Health IT

Foundation and Flatiron launch expansive clinico-genomic cancer database

Two major players in the cancer space are launching one of the largest-ever clinico-genomic databases, commercializing the electronic health records of 20,000 cancer patients

Skull CT scan picture on the wall

Foundation Medicine and Flatiron Health today announced a new initiative to assemble and curate one of the largest-ever clinico-genomic databases, built around the electronic health records of 20,000 cancer patients.

It’s not the first time Foundation and Flatiron have partnered and the initiative is close to home. They share a core group of highly involved investors, including Roche and GV (formerly Google Ventures) and are both committed to the cancer genomics space.

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Each has a different-yet-complementary area of expertise: Flatiron is health IT, Foundation is diagnostics.

Combined, the companies have sequenced, interpreted and managed tens of thousands of tumor samples. They have access to those genomic files, said Vineeta Agarwala, director of product management at Flatiron Health, in a phone interview. The aim now is to comb through the electronic health records (EHRs) of those patients to add a rich layer of contextual information.

“We very much hope that we can bring to life more data for more patients across the country,” said Agarwala. “Only about 4 percent of all cancer patients in America go on a clinical trial. Those other 96 percent of patients are leaving a very rich digital trail of their care, of their outcomes, of their treatment, because of electronic health records. But typically it’s only being used in the care of those individual patients and really nobody is learning from those patients’ experiences.”

It could be a powerful tool for researchers — but there is a catch.

None of the 20,000 cancer patients that generated the data have directly consented to the use of their information. In a strange twist, Flatiron and Foundation can use the EHRs, but individuals and their families struggle to access them.

It’s a situation that cardiologist and digital health leader Eric Topol calls a matter of “civil rights.” Patients don’t have ownership of their own genetic data, but at the same time, organizations are amassing information about hundreds of thousands of individuals’ genomes, which he says creates a risk for computer hacking.

To add insult to injury, Foundation and Flatiron’s new database will not be open access. In other words, the companies stand to financially benefit from the medical information of cancer patients that haven’t consented to the program and who won’t be getting a dime.

In response, Agarwala underscored that the patient data would be fully anonymized and that the entire database is HIPAA-compliant.  

She was reluctant to share specifics about how researchers would negotiate access to the database, other than to say the curated information would be mediated through one-on-one partnerships at an institutional level, such as with university, a cancer center, or a life science company.

“It really depends on the institution and the group that wants to access it. We’re really open to coming up with creative collaboration strategies.” Agarwala said. “It’s not a completely open dataset today, for a number of reasons, including patient privacy.”

Rather than make the information publicly available, the company aims to work with scientists on a particular research question, ultimately delivering a package solution that makes sense for their work.

As Agarwala explained, the value is in the annotations — how the data is flagged and categorized.

“If you think of electronic health records as sort-of a filing cabinet of everything a provider team knows about their patient, everything from diagnosis codes that they enter into the chart, medication orders, a ton of free text of describing the oncologist’s visit with the patient, pathology reports that are often scanned or faxed into an oncology patient’s EHR,” Agarwala said.

“What Flatiron does is create a curated process data layer that sits on top of that electronic health record where that data is normalized and harmonized. Free text is processed into database details that we can then use for research”

Right or wrong, this could advance cancer treatments and care. It may also add to the debate about ownership of genetic data, access to EHRs and patient consent.

Photo: Sudok1, Getty Images