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Thermo Fisher's Oncomine Knowledgebase Reporter Aims to Simplify NGS Analysis


CHICAGO (GenomeWeb) – An early adopter of Thermo Fisher Scientific's Oncomine Knowledgebase Reporter genomic analysis software is reporting mostly positive results with the new product, but knows the technology is far from reaching its full potential.

"It's a very good product," said Karl Kashofer, manager of translational genome analysis in the Institute for Pathology at the Medical University of Graz, Austria.

For one thing, it makes pathologists more efficient and more accurate when making sense of genomic data. Plus, Thermo offers a locally hosted client-server version in addition to a cloud option, an important consideration for Medical University of Graz, since Austrian privacy laws do not allow for web-based analytics of sensitive data such as genomics, Kashofer said.

There still are some shortcomings, though. For example, the institute prints out reports as support information for pathologists, though reports tend to be dozens of pages long. "We are working on filtering information or summarizing," Kashofer noted.

Thermo Fisher introduced Oncomine Knowledgebase Reporter at the American Association for Cancer Research Annual meeting in April. Knowledgebase Reporter is part of the Oncomine suite of products for next-generation sequencing.

A month ago, the US Food and Drug Administration cleared a related product, the Oncomine Dx Target Test, an NGS-based companion diagnostic that can analyze alterations in a panel of genes to predict response to three non-small cell lung cancer treatments. Shortly thereafter, Thermo Fisher said it would seek rapid expansion of indications for this test.

Oncomine Knowledgebase Reporter is reporting software, taking results off sequencers and converting the output into actionable information. Thermo Fisher has had a reporting tool for about two years, and in 2016 launched a web-based version of that technology called the Thermo Fisher Connect cloud platform.

This new product, available in 10 different languages, is meant to simplify NGS results reporting and management, according to Jody McIntyre, Thermo Fisher's associate director of oncology products.

"There is a data bottleneck because there are so many variants in sequence samples," McIntyre said. Knowledgebase Reporter is a centralized hub for information on how to act on variants.

Graz hosts one of the largest biobanks in Europe and the molecular pathology lab relies heavily on NGS. The institution, which performs four to five NGS runs a week, has had Thermo Fisher Oncomine sequencing technology since 2012.

The lab uses Thermo Fisher's Ion Personal Genome Machine sequencers to handle longer read lengths and Ion Reporter software for mutation detection. Data gets transferred to reports.

The Oncomine platform "annotates and tells where and what the variants are," Kashofer said. "This is the technical information needed to describe a variant," he said.

The new Knowledgebase Reporter pulls in relevant medical knowledge from data sources such as the FDA, the US National Comprehensive Cancer Network, the European Society for Medical Oncology, the European Medicines Agency, and clinical trials from around the world, she said.

Carlsbad, California-based Thermo Fisher has a curation team for Knowledgebase Reporter that came over in the acquisition of Life Technologies in 2014. Thermo updates the database at least every quarter.

This ability to stay current attracted Medical University of Graz, which became a beta tester of Knowledgebase Reporter about six months ago, prior to the formal launch.

"There is lots of overlap between what pathologists know and what Oncomine says," according to Kashofer. However, there are 409 known genes associated with cancer, and physicians simply cannot understand and recall all of them when making decisions without the help of technology, he noted.

In doing so, Kashofer channeled the work of the recently deceased Lawrence Weed, 93, the medical informatics pioneer who envisioned clinical decision support 60 years ago. "The unaided mind does not know what data to collect, and does not see many of the significant relationships buried in whatever data are collected," Weed said in a 2004 interview.

Kashofer also noted that regular updates make Oncomine more useful to researchers and clinicians alike than static databases. "Quality is determined by the data that goes in," Kashofer said.

There is a three-step process for creating reports. Users first click a "create analysis" button to load genomic sample and filter results to customize what fields they want in their reports. The system shows evidence and suggests relevant therapies from multiple sources. Researchers then can filter by location to find suitable clinical trials, McIntyre said.

Knowledgebase Reporter can produce reports for clinical settings, but Medical University of Graz only is using it for research purposes now. Kashofer eventually wants to apply it to clinical decision support as the technology matures and as the university trains clinicians on the Oncobase platform.