Genexus system chip
The chip used in the Genexus system is designed to run smaller batches, a key consideration for health systems that want to deliver results quickly but don’t generate a high volume of tests.

In today’s world of precision medicine, the more information you have on a patient, the better, in terms of treatment options. The field of oncology is perhaps the most dependent on patient information being used for treatment, and where genomic information can determine which treatment will be best suited for a specific mutation or set of mutations, and anticipating the cancer’s behavior and development.

However, performing a full genomic screen of a patient’s tumor can be costly, time consuming, and in some rural areas, simply not available to the patient populations. Oftentimes, a full panel of tests can be confusing for the treating oncologist, and biomarkers are not identified in a timely manner.

Outsourcing next-generation sequencing (NGS) testing was also known to be very expensive, and stringent sample requirements often lead to results being of poor quality and inconclusive. Recent clinical research studies show this issue effects approximately 20% of patients, excluding samples not submitted because they failed to meet sample quantity criteria.

A study published in the journal Clinical Lung Cancer underscores the logistical challenges that limit local hospitals from providing NGS-based genomic testing, even though most patients are treated in a local setting. These NGS adoption barriers—including coordination of sample handling, cost, product complexity, long turnaround times, access to targeted therapies, insufficient amounts of tissue, and patient harm from the repeat biopsies, must be addressed if the healthcare industry is serious about advancing precision medicine.

These factors often result in the majority of local molecular laboratories relying on limited single-gene tests.  Frequently, the treating oncologist is unaware which genes, or biomarkers, to test for due to the fast pace of new discoveries about the genetic influences on disease, and drugs and clinical trials becoming increasingly unique to certain mutations in patient populations.

But some companies are aiming to make genomic analysis for patients more accessible and easier to order for community oncologists, including Thermo Fisher Scientific and Contextual Genomics. Thermo Fisher has developed a tool that allows a hospital lab to consolidate all genetic testing into a single molecular test, and Contextual Genomics has developed genetic tests and a cloud-based informatics tool that can suggest relevant clinical trials and treatment options for cancer patients.

on Torrent Genexus System
The Ion Torrent Genexus System was designed specifically to be able to run even a single test at a time to make the power of NGS testing available to smaller health systems while providing quick turnaround of results.

Contextual Genomics has developed patient cancer panels including FIND IT (a tumor tissue sequencing test) and FOLLOW IT (a liquid biopsy test). Both panels are multiplex, NGS genomic assays, with each test searching for 146 well-characterized mutations with the greatest potential to impact treatment decisions and relevance to available clinical trials. A unique aspect of this company is that it provides the bioinformatics expertise to oncologists directly, so that much of the laboratory work can be conducted in house, and the genomic analysis can be conducted though a cloud-based learning system.

Thermo Fisher announced the launch of its Ion Torrent Genexus System late last year, as a fully integrated, next-generation sequencing (NGS) platform featuring an automated specimen-to-report workflow. Impressively, it can deliver results economically in a single day, and was designed to enable local hospitals to adopt NGS testing. Thermo has also introduced the Oncomine Precision Assay, an innovative pan-cancer panel for the Genexus platform, which enables comprehensive genomic profiling from formalin-fixed, paraffin-embedded (FFPE) tissue and liquid biopsy samples with a single assay.

“Our goal is to advance precision medicine in every clinical setting by enabling clinicians to leverage the power of comprehensive genomic information,” said Mark Stevenson, executive vice president at Thermo Fisher Scientific. “We can envision a time when patients at local hospitals will have faster access to comprehensive test results that can guide more effective, targeted therapy selection and improved health outcomes.”

Mark Stevenson
Mark Stevenson
Thermo Fisher Scientific

Recently, LabCorp announced that it will adopt Thermo’s Genexus System and Oncomine Precision Assay to support the research and development of new companion diagnostic innovations.

“We are very excited to collaborate with Thermo Fisher and leverage the capabilities of the Genexus system,” said Marcia Eisenberg, Ph.D., chief scientific officer of LabCorp Diagnostics. “This streamlined platform, with fast turnaround time and automated workflow, has the potential to bring the power of next-generation sequencing to a broader range of settings and to stimulate significant advances in the future for the diagnosis and treatment of a broad range of cancers.”

“The speed is amazing, but to me, the real value of the Genexus System is how easy it is to use,” said early access user José Luis Costa, Ph.D. at the University of Porto in Portugal. Costa was particularly impressed by the ability of this system to take a biological sample and produce a report with, “practically zero intervention from the operator.”

With the Genexus system laboratories can scale their sequencing runs with a special sequencing chip that allows in-house sequencing facilities to process small batches of samples as they arrive at the lab.

A lab technician loads reagents into Thermo Fisher Scientific’s Ion Torrent Genexus System
A lab technician loads reagents into Thermo Fisher Scientific’s Ion Torrent Genexus System that the company designed to make NGS testing more accessible to smaller health systems and testing labs.

Michael Ball, the CEO of Contextual Genomics and formerly of Illumina, is also motivated to expand the reach of genomic testing to more patients. “Our objective is to bring that testing, in a cost-effective way, out to the communities, such that patients get better access to those tests and ultimately, better therapies and better outcomes.”

Brady Davis, senior vice president of business development at Contextual Genomics, added that the product they are launching is focused on developing a rapidly learning healthcare system. “Being able to aggregate that data and create a rapid learning system where we can improve the accuracy and the sensitivity of the test, and support pharma companies in their need for additional multimodal data sets—that will help drive accelerated discovery.”

The systems developed by Thermo Fisher and Contextual Genomics have the potential to change the current paradigm, as well as provide data to improve future research and trials.

Several factors in the healthcare space have prevented patients for accessing genomic tests in the past, including costs and oncologist education.  Building cost-effective tests, educating oncologists on the value of testing for targeted therapies, and then simplifying the information that is provided would change that.

Bell explained, “Our model is to work directly with the health providers, and have them to actually implement these tests within their own lab system and within their own hospital system. We then work with the oncologist to make sure that the reports are meaningful and actionable for them in the context of their own communities.”

David Huntsman, a founder of Contextual Genomics, added the assays were developed based on the desire to reach as many patients as possible. “We needed to produce an assay where you didn’t have to be a frontline, research-orientated oncologist to understand the data, and [the tests would be] cost effective enough to fit into a parsimonious, public funded healthcare systems, or for people who [cannot] spend large amounts of money on their testing. It has been a drive of the company to be able to reach as many people as possible, because, sadly, many years after we thought people [would be] getting very broad scale sequencing routinely, most people still don’t get any testing done.”

Michael Ball, CEO, Contextual Genomics

Ball stated, “When you think about these mid- and even large-sized healthcare systems that maybe aren’t quite as sophisticated as some of the well-known institutions like MD Anderson, Mayo, and others, you see their drive towards trying to engage and enter into the precision oncology movement. And when you think about the collective opportunity we have in grabbing all of our customers inside of our ecosystem— we have a product called Quality Nexus that pulls all of the aggregated, de-identified data sets together—we are really improving the accuracy and sensitivity of these tests. So it becomes what I refer to as this really rapid learning loop. When a midsize healthcare system has maybe five or seven hospitals and 3.5 million patients, they might see 1,000 patients or 500 patients a year and do testing on a small percentage of them.” He continued that by using the system his company has developed, providers will have access to their own data, as well as data from other sources.

“We’re able to centralize [the information to] make it easier for these organizations who don’t have the bioinformatics expertise to get a report, [to make a clinical decision, and to provide], better treatment, and monitoring to their patients.”

Davis added, “It’s not trivial to set up a lab. It’s not trivial to validate an essay. And it’s really not trivial at all, to be able to wrap a bioinformatics program around that to get an answer and sign out a report. I think there are a lot of labs, a lot of systems out there that really look at people who are doing precision oncology, and think, ‘We’re not there, because we can’t get there. We don’t have the people. We don’t have the tools. We don’t have the bioinformatics expertise. So how are we going to catch up with them?’ Well, guess what? There is an option now, and you actually can play in this space.”

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