NEW YORK (GenomeWeb) – In the two years since it launched proprietary software solutions for next-generation sequence data analysis, GenomOncology has expanded its platform to include a number of additional applications that cater to a much broader range of analysis and interpretation needs.
GenomOncology emerged from stealth mode in 2014 with proprietary software solutions for managing and interpreting oncology data — the GO Clinical Workbench and the GenomeAnalytics platform — which were intended for clinical and research uses, respectively. Although it still offers the research product, the company now focuses almost entirely on supporting the clinical genomics market and offers a set of solutions that it believes are uniquely tailored to the needs of the space, according to Baiju Parikh, the company's vice president of sales and marketing.
The company now refers to its product as the GO Precision Medicine Portfolio. The portfolio encompasses its flagship GO Clinical Workbench and GenomeAnalytics products as well as more recent additions, such as the GO Knowledge Management System (GO KMS), which provides programmatic access to curated content from the My Cancer Genome database, a curated repository of cancer genomic variants and treatments, developed by researchers at Vanderbilt University's Ingram Cancer Center and released in 2013. GenomOncology and Vanderbilt-Ingram signed an agreement in 2014 that allows GenomOncology to offer commercial licenses to My Cancer Genome's content.
"The need that we are addressing is the ability to aggregate as much knowledge as possible to apply towards clinical reporting," Parikh explained to GenomeWeb. In addition to My Cancer Genome, there are several publicly databases that have valuable annotation content that customers wanted to be able to use in their workflows, including resources such the Catalogue of Somatic Mutations in Cancer (COSMIC) and the Cancer Genome Atlas (TCGA) repositories, as well as the National Center for Biotechnology Information's ClinVar database.
The GO KMS application makes it possible for researchers to incorporate data from My Cancer Genome as well as from third-party resources like COSMIC and internally developed databases. This enables customers analyze and aggregate variant data in the context of genes, pathways, drugs, alterations, and transcripts. They also have access to guidelines from the US Food and Drug Administration, the National Comprehensive Cancer Network, and the American Society of Clinical Oncology through the system, according to the company.
Other tools in the GenomOncology portfolio include the GO Validation Toolkit, which, as the name implies, provides tools that help pathology and medical genetics laboratories validate next-generation sequencing-based tests. A step-by-step workflow guides users through the planning, analysis, and implementation phases of the validation process, including making cost projections and power calculations for determining sample needs and run counts, breaking down results by variant type, and crafting suitable reports for regulatory review.
In addition, GenomOncology now offers what Parikh described as a "molecular tumor board clinical consult application" that lets clinical labs more easily communicate with oncologists about the results of testing. Furthermore, "we [have] the ability to aggregate as much knowledge as possible to apply towards clinical reporting," Parikh said. For example, in addition to genomic data, customers can also access guidelines from the US Food and Drug Administration, the National Comprehensive Cancer Network, and the American Society of Clinical Oncology through the system, according to the company.
However, exclusive access to the My Cancer Genome content sets it apart from competing solutions from companies like Syapse and PierianDx, both of which offer tools for clinical NGS-based testing, according to Parikh. Syapse offers applications based on its precision medicine platform for oncology and pharmacogenomics with plans to target infectious diseases as well as rare and undiagnosed diseases, while PierianDx offers tools for analyzing, interpreting, and reporting the results of tests for somatic cancers and constitutional disorders. Syapse and PierianDx signed an agreement last year to combine their respective products to provide an end-to-end genomic testing workflow for clinical pathology laboratories.
In the last year, GenomOncology has added eight new customers to its roster, Parikh told GenomeWeb. The bulk of its current clients are large academic medical centers, he said, about 14 of them being NCI- or AACI-designated cancer centers. Its customer base includes Ohio State University, the University of San Francisco, the University of Wisconsin, the New York Genome Center, and, most recently, Genomics England, which will use the company's GO KMS to handle clinical reporting requirements for the UK's 100,000 Genomes Project's cancer program.
Specifically, the partners will combine information from Genomics England's curated database with data from My Cancer Genome to generate clinical reports that cover treatment, prognoses, and clinical trials. In addition, GenomOncology and Genomics England will work on adding UK-specific resources to the platform, including guidelines from the UK's National Institute for Health and Care Excellence and information on UK-specific clinical trials.
Commenting on Genomics England's reasons for selecting GenomOncology's platform, Augusto Rendon, director of bioinformatics at Genomics England, said in a statement that the company's "consistent variant nomenclature" made it easy to integrate the My Cancer Genome data into variant annotation and interpretation pipelines. They have "made great progress in solving the difficult problem of representing cancer variants consistently in order to support genomic workflows," he said.
Another customer, Samuel Strom, an assistant clinical professor at the University of California Los Angeles School of Medicine and associate director of the UCLA Molecular Diagnostics Laboratories, found the platform's visualization capabilities particularly compelling. GenomOncology's tests support a number of diagnostic cancer tests that the lab offers. "GenomOncology has a very effective platform for allowing the user to actually visualize the raw data in a way that allows us to review cases much faster," he explained.
Specifically, "for every variant, it brings up a pileup view or an alignment view similar to the [Integrated Genome Viewer] or other NGS browsers and displays the raw data with color codes and easy-to-see text," he said. Also, compared to a number of unnamed solutions, including offerings from some sequencing instrument vendors, "it's the only product that we saw that helped streamline the analysis of the quality of variant calls," he added.
Strom also highlighted GenomOncology's openness to collaboration and suggestions, which also proved attractive. "A lot of larger companies with more established products [give you] what they have and [you] take it or leave it," he said. With GenomOncology, "we've really worked together to build a new product that's tailored to us and that's been tremendously useful."