Twenty academic institutions, diagnostic and drug developers, and government agencies have begun creating an open database for liquid biopsy data—a pilot project of Vice President Joe Biden’s “Cancer Moonshot”—aimed at advancing development of blood profiling diagnostic technologies.
The Blood Profiling Atlas pilot plans to aggregate, make freely available, and harmonize raw datasets from circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and exosome assays. It will also include select clinical data.
“Our goals are to start producing in the next 45 to 60 days; for the group to have actual data flowing through an actual location; and [have] some understanding of what's in that data,” Andrew Gruen, director of marketing with Seven Bridges, told Clinical OMICs.
Seven Bridges, a developer of biomedical data analysis tools, is partnering with University of Chicago to curate the pilot’s datasets. The company has committed to providing six months of engineering, bioinformatics and project management resources, and up to $500,000 of computing and storage to facilitate use of the analytic tools, as well as data donated by stakeholders.
“Should we really get this up and running, and we start to do prospective studies, we could be talking about exabytes of data,” Gruen said.
The pilot will include sample preparation and handling protocols from studies by 13 of the 20 stakeholders—AstraZeneca, Eli Lilly, Epic Sciences/Memorial Sloan Kettering Cancer Center (MSK), Foundation Medicine, Genentech, Guardant Health, Novartis, Personal Genome Diagnostics (PGDx), Pfizer, Thermo Fisher Scientific, University of Michigan (U-M), and University of Southern California.
MSK said it will share methods of blood sample collection, comparative results of different processing methods for cell-free nucleic acid analysis, and CTC data from metastatic prostate cancer patients. The data could help answer how outcomes are influenced by prior treatment, said Howard I. Scher, M.D., chief of MSK’s Genitourinary Oncology Service at the Sidney Kimmel Center for Urologic and Prostate Cancers.
“Prostate cancer is a tumor type where it’s very difficult to get cancer from biopsies to actually do this kind of profiling. If you think about prostate cancer, it doesn’t spread in lumps. It infiltrates bone, which is very hard to measure. That’s what stimulated the interest in circulating tumor cells,” Dr. Scher said.
MSK will also use Epic Sciences’ No Cell Left Behind CTC detection and characterization platform to provide further characterization of prostate cancer CTCs, both at phenotypic and genomic levels.
“What we’re working on with Epic is a way to classify cells based on how they look,” Dr. Scher said. “If cells look similar to each other, they may have similar genetic alterations.”
PGDx plans to submit data from 500 samples, and work with its academic, biopharma and molecular lab partners to transfer datasets generated for them to the Atlas at no additional charge. PGDx will share expertise, protocols, and non-proprietary ctDNA profiling data generated through its PlasmaSELECT 64 tumor-profiling platform.
“This really is an important early step for the field of oncology, to understand and think more comprehensively about how to use liquid biopsy, and what factors affect the information that you can gain from liquid biopsy profiling,” John Simmons, Ph.D., manager of translational science and diagnostics at PGDx noted.
He said PGDx will contribute data that includes comparisons of pre-analytical factors, such as what types of tubes are used to collect blood, and how processing affects the data.
At U-M, four research teams will share data that “includes low-pass whole-genome sequencing data from plasma of patients with a variety of cancers, plasma cell-free tumor DNA digital PCR data from breast cancer patients, plasma RNAseq data from a cohort of healthy individuals, and enumeration and protein marker data from circulating tumor cells isolated from blood samples from breast cancer patients,” Muneesh Tewari, M.D., Ph.D., told Clinical OMICs.
Novartis plans to evaluate ctDNA testing methods, including PCR-based methods and next generation sequencing-based methods.
“Novartis will share (i) SOP(s) for plasma collection for ctDNA; (ii) results from evaluation of different commercially available ctDNA extraction kits; and (iii) evaluation of ctDNA technology performance using contrived samples. In addition, Novartis will share data and/or samples generated from these evaluations,” according to spokeswoman Tina Tuttle.