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DNAFeed Adds Genetic Counseling to Scripps Polygenic Risk Study


CHICAGO — Scripps Research Translational Institute (SRTI) has augmented an ongoing study on polygenic risk for coronary artery disease by adding remote genetic counseling, courtesy of a new partnership with DNAFeed. The institute also has widened its potential study base by making its mobile interface available to Android users in addition to those with iPhones.

San Diego-based DNAFeed and SRTI, in nearby La Jolla, California, launched their collaboration last month, in conjunction with the research institute issuing an update to its polygenic risk scoring platform. Changes include refining Scripps' algorithm and the release of an Android mobile app to complement an existing app for the Apple iOS platform.

The most recent release also added a Spanish-language option and an update to how genetic risk scores are calculated.

DNAFeed is now supplying remote genetic counseling services — online and phone — for study participants. DNAFeed Founder and CEO Ahmed El-kalliny said that this partnership makes the project among the first studies of polygenic heart disease risk scoring to include online and phone/video counseling.

The study is trying to apply genetic information to preventive health settings.

"Generally, genetic information is used as more of a reactive test at this point in time. You either have very high cholesterol levels or a family history of cancer or something like that," said Ali Torkamani, director of genomics and genome informatics at SRTI. The genetic test then helps clarify phenotypic observations.

Scripps wants genetics to identify risks ahead of time so physicians can prescribe interventions or help patients change behaviors to prevent the onset of symptoms.

SRTI chose to partner with DNAFeed because genetic counselors at the affiliated Scripps Health mostly specialize in familial cancer counseling; the organization does not have its own counselors for cardiology, according to Torkamani.

"This takes it even a step further with polygenic risk versus monogenic risk," said Torkamani, an integrative structural and computational biologist at Scripps Research.

DNAFeed offers a mix of telephone-based counseling, video, and online chat backed by both artificial intelligence and human genetic counselors and pharmacists — the latter for pharmacogenomic applications, which do not apply to the Scripps study.

After DNAFeed schedules a call with a patient, any family history collected by the testing laboratory or ordering physician shows up in the system to guide the conversation, and the counselor will confirm that information. Following the session, the counselor writes up consult notes, which then get sent back to the ordering lab or clinician. At that point, DNAFeed can open up an asynchronous chat line for the physician to ask follow-up questions of the counselor.

DNAFeed's system has several AI components, including a library of responses. For this, the company has a HIPAA business associate agreement with Google to use an application programming interface for scanning keywords in the chat, then matching the keywords with the DNAFeed library to propose responses.

The company has direct links to ClinVar and other databases to help counselors find citations and evidence. El-kalliny said that that feature is more often used for inquiries related to direct-to-consumer tests than for professionally ordered screening.

DTC tests are exactly what SRTI is relying on for its study, specifically 23andMe panels.

Users download a Scripps-developed app called MyGeneApp, consent to participate in the research study, then connect their 23andMe accounts. Only those with 23andMe test results are able to take part in the study.

Scripps chose 23andMe because of the availability of an API to connect individual data with myGeneApp, according to Torkamani.

"We're just trying to leverage the pre-existing genetic data that's out there," Torkamani said. He would like to expand the study to other consumer genetic testing sites as public APIs become available.

Scripps allows participants to upload lifestyle data about diet and exercise, including information from wearable fitness and step trackers, to inform risk score.

"That is part of our discussion with the participant: What are the kinds of things that can lower your risk for heart disease, for instance? And what are some of the things that would increase the risk even if they're not genetic?" El-kalliny said.

"Even though it's just a study, it could have a lot of value to the participant, and especially if they're taking this and having a follow-up discussion with their healthcare provider about a particular insight that they had."

After receiving the data, Scripps provides a questionnaire through the app, then returns a genetic risk score for coronary artery disease, with context on specific health risks. After this score, study subjects discuss their risk with a counselor by phone, video call, or online chat to understand what lifestyle and behavioral changes they could take to reduce their risk for heart disease.

Participants have the option to provide data from activity trackers and from the Apple Health and Google Fit platforms as well. Seqster aggregates data from wearables and from electronic health records on behalf of SRTI.

Within the app, users can turn on and off various behavioral factors related to diet, exercise, and other lifestyle choices to see how those factors influence overall health risk. Six months later, study participants get a follow-up questionnaire to see how risk has affected behavior.

"We can see over a period of time how people respond to this genetic information," Torkamani said "Do they change their behavior? Do they increase their activity? And how does that relate to their usage of the app itself?"

Following the consultation, DNAFeed summarizes the conversation and shares the note with patients and researchers. Patients also can give permission to share the note with their physicians.

As part of its service, DNAFeed offers genetic counselor support to physicians for a specific period of time, usually 60 or 90 days.

"We can schedule phone calls with the physicians, but in most cases, we're able to answer a lot of their questions online," El-kalliny said, noting that it can be difficult to schedule phone calls between physicians and genetic counselors.

"Many physicians may not be equipped to handle these questions. Having that open line of communication between the physician and our genetic counselor really helps," El-kalliny said. "Not only does it aid them in being able to answer the patient's question, but then physician may also learn something in the process that might help them in dealing with their next patient's genetics-related question."

The updated polygenic risk score is based on 57 specific SNPs related to coronary artery disease. "That's the only condition we're looking at, common variants related to that risk," Torkamani said.

"In this latest update, everyone gets an updated score based on a more powerful score now that our knowledge of the genetics of coronary artery disease has improved over the past couple of years," he added.

Counselors are tasked with explaining whether changes in risk scores are clinically relevant. "Some people might get concerned about a move from, say the 50th percentile to the 60th percentile," Torkamani said. "It seems like it might be a pretty big move, but not in terms of clinical implications."

Another concern in defining guidelines was for people who have a low polygenic risk score but have high clinical risk factors, such as elevated cholesterol.

"We want to make sure that we have guidelines in place that essentially warn people that they're not they're not necessarily out of the woods just because they came out with a low genetic risk score. There are other things like familial hypercholesterolemia that are not being tested," Torkamani said.

Following this recent update, Torkamani will start looking at improving the actionability of information by providing material through the app to help individuals cut their disease risk.

Later on, Scripps will expand its risk scoring to include other medical conditions, possibly beyond cardiology, Torkamani said. He did not commit to a specific timeline.