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M2Gen Builds Cancer Research Database, Bets on Data Harmonization


CHICAGO – Since the time media giant Hearst invested $75 million in M2Gen in 2017, the oncology-focused informatics company has widely augmented its flagship cancer research database, brought in new management, and has begun making ambitious expansion plans, albeit without any current target dates.

The investment gave Hearst — which has a healthcare portfolio including drug knowledge database First Databank and clinical decision support content provider Zynx Health — a foothold in precision medicine. Moffitt Cancer Center in Tampa, Florida, which birthed M2Gen in 2006, remains a shareholder as well.  

The 2017 Hearst investment also helped support the expansion of the Oncology Research Information Exchange Network (ORIEN), which Moffitt, M2Gen, and Ohio State University's James Cancer Hospital and Solove Research Institute created in 2014 to support data sharing among cancer centers. ORIEN now connects 18 US institutions and other partners, including Takeda Pharmaceutical.

ORIEN has a research program called Avatar that collects deidentified genomic and clinical information from consenting patients, including disease stage, demographics, and treatment history. Participating cancer researchers can receive rich molecular data plus access to a network of potential collaborators for the discovery and clinical development of novel cancer therapeutics.

At the time Hearst invested, the Avatar database had about 2,000 patients. Today, it includes more than 17,000 annotated, longitudinal molecular records, and is growing at the rate of at least 5,000 per year, according to CEO Helge Bastian, who joined the company in August 2019.

Bastian is a molecular biologist by training who previously ran the synthetic biology business of Thermo Fisher Scientific. He also is a former vice president of molecular diagnostics at Qiagen and ex-managing director of German oncology-focused contract research organization Indivumed.

Bastian said that his hiring from a commercial background represented a strategic change for the company as it tries to step out of the shadow of academia. M2Gen is building up its human resources, marketing, and project management teams, and recently brought in a new sales vice president.

Clients include pharmaceutical, molecular diagnostics, and companion diagnostics companies. "The world has changed. Data belongs to patients, and therefore, in this regard, patients are our partners, too. Patients consent through the clinics that we work with, which is our next stakeholder, the clinics," Bastian said.

Through a network of laboratory partners, M2Gen sequences whole exomes and collects clinical data at the time a patient presents with cancer.

ORIEN, and thus Avatar, are dependent upon Total Cancer Care, a protocol that M2Gen Founder, Chairman, and former CEO William Dalton came up with in the mid-2000s when he was president and CEO of Moffitt. Total Cancer Care is now co-owned by M2Gen and Moffitt and licensed to partners. "Under the protocol, we are now approaching 300,000 patients that have consented," Bastian said.

Patients consent to being part of Total Cancer Care, allowing M2Gen to follow them for the rest of their lives. Because Total Cancer Care is a lifelong commitment, the data is longitudinal. Bastian called this protocol part of the company's value proposition.

"We are a data-driven company that lives under the credo that it's always better to know than not to know and that data is knowledge," Bastian said. "We harness the power of the data to redefine cancer care, so we try to be more clear in our methods, in all directions toward the ORIEN members, toward the patients, and toward the pharma/diagnostic industry that benefits from getting access to it in time."

Avatar features comprehensive genomic and transcriptomic data on its 17,000 patients, with 600 data elements per patient on the clinical side. "It's very deep and very solid," Bastian said.

Potential partners have been coming to M2Gen in search of real-world data, he said.

Avatar is a prospective collection service in a way, according to Bastian. "People can jump on this, get access to the 17,000 [patient records], but then they can let us know going forward what data they are looking for so that we can go in that direction," Bastian said.

And because Avatar is longitudinal, it is constantly expanding as new clinical data is generated.

"I think these are the three cornerstones for us, Avatar, real-world data, and oncology projects," Bastian said.

Another relatively recent addition to the company is Oliver Hampton, who became VP for bioinformatics and biostatistics in April 2019.

Hampton, in his former role as founding group leader of platform informatics at Memorial Sloan Kettering Cancer Center's Center for Molecular Oncology, designed pipelines to support research and care there and developed the laboratory information management system there. That is where the New York-based organization created its MSK-ACCESS liquid biopsy test for noninvasive cancer genomic profiling and disease monitoring.

Among Hampton's tasks at MSK was to standardize algorithms and pipelines so they could be accessed not only internally, but also with outside collaborators and business partners.

Now, M2Gen has called on Hampton to lead the important task of standardizing and harmonizing data across ORIEN and Avatar to support researchers in academia, biopharma, and molecular diagnostics.

"We need to work closely with sequencing partners to get what we really want out of the data, and harmonization is really key," Bastian said.

"It's the diverse data harmonization which is key to unlocking the knowledge and the new findings within the data we have," Hampton added.

Hampton said that M2Gen takes cues from the Cancer Genome Atlas (TCGA) project, which, he noted, tried for a "pristine" dataset. But M2Gen adds more real-world data.

"Patients are getting seen in the hospitals and precision oncology and research is happening," one of the goals of TCGA, he said. Harmonization is making that happen.

At previous jobs, Hampton participated in TCGA and in follow-on efforts funded by the US National Cancer Institute, including the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. He said that M2Gen is applying lessons from the construction of those publicly funded datasets.

"We leverage semantic and graph data models for clinical and molecular data integration," Hampton said. The company has a bioinformatics staff that is building algorithms to improve the sensitivity of somatic mutation detection.

Harmonization goes beyond data. TCGA and TARGET used fresh-frozen specimens, but M2Gen's lab partners also are receiving formalin-fixed, paraffin-embedded samples. The company harmonized capture protocols for sample extraction, probe captures, and sequencing across the chain of data generation at different labs.

M2Gen designed its protocols to be oncology-specific, targeting specific genes within exome sequences for double coverage, and performs tumor-normal comparisons, according to Hampton.

"We've learned the lessons by leveraging the entire ORIEN network because these are not coming just from one cancer site," Hampton said.

Hampton said it is difficult to make accurate molecular assessments of cancer patients in trials that did not collect tumor-normal data, but the M2Gen database facilitates that analysis.

"You can obtain extremely accurate assessments [with the Avatar dataset] without having that companion normal if it just isn't available when they ran their clinical trial," he said. "We are traditionally a data company, but we are flexing toward more analytics application of the data from three years ago," he added.

M2Gen has established a scientific affairs team in the last three years to manage projects between ORIEN members. There now are about 30 of these so-called intermember projects," Bastian said. The company also has an advisory council called the patient engagement team.

"We want to make sure that the patient understands where the data is going and what researchers do with the data to the benefit of the patient," Bastian said.

M2Gen has begun the development of a more automated platform for enrolling patients in trials to improve and accelerate trial matching, according to Bastian. He said there cannot be precision oncology without deep involvement of patients.

"It's not just about gathering the data, but analyzing the data, making sense of the data and giving a higher-value kind of information to those that we believe can benefit from this data," Bastian said.

M2Gen is mostly supporting translational and clinical research, but not clinical care. Longer-term, the company wants to work with providers and payors as well, Bastian said, perhaps expanding from its academic base into community hospitals as well.

The company plans on taking ORIEN beyond the borders of the US in the future. "We want to go international because that's the demand of our clients, too, and it makes perfect sense to get all the ethnicities and cohorts that people are looking for," Bastian said.

Bastian said that he does want to move into other medical specialties at some point, but not by losing focus on cancer. He named neurological conditions including Alzheimer's and Parkinson's diseases as possible future areas of interest, but said that there are no current plans to go beyond oncology.