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Thermo Fisher's Precision Medicine Science Center Supports Biomarker, Clinical Assay Development


NEW YORK (GenomeWeb) – With its newly opened Precision Medicine Science Center (PMSC) in Cambridge, Massachusetts, Thermo Fisher Scientific plans to help customers develop analytical workflows for mass spec and sequencing projects more quickly, allowing them to generate molecular profiles of patient samples on a large scale for biomarker discovery and clinical assay development.

The center, which formally opened last week, grew out of the company's realization that it is not enough to sell instrument platforms but that it also needs to support customers with the development of workflows and protocols to solve biological problems, according to Emily Chen, senior director of the PMSC. "Particularly, we wanted to accelerate the path for biomarker discovery to actually make an impact in the clinic," she said.

The PMSC is an expansion of an earlier effort by Thermo Fisher, the Biomarkers Research Initiatives in Mass Spectrometry (BRIMS) Center, which the company opened in 2004, in collaboration with Massachusetts General Hospital.

While the PMSC is located in the same facility as the BRIMS Center, it offers more technologies and has a wider scope. Work at the BRIMS, Chen said, tended to be on a smaller scale, often involving just a few patient samples, and did not require the same type of robustness and throughput that projects tackled by the PMSC do. Instead, BRIMS was more focused on supporting individual users' applications and developing customized methods. "Here, we are trying to work with the entire community as opposed to individual customers only," she said.

For example, she said, the PMSC will focus on developing robust, scalable, and cost-effective workflows that enable large numbers of samples to be analyzed, which she said is something academic researchers often don't have the resources for. In addition, the PMSC will serve as an educational center to provide training and protocols for customers.

In terms of technologies, the PMSC houses Thermo Fisher's latest platforms for both mass spectrometry and nucleic acid sequencing. "Our message is multi-omics, as opposed to single-omics," Chen said. The center has a staff of three scientists at the moment, which will grow to six or seven in the near future, she added.

On the mass spectrometry side, the PMSC is equipped with the Orbitrap Fusion Lumos Tribid as well as Q Exactive HF and HF-X Quadrupole-Orbitrap mass specs. In addition, it will soon receive the new Orbitrap ID-X Tribrid, Chen said, which Thermo Fisher launched at the American Society of Mass Spectrometry annual meeting last week and which is particularly suited for metabolomics work. Customers have shown an interest in both proteomics and metabolomics projects, she noted, including some that integrate both technologies.

With regard to sequencing, the center is equipped with the Ion GeneStudio S5 Prime next-gen sequencing system, the Ion Chef for NGS library and template preparation, and the Applied Biosystems SeqStudio Genetic Analyzer for Sanger sequencing. "Our NGS clinical sequencing group has been supplying us with the latest equipment to be placed in the center," Chen said.

The center is currently looking for collaborators across sectors – including academia, biotech, and pharma – with interesting biomarker and assay development projects that could benefit from its expertise and resources. These could be groups, for example, with interesting clinical studies and a large biobank, where Thermo Fisher could apply its technologies "to be able to produce biomarker panels or develop the downstream assays that can have an impact and be translated back to the clinic," Chen said.

For promising projects, the PMSC will provide its resources, including its equipment and application scientists, with the goal to create success stories that can give others "an idea of what you can do, how you can move forward with precision medicine projects," Chen said, noting that the center will be very selective in who it will work with.

Chen said the center doesn't have a fixed budget for its collaborations but will consider projects – both short-term and long-term ones – individually based on their promise. It also asks to be actively involved in the design of experiments and will define milestones for the success of a project. One result might be application notes for other customers, for example, that describe a workflow the company developed for a project.

One ongoing project of the PMSC is a collaboration with Jennifer Van Eyk, a professor of medicine at the Cedars-Sinai Medical Center, to develop a plasma proteomics workflow to quantify several hundred plasma proteins by mass spectrometry for the development of biomarkers. "She's now at the stage of implementing our workflow; she has a biomarker panel that's ready to be developed into a clinical assay," Chen said. "That was an early collaboration, a demonstration of how our involvement can help with developing the biomarker, as well as accelerate that biomarker into a clinical setting."

In addition, the PMSC is involved in a project that is part of the Applied Proteogenomics Organizational Learning and Outcomes (APOLLO) program, funded under the National Cancer Institute's Cancer Moonshot program, where it developed standardized protocols for sample prep, quality control, and more that could be transferred to other labs involved in the Cancer Moonshot initiative, Chen said.