Alex Philippidis Senior News Editor Genetic Engineering & Biotechnology News

Thermo Fisher Scientific, University Hospital Basel Partner to Develop, Validate NGS Cancer Diagnostics

A partnership launched by Thermo Fisher Scientific with the Institute of Medical Genetics and Pathology at University Hospital Basel aims to accelerate clinical research into oncology and immuno-oncology by developing and validating next-generation sequencing (NGS)-based cancer diagnostics.

The Institute is the first partner in Thermo Fisher Scientific’s Next Generation Sequencing Companion Dx Center of Excellence Program. The Institute will serve as one of the program’s global sites focused on developing and refining Thermo Fisher Scientific’s NGS-based research assays from its Oncomine oncology portfolio, with the goal of eventually introducing them into clinical use as companion diagnostics.

Both organizations are cooperating in forming global alliances and strategic partnerships with hospitals, testing facilities, and biopharma groups.

“The partnership with Thermo Fisher will further enhance our potential by increasing our throughput capacity up to several thousand samples per year, thus allowing us to be able to satisfy the typical needs of large international multicenter trials,” Markus Tolnay, M.D., manager of the Institute, told Clinical OMICs. “Eventually, new gene panels tested within the context of a clinical trial could expedite the routine molecular diagnostic setting.”

The partnership envisions introducing new solutions for routine genomic analyses, such as gene panels in sarcoma and CNS tumors, as well as improving current bioinformatic pipelines for complex variant calling. “We intend to increase both sensitivity and specificity of currently used kits and increase the quality of data produced by Thermo Fisher instruments,” Dr. Tolnay added.

He said the Institute’s contributions will include its experience in human Formalin-Fixed Paraffin Embedded (FFPE) tissue handling and its Institute BioBank of tissues, consisting of about 3.2 million FFPE blocks and some 35,000 fresh frozen samples from a variety of pathological and normal tissues.

The Center of Excellence builds on previous collaborations by the Institute and Thermo Fisher Scientific. About three years ago, the Institute concluded Thermo Fisher’s Ion Torrent sequencing system could best address testing limited material from FFPE tissue. The Institute was among the first in Europe to switch from Sanger sequencing to NGS for routine genomic profiling of cancer patients.

That transaction led to other efforts, from working to improve commercialized NGS-related solutions, such as the company’s Ion Reporter software, to participating in early access customer programs involving Oncomine.

A year ago, the Institute began using Oncomine’s liquid biopsy panels and immune response panels in immunotherapy applications. The Institute is one of 11 institutions within a network of researchers organized by Thermo Fisher Scientific, called the OncoNetwork Consortium. Initial promising results from that collaboration were presented in April at the Association for Molecular Pathology (AMP) Global Congress on Molecular Pathology in Berlin.

“The Institute has served as an early access opinion leader, and has been approached by many other groups outside of Switzerland to receive clinical training on their technology. They also worked with other hospitals who hadn’t yet had access to the technology, to help patient decision-making,” said Mark Stevenson, president of life sciences solutions for Thermo Fisher Scientific. “We saw they were good not only in using new technology, they were good in training other centers. And as we look to introduce future new technology, we thought they’d be a great partner with which to work together.”

Through the partnership, Stevenson said Thermo Fisher will take existing Oncomine assays for solid tumors—including non–small cell lung cancer, colon cancer, and breast cancer—and put them into a format for monitoring via liquid biopsy. The number of genes typically being monitored is in the range of 10 to 50.

Thermo Fisher Scientific and the Institute have also focused on early detection of mutations. The company is a group partner in the Blood Profiling Atlas in Cancer Consortium, which aims to develop an open database for liquid biopsy data. The Atlas is a pilot project of the “Cancer Moonshot” championed by former vice president Joe Biden.

The growth of cancer immunotherapy has been a key driver for the development of Centers of Excellence for Thermo which is working with two developers of cancer immunotherapies, Novartis and Pfizer. The treatments involved have not been disclosed.

Stevenson said the Center of Excellence launched with the Institute is the first of several such partnerships envisioned worldwide. Talks have begun with prospective partners in North America, with announcements expected in coming months: “We really expect to have maybe five to 10 centers of excellence around the world.”

Such partnerships, the company reasons, will inform a standard for companion diagnostics product development that will help speed up oncology and immuno-oncology trials. That acceleration will entail, in part, reducing the time to generate a full molecular diagnostic report, which now stands at about nine working days.

“Through this partnership, we will work together with Thermo Fisher to find the best solutions to drastically lower this time,” Dr. Tolnay said. “We aim to reduce it down to a maximum of five working days and we will help all Ion Torrent customers to reach the same of proficiency.”  

This article was originally published in the May/June 2017 issue of Clinical OMICs. For more content like this and details on how to get a free subscription to this digital publication, go to

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