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Following the Spread of APIs in Health: BaseHealth’s Genomic Health Analysis

Posted on June 3, 2015 I Written By

Andy Oram is an editor at O’Reilly Media, a highly respected book publisher and technology information provider. An employee of the company since 1992, Andy currently specializes in open source, software engineering, and health IT, but his editorial output has ranged from a legal guide covering intellectual property to a graphic novel about teenage hackers. His articles have appeared often on EMR & EHR and other blogs in the health IT space.

Andy also writes often for O’Reilly’s Radar site ( and other publications on policy issues related to the Internet and on trends affecting technical innovation and its effects on society. Print publications where his work has appeared include The Economist, Communications of the ACM, Copyright World, the Journal of Information Technology & Politics, Vanguardia Dossier, and Internet Law and Business. Conferences where he has presented talks include O’Reilly’s Open Source Convention, FISL (Brazil), FOSDEM, and DebConf.

Because health care has come late to the party, companies in that field have had plenty of time to see the advantages that Application Programming Interfaces (APIs) have brought to other areas of computing and commerce. BaseHealth Enterprise, which has been offering comprehensive health assessments based on a patient’s genetic information and other health factors for five years through a Software as a Service (SaaS) platform, is now joining the race to APIs. The particular pressures that led to the development of their APIs makes an interesting case study.

Although the concept of an API is somewhat technical and its details call for a bit of programming background, the concept driving API use is simple. We all use web sites and mobile apps to conduct business and interact, but an API allows two applications to talk to each other, serving as a pipe of information transfer. Thus, crucial tasks can be automated and run on a routine basis using an API. BaseHealth modestly suggests in their press release that their API “marks the first time in human history that genomic data is on-call for developers across the globe.”

Example of request for sleep apnea information

Example of request for sleep apnea information

I talked last week to BaseHealth’s CEO Prakash Menon and to Hossein Fakhrai-Rad, founder and Chief Scientific Officer. They offer five basic services, all based on evaluating the genomic and phenomic (observed) data from a patient. A developer can call for such information as:

The patient’s risk for a particular common complex disease, along with risk factors that make it more likely and recommended lifestyle changes The likely effectiveness of a particular drug for a condition, given the patient’s genetic makeup Likely patient responses to various nutrients

Genomic testing is done by companies such as Illumina. Different testing services make very different judgments about the significance of various genes, but there are now evaluation sites (which perform a kind of crowdsourcing to accumulate information validating these judgments) to offer more confidence in the tests. BaseHealth accepts this data along with information about family history, lifestyle, and the patient’s environment to make useful recommendations about handling diabetes, cancer, stroke, gout, sleep apnea, and many other common conditions.

Previously, many health plans and hospitals were interested in the BaseHealth SaaS platform, but did not want to adopt a new application and UI into their existing systems because of the cost of implementation and the time it would take to train healthcare professionals on a new system. The BaseHealth API allows developers at these organizations to use specific features of BaseHealth’s comprehensive health assessment without having to overhaul their existing systems.

Furthermore, large genetic sequencing results are time-consuming and expensive to transmit, and it was wasteful to store them twice (at the provider and at BaseHealth). Some countries also prohibit the transfer of genetic data outside the country’s border for privacy reasons.

BaseHealth’s APIs therefore allow a totally different interaction model. Data can be stored by health care providers and patients, then combined by an application (usually run at the provider’s site) and submitted as a JSON data structure to the API. Only the specific information required by the API needs to be transferred. It is conceivable that apps could be developed for patient use as well. However, because BaseHealth does not offer direct-to-consumer genetic testing, they have none of the problems that 23andMe suffered.

In a field where many vendors scrutinize and limit access to APIs, it’s important to note that BaseHealth’s API is available for all to use–there is no gateway to get through, only a short registration process in which BaseHealth collects a developer’s email address. One can submit 1,000 requests each month for free-making participation easy for small providers-and then pay a small fee for further requests.

APIs hold the promise to streamline health care just as they have reduced information friction in other industries. The BaseHealth experiment illustrates why an API is useful and how it can alter the business of health care.

Insights from Dr. Eric Topol at #SHSMD14

Posted on October 16, 2014 I Written By

John Lynn is the Founder of the blog network which currently consists of 10 blogs containing over 8000 articles with John having written over 4000 of the articles himself. These EMR and Healthcare IT related articles have been viewed over 16 million times. John also manages Healthcare IT Central and Healthcare IT Today, the leading career Health IT job board and blog. John is co-founder of and John is highly involved in social media, and in addition to his blogs can also be found on Twitter: @techguy and @ehrandhit and LinkedIn.

Patient care will eventually win, but sacred cows still have a lot of fight in them.

I’m still chewing on this one. I definitely love the idea of remote visits. Not sure it’s the smartest patient room.

This trend is definitely happening. Although, if you sound out Iwwiwwiwi, it sounds a lot like whining. I’m not sure that’s a good thing. Either way, I think the market is going to push towards on demand medicine.

I’d love to hear more about this topic. I think the first step is identifying the real cost problem. Seems like these top drugs could provide a really good start.

NY Hospital Links DNA Profiles With EMR

Posted on May 6, 2013 I Written By

Anne Zieger is veteran healthcare consultant and analyst with 20 years of industry experience. Zieger formerly served as editor-in-chief of and her commentaries have appeared in dozens of international business publications, including Forbes, Business Week and Information Week. She has also contributed content to hundreds of healthcare and health IT organizations, including several Fortune 500 companies. Contact her at @ziegerhealth on Twitter or visit her site at Zieger Healthcare.

New York’s Mount Sinai Medical Center has launched a new program designed to link patient DNA to optimal treatments, in which patients consent to DNA sequencing, contact with researchers and longitudinal studies related to data within their EMR.

To date, 25,000 people have signed up to participate in the biobank program, BioMe. BioMe is designed to access a broad range of clinical and environmental information stored in the EMR and link it with genetic information provided by patients.  BioMe also offers doctors the opportunity to give patients more targeted care based on their DNA profile. The program is funded by The Charles Bronfman Institute for Personalized Medicine at Mount Sinai.

As part of this effort, a team of doctors, genetic scientists and IT experts at Mount Sinai are gradually implementing a new program called CLIPMERGE (Clinical Implementation of Personalized Medicine through Electronic Health Records and Genomics).  CLIPMERGE is using a new tool, developed at Mount Sinai, which gives doctors real-time therapeutic suggestions based on patient genetic profiles. The idea behind these technologies is to link CLIPMERGE and BioMe, bringing up to the moment information on genetic responses to certain medication to the patient bedside.

Right now, real-time feedback on ideal medications based on DNA profiles is available for three conditions related to cardiovascular disease, blood clots and high cholesterol. The idea is that as scientists discover other DNA-specific responses to therapeutics, CLIPMERGE and BioMe will help bring them to practicing physicians quickly.

According to Healthcare IT News, the BioMe databank will include diverse human ancestry, with self-reported 25 percent of African ancestry, 30 percent of European ancestry, 36 percent of Hispanic Latino, and 9 percent of other ancestry.

Genomics Based EHR

Posted on January 10, 2012 I Written By

John Lynn is the Founder of the blog network which currently consists of 10 blogs containing over 8000 articles with John having written over 4000 of the articles himself. These EMR and Healthcare IT related articles have been viewed over 16 million times. John also manages Healthcare IT Central and Healthcare IT Today, the leading career Health IT job board and blog. John is co-founder of and John is highly involved in social media, and in addition to his blogs can also be found on Twitter: @techguy and @ehrandhit and LinkedIn.

This is a pretty old tweet that I’d stored away, but I’m completely interested in the idea of a Genomics based EHR. I meant to reach out to Don Fluckinger to see what he was talking about. I don’t think that there is any EHR that is based on Genomics. Although, if there is I’d love to know about it. Instead, I’m pretty sure that Don is just talking about integrating Genomics into EHR software.

I’ve made this prediction for a number of years now: Genomics will be part of the EHR software of the future. Genomics is one of the core elements that I think a “Smart EMR” will be required to have in the future. I really feel that the future of patient care will require some sort of interaction with genomic data and that will only be able to be done with a computer and likely an EHR. I love some of the quotes by Shahid Shah in this eWeek article about Digital Biology and Digital Chemistry.

As I think about genomics interacting with EHR data and the benefits that could provide healthcare going forward, I realize that at some point doctors won’t have any choice but to adopt an EHR software. It will eventually be like a doctor saying they don’t want to use a blood pressure cuff since they don’t like technology.