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BaseHealth Seeks New Model for Offering Patients Genetic Health Information

By Aaron Krol  

April 22, 2014 | “We are well aware of the fact that the FDA is looking at this very closely,” says Prakash Menon, CTO of the Los Altos-based startup BaseHealth, which just emerged from stealth mode this morning to announce the launch of its genetic health platform Genophen. Menon is explaining to me why Genophen should not be compared to 23andMe’s Personal Genome Service, which recently and famously became subject to some harsh FDA intervention.

I had asked about 23andMe because of the teaser email that Bio-IT World received from BaseHealth two weeks ago, asking if we would like to learn more about “a doctor-driven 23andMe.” It’s a revealing statement about the market for genetic health services that part of our interview with BaseHealth’s executive team consists of walking back the elevator pitch. Plenty of companies would like to harness the popular excitement that 23andMe has generated for learning about one’s own genome, tapping into a clear, and now unsatisfied, demand for genetic insights into personal disease risk. At the same time, the regulatory waters of personal genetic testing have always seemed murky, and now they are looking downright perilous.

The growing consensus is that 23andMe, and early competitors like Navigenics that have left the direct-to-consumer market, made their misstep in trying to deliver health information straight to customers – a red flag for the FDA, which worries about patients taking drastic actions without expert medical advice. (For a more detailed discussion, see: “23andMe Pursues Health Research in the Shadow of the FDA.”)

“The first wave of companies in this field essentially went directly to consumer, without placing what they do in context,” Menon continues. “We specifically, by design, wanted to place the data we are presenting in a context provided by a physician. This is complex information, and most people need some help to understand it, and to make behavioral modifications based on what they see on this platform.”

BaseHealth is not the only company experimenting with a physician-mediated model for offering customers access to their personal genetic data. Coriell Life Sciences, a commercial spinoff from the non-profit Coriell Institute for Medical Research, recently launched a suite of products that can store patients’ whole genomes in a secure database, and allow their physicians to run specific tests on that data, one indication at a time. (See: “Coriell Life Sciences Prepares for the Whole-Genome Health Environment.”)

But the Genophen platform stands out in two respects. First, it edges a little bit closer to a direct-to-consumer model, giving patients full access to their profiles at home, after an initial consult with a physician. And second, it considers genetics as just one small piece of a broader view of health, a perspective that will appeal to both physicians, and end users interested in the quantified self environment of calorie counting and Fitbits.

“BaseHealth is the first company to make a health management platform that integrates genomic data with lifestyle and medical data,” says CEO and co-founder Hossein Fakhrai-Rad, who before forming BaseHealth served as director of the genotyping service at Affymetrix. “Genophen uses patients’ genetic information, lifestyle information, and medical information, and provides a comprehensive health assessment for the patients and physicians.”

Hossain Fakhrai-Rad    Menon 

Hossein Fakhrai-Rad (L), CEO, and Prakash Menon (R), CTO, of BaseHealth. Image credit: BaseHealth 

When a new user joins the Genophen platform, she uploads basic lifestyle and background information like her physical activity, tobacco and alcohol use, and family history. Her physician contributes some clinical data – medication history and biometrics like cholesterol levels – and the genetic data is gathered courtesy of a partnership with gene sequencing company Illumina, running either genotyping arrays or whole genome sequencing in a CLIA-certified lab. All this information will be combined into an overall health assessment that calculates each user’s risk for a variety of diseases, and delivers specific lifestyle recommendations to reduce those risks.

The platform is designed so that the patient’s first encounter with her health profile occurs during a one-on-one visit with her physician. “The physician runs the assessment first, studies the assessment, and then has a consultation with the patient and walks them through the assessment,” says Menon. “After this consultation, the physician gives full access to the patient.”

“We think the primary physician is the best person to make some of these recommendations, because they probably know more about the patient than was entered in our system,” he adds.

Predisposition and Prevention 

Genophen is designed to educate users about common complex diseases that can be controlled and prevented.  “Our focus is on multifactorial diseases,” says Fakhrai-Rad, “where if you learn about your genetic predisposition, that doesn’t mean you’re going to get the disease 100%. There are certain modifiable risk factors that you can start taking action for, and reducing your risk.”

More than 40 of these diseases are analyzed in the launch version of Genophen, including widespread chronic conditions like type 2 diabetes, sleep apnea, and heart disease. Genophen also prioritizes the highest-risk diseases for each user, to show where preventive health actions could be most beneficial.

The question of how to communicate health risks has been a vexed one for companies like BaseHealth, which have to balance a desire to be fully informative against the inherent uncertainty of predicting future disease. Where 23andMe presented lifetime disease risks as absolute percentages, Genophen shows each user’s lifetime risk on a relative scale, compared to a hypothetical control patient of the same gender and ethnicity. This assessment is also broken down by specific risk factors: a user might see, for instance, that her genetic profile lowers her risk of developing diabetes twofold, but her cholesterol level raises her risk by a factor of four. The risk factors are divided into those that are non-modifiable – genetic variants, but also characteristics like family history and past smoking – and modifiable risk factors that can be controlled with new health behaviors.

The stress is on interventions, and a number of features have been built to encourage users to take behavioral steps that could protect against future disease. “We know that people are more likely to follow on recommendations and actions that are specifically tailored to their needs, rather than what is good for the average population,” says Fakhrai-Rad. With that in mind, Genophen displays not only a patient’s current risk, but also her “achievable risk,” a best-case figure that could be reached by controlling modifiable risk factors like high blood pressure or poor diet.

There is even an interactive element, a “what-if” analysis where users can see their modifiable risk factors displayed with sliders. By moving those sliders up and down, a user can see how changes in risk factors impact overall disease risk. A patient at high risk of heart disease, for instance, might use this feature to visualize how much benefit could be achieved by giving up cigarettes.


The "what-if" analysis feature in Genophen lets users see how changing their lifestyle behaviors can impact their risks of developing chronic diseases. Image credit: BaseHealth 

“Any data we use to make the assessment comes from peer-reviewed articles that have been replicated,” says Fakhrai-Rad, and users can view the literature citations for any risk claim in Genophen. In principle, adds Menon, this transparency and rigor in making health claims should help the FDA view the platform’s recommendations as well-validated. “Most of the recommendations and assessments we do can actually be replicated given the data that we have provided, with the citations,” he says.

When it comes to genetics, most of BaseHealth’s claims are derived from a collaboration with NextBio, an Illumina-owned company that maintains what it calls “the world’s largest repository of curated genomic data.” The BaseHealth curators have mined the NextBio database for associations between known genetic variants and complex diseases. Genophen users can view their genetic risk factors at the level of individual variants: by selecting the “DNA data” tab for a particular disease, users reach a graphic representation of the 23 human chromosomes, with any variants they carry that impact their disease risks highlighted at the appropriate chromosomal locations.

Access to NextBio’s database has also allowed BaseHealth to build pharmacogenomic and nutragenomic profiles for each patient, identifying which drugs and dietary choices may be impacted by genetic factors. The pharmacogenomic component concentrates on a few well-known drug-gene interactions, such as variants affecting response to blood thinners. At present, the nutragenomic component is used mainly to supplement basic nutritional advice, considering genetic factors like lactose intolerance or celiac disease before recommending dietary changes. Any recommendation made in Genophen can be manually overruled by a patient’s physician, if she disagrees with the platform’s findings or has more complete information.

A Platform for Care Providers 

A select group of customers has already enrolled in the Genophen platform, through a pilot program based around 50 physicians who have become early adopters. “We are not reaching out to customers individually,” says Fakhrai-Rad. “We reach out through larger physician groups and other organizations,” so that physicians who aren’t comfortable using Genophen don’t find themselves serving patients on the platform.

“It turns out going through the physician actually helps us be in compliance with a lot of what the FDA is looking for,” adds Menon. “We are in compliance right now, and obviously the policies are in flux as the industry matures.” He also says that BaseHealth has agreed to certain disclaimers suggested by FDA consultants, to make the intent and limitations of genetic health reports clear to users.

Providing a service to larger care organizations lets BaseHealth pursue a very simple revenue model. Genotyping services, and especially whole genome sequencing, are expensive propositions, and few consumers are in a position to pay for their whole genomes. Care organizations, however, may see the promise of large cost savings across their patient populations if Genophen leads users to improve their overall health and head off disease risks. BaseHealth charges for the platform on an annual subscription basis, and Fakhrai-Rad says he sees no need to supplement these subscriptions with other sources of revenue, like selling anonymized data to commercial partners.

With preventive care as a guiding principle, BaseHealth also has less interest than some of its potential competitors in mining as much information as possible from the genome. Although the company will gather enough genetic data to flag rare, single-mutation disorders, Genophen will not report carrier status or other information that could cause users anxiety without suggesting future actions that can be taken. “We have been working very closely with physicians, and this has been a request from physicians,” says Fakhrai-Rad. “We do not want to get into monogenic or Mendelian diseases, where we have no idea how to deal with it.”

Genophen is also uninterested in non-health-related traits, which have been a playful feature of direct-to-consumer services like 23andMe, giving customers small insights into traits like unibrows and distaste for cilantro. One trick BaseHealth may borrow from the 23andMe playbook, however, is using its customers’ genetic data for original in-house research, which could feed new health information into the system. “We haven’t done that yet,” says Fakhrai-Rad, “but as we build our database, and bring enough participants onto the platform, definitely that is something we could do.”

At launch, around 250 pilot users have created Genophen profiles. Even bringing the platform to this point of development has been a massive investment, with BaseHealth spending over $5 million of a $6.3 million round of initial funding by angel investors. The market the company has entered is also uncertain – though patients are gaining interest in personal genetics, no company has yet been able to translate a genetic health service into sustained profits.

The BaseHealth executive team hopes that a focus on preventive care will prove to be the missing ingredient that brings large care organizations on board. “The current health assessment platforms are not supported by providing a personalized and specific action that is tailored to the patient,” says Fakhrai-Rad. “[Genophen] intervenes physicians early, so the physician can take actions and provide recommendations and advice to the patients to start managing their health.”


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