. Learn more about his experience as a kidney cancer physician scientist and TCGA contributor in this TCGA in Action Researcher Profile.
CASE STUDY: New Tool Combines Many Types of Genomic Data
Rachel Karchin, of Johns Hopkins University's Department of Biomedical Engineering, is developing a tool that will help researchers sort through the massive amounts of genomic data gathered from TCGA's ovarian cancer tumor samples. Learn more about her progress in this TCGA in Action case study.
CASE STUDY: Using TCGA Data to Validate GBM Signaling Pathways
Neurosurgeon Cameron Brennan of Memorial Sloan-Kettering Cancer Center used TCGA data to define subgroups of patients with a deadly brain cancer called glioblastoma multiforme. Learn more about his research in this TCGA in Action case study.