CHICAGO – Earlier this month, French bioinformatics and genomic services company IntegraGen said that it has received CE marking for Mercury, an oncology-specific software platform that helps cancer centers manage bioanalytical pipelines, annotate exome and transcriptome sequencing data, and produce reports for both research and clinical trials.
In the US, the Dana-Farber Cancer Institute in Boston will adopt Mercury to manage the analysis and reporting of tumor sequencing data, including small and large targeted panels and both exome and genome sequencing data, IntegraGen said last month.
Keith Ligon, director of the Dana-Farber Center for Patient Derived Models and codirector of the recently established interpretive genomics program in the Department of Oncologic Pathology, said that Dana-Farber will be using the IntegraGen software to build the new program's services. He expects to have Mercury online at Dana-Farber in the next few weeks as IntegraGen completes its customization of the product for the cancer center.
IntegraGen's Mercury will allow different constituencies within Dana-Farber to run analyses that suit their particular needs, according to Ligon, whether building research cohorts or recruiting patients for clinical trials.
Indeed, IntegraGen General Manager Larry Yost, who works out of the company's US headquarters in Cambridge, Massachusetts, said he sees market potential for the company in clinical reference labs that lack bioinformatic specialists to develop and manage pipelines because Mercury is highly adaptable to each user's requirements.
"We're looking at it all, from variants to tumor mutational burden to microsatellite instability, but if you're looking at a smaller panel, you may be only interested in [copy-number variations]," Yost said. "It allows for that separation. You don't have to have all or none."
Ligon is particularly interested in using the tool for a glioblastoma research initiative that he started several years ago. Working with the Broad Institute and a foundation called Accelerate Brain Cancer Cure (ABC2) on an initiative called the Allele Project, Ligon's laboratory sequences tumors from glioblastoma patients and identifies candidates for clinical trials.
Mercury fills an urgent need for Dana-Farber and the Allele Project for managing the sequencing data.
"We didn't have great software options. I can tell you I started with Excel spreadsheets," Ligon said. A vendor whose software Ligon and ABC2 helped customize for the project went out of business, and Ligon eventually found IntegraGen.
In Mercury, Évry-Courcouronnes, France-based IntegraGen incorporates reference tools from a variety of sources, including the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, and OncoKB. Clinical trial data comes from the US government's ClinicalTrials.gov site.
Since clinical reference labs in the US are not always performing whole-exome or RNA sequencing because of lack of insurance reimbursement, IntegraGen adapted Mercury to support small and large gene panels, according to Yost.
"We've adapted Mercury to make sure that we can meet the needs of a broader audience rather than just researchers looking at this big data type of stuff coming up from their research," he said.
Ligon cited the need to work within the confines of reimbursement issue as one reason Dana-Farber chose IntegraGen.
Mercury is one of three bioinformatics products that IntegraGen offers, all hosted on the Google Cloud.
Sirius is a research tool to help investigators find genomic markers for rare Mendelian disorders. The newest release, Galileo, is a visualization app for RNA sequencing data. "Researchers use this instead of finding somebody else to go out and do the plots, the graphs, and produce images for publications," Yost said.
Historically, IntegraGen performed genotyping services for academic researchers and hospitals, but the firm has branched out in recent years to offer whole-exome, partial exome, RNA-seq, and genome sequencing services. Its laboratories contain instruments from Illumina — including some recently acquired NovaSeq machines —, 10x Genomics, and Fluidigm.
"We consider ourselves pretty good at being able to pull the genomic data from these samples," Yost said.
IntegraGen formed a US subsidiary in 2010, initially to support research into early identification of autism risk in children.
In the last five years, IntegraGen has moved into clinical research by installing its technology and stationing employees away from its headquarters in a genomic research and biotechnology hub near Paris called Genopole.
Notably, the company has operated a clinical research sequencing platform and lab at the Institut Gustave Roussy cancer center in the Paris suburb of Villejuif.
IntegraGen later established a similar relationship with Institut Pasteur in the French capital, and recently announced that it has extended its contract with that research organization through December 2021.
The Gustave Roussy facility performs tumor-normal and RNA sequencing, while at Institut Pasteur, IntegraGen is now supporting research into the SARS-CoV-2 coronavirus and COVID-19.
In July 2018, the Sequencing Omics Information Analysis (SeqOIA) cooperative health group, which involves Assistance Publique-Hôpitaux de Paris, the Institut Curie, Gustave Roussy, and Institut Imagine selected IntegraGen for technology services.
The company will receive €18 million ($19.5 million) over five years to provide SeqOIA with access to exome as well as genome and RNA sequencing data from patients with cancer and rare diseases. In this role, IntegraGen installed a couple of NovaSeq machines and set up a laboratory information management system to support this collaboration.
IntegraGen, which is publicly traded on the Euronext Paris exchange, released its 2019 financials in early April, reporting a net loss of €285,000 for the year, compared to a loss of €1.1 million a year earlier. Revenue increased by 18 percent to slightly more than €8.3 million from €7.1 million in 2018.