Seven Bridges visits Dana Farber

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Seven Bridges visits Dana Farber

Last week Seven Bridges spent some time at the Dana Farber Cancer Institute, at the annual genomic approaches towards precision cancer medicine symposium. This event, organized by the Center for Cancer Genome Discovery showcases the work of Dana Farber researchers.

Genomic profiling methods are increasingly used to study cancer alterations in individual patients, enabling precise diagnosis and patient stratification for the development of more efficient therapeutic options.

The aim of this symposium was to present and discuss the latest technologies and applications used in cancer genomics and their application in personalized clinical practice. The attendants were clinicians, clinical researchers and basic researchers.

Things we liked

Barrett Rollins gave an update on Profile, a huge project that aims to make accessible genomic profiles of all patients with cancer treated at Dana Farber, Brigham Women’s Hospital and Boston Children’s Hospital—approximately 16,000 patients per year.

The project uses a 309-candidate panel to identify mutations and other DNA alterations that drive a patient’s cancer. The tumor genetic profiles are linked to clinical information, and are used both for research and to guide clinical decision making.

Ethan Cerami discussed computational infrastructure for precision medicine. He presented cBioPortal, a web-based exploratory data analysis portal explicitly designed for biologists and clinicians. A visualization tool (OncoPrinter) provides compact visualization of discrete genomic events in specific samples. Here’s OncoPrinter in action, for TP53, MDM2 and MDM4 alterations in glioblastoma. More features of this dataset can be explored here.

OncoPrinter output showing genetic alterations in three genes among 91 glioblastoma samples from The Cancer Genome Atlas. Image from

Geoffrey Oxnard discussed cell-free plasma DNA genotyping in clinical care and cancer discovery. Tumor cells release small pieces of DNA into the bloodstream, which can be detected by droplet digital PCR (ddPCR) diagnostic assay, a target-gene PCR method with high amplification efficiency. Applied to lung cancer, testing for common driver mutations in EGFR and KRAS is used to follow treatment response, disease progression and drug resistance. The next goal is to investigate the effects of treatment based on plasma rather than tumor genotype.

Many thanks to Rene for providing detailed notes on the day’s activities.