The Variant Rich Biobank: An Insider's Look
A Scientist.com and Precision for Medicine Webinar
Precision for Medicine® hosted a webinar called The Variant Rich Biobank: An Insider’s Look. Precision for Medicine is a global clinical research organization (CRO) that supports biomarker-based research and development (R&D) activities from bench to market, supplying biospecimens, lab services, and clinical trial solutions to the life sciences community.
Anuj Kalsy, Scientific Director, Precision Biospecimen Solutions and Robert Snyder, Associate Director of Genomics at Precision for Medicine discussed how biobanks with well-characterized biospecimens address unmet needs within the scientific community.
Kalsy began by talking about the critical issue of experimentation reproducibility.
"According to a Nature survey conducted in 2016, over 70% of researchers have tried and failed to reproduce another scientist's experiments," he said. "This observation was confirmed in a later survey where nearly 9 out of 10 acknowledged that poor reproducibility is a problem."
Biospecimens are the key to providing a solution to this problem. By delivering fit-for-purpose samples, biobanks support the research community, saving valuable time and resources. Precision for Medicine's broad base of biobanks provide a vast array of high-quality, clinically annotated samples to support preclinical and clinical research (see Figure 1).
With our global footprint for patient sampling and data collection, Precision for Medicine has an extensive biorepository of over 30 million biospecimens and 7 laboratories across North America and Europe processing millions of samples per day. Precision for Medicine also has robust custom collection capabilities, with a clinical network spanning more than 150 investigator sites, 90 therapeutic areas, 25 countries, and 500 actively enrolling studies.
Figure 1. Biospecimen types available
Kalsy shared a personal experience on how biobanks supported his prior work as a researcher in a breast cancer drug discovery program.
“We were trying to figure out the HER2 status of a particular sample type, and tumor samples from HER2-driven breast cancers were rare,” recalled Kalsy. “Precision for Medicine was able to provide samples that enabled us to profile the HER2 expression pattern in our chosen sample type. This is just one of many examples of how well-characterized biospecimens can be critical tools for fueling research and innovation and driving drug discovery forward.”
Dr. Snyder then introduced Project Precision Oncology Sequencing Initiative (P.O.S.I.), a novel and ambitious next-generation sequencing (NGS) initiative. Phase 1 of Project P.O.S.I., comprising Project Spawn and Project Lumispawn, focuses on screening formalin-fixed, paraffin-embedded (FFPE) blocks across 12 cancer indications. Project Spawn involves screening on the Thermo Fisher Genexus platform using the Oncomine Precision Assay, while Project Lumispawn utilizes the Illumina Novaseq platform to sequence FFPE samples using the TSO500 assay.
“We are currently screening at a rate of about 800 samples per month but are ramping up to 1,600 samples per month,” reported Snyder. “To date, we have screened nearly 9,000 tumor cases.”
Phase 2 of Project P.O.S.I. involves ongoing prospective collections for liquid biopsy assays. Approximately 350 donors are enrolled across a range of cancer indications. These donors are first screened with tissue-based assays and then followed with plasma-based assays, creating a biorepository and database of matched tissue-plasma samples.
Project P.O.S.I. is supported by Precision for Medicine's robust and expanding genomics and molecular laboratory infrastructure (see Figure 2). This screening infrastructure was purposefully designed to be platform and assay agnostic, allowing the data to speak for itself and enabling unbiased head-to-head comparisons.
Figure 2. Advanced equipment and assays supporting Project P.O.S.I.
Snyder reflected on his previous work in companion diagnostics product development and reinforced that the biggest bottleneck, particularly when running accuracy assays, is samples.
“When I was developing a plasma assay, the best that I could find was matched tumors, and when we ran out of that, I was sequencing as many unscreened samples as I could, hoping to find the rare variants we needed for our submission,” said Snyder. “And this was really hard, not just technically, but also emotionally because we had so much on the line. What I wish I had was an easily searchable database of samples and their associated variants to choose from, ideally with the demographics, metadata, and raw sequencing data. Precision for Medicine's biorepository would have been a gold mine for me.”
As a solutions provider and partner to therapeutics and diagnostics developers, Precision for Medicine has created a library of deeply phenotyped, data-rich samples that researchers can leverage to accelerate the advancement of precision medicine.
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