Clinical Geonomics Innovative Healthcare
February 10, 2016

Clinical Genomics on FHIR - Innovative Healthcare

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Have you or a loved one ever received a terrifying medical diagnosis? In my case, it was “multiple sclerosis." For other people in my life, the news has been “Cancer”, “Parkinson’s,” and other chronic, debilitating diseases and syndromes. The moment is etched in my brain for life. The seconds seem to stand still as your brain is processing the news. At first, there’s shock, then relief that you finally have a diagnosis to explain the strange things that are happening to you… finally you wonder how can you fight it?

What are your odds and can you beat those odds? What are your specific odds? That’s the key thing to understand. Everyone is different. With MS, for example, the range of outcomes of how it will affect you in the years to come is extremely wide. When you ask your doctor how he thinks you will fare and what will your life look like now, the answer is often, “wait and see.” This is especially true for MS. You leave the office with more questions than answers. Talk about living on eggshells for months/years! Cancer is similar, as there is a wide range of outcomes for how patients will respond to their diagnoses and particular treatments.

Clinical Genomics


My diagnostic experience was on my mind a few of weeks ago when I participated in the HL7 Working Group Meeting (WGM) in Orlando. I attended the “Clinical Genomic Apps via FHIR: From Design to Deployment” tutorial, presented by Gil Alterovitz and Jeremy Warner. It was an extremely interesting, hands-on tutorial. I highly recommend attending the HL7 WGMs and this tutorial if it is offered again. This tutorial focused on leveraging Genomic data surfaced by HL7 FHIR for use by clinicians and patients. Dr. Jeremy Warner painted a picture where clinicians could utilize the genomic information exposed through HL7 FHIR, in combination with the patient’s genetic, environment and lifestyle make up, for determining the therapy or drugs that will work well or not so well together. This information could possibly help predict the outcome of the treatments or help in determining the patient’s eligibility for clinical trial.

There are many other scenarios where, if the clinician and the patients had this information at their fingertips at the moment they need it, it would help. In other words, it can be use in Precision Medicine. He also described a scenario where, when giving the patient their diagnosis, the clinician has the patient’s personalized genomic data on hand to help answer some of the questions, instead of leaving the patient with the “wait and see” type of response.

Why is all this so exciting? Today, this genomic information is rarely integrated into an electronic health record (EHR) product. It is hard to get and interpret when the clinician needs it. It is not currently at their fingertips. The work done by the HL7 FHIR community and the SMART team is changing this.

HL7 FHIR is Key

The HL7 Fast Healthcare Interoperability Resource (FHIR) specification is an open, community-developed specification led by the HL7 group that provides a mechanism to represent and exchange electronic health records. This exchange can be implemented using the four paradigms of REST, Documents, Messages and SOAP. The support of the four paradigms gives implementers great flexibility to leverage the paradigm best suited for the job. REST is the paradigm of choice because of its flexibility, ease of use, and market adoption.

The FHIR specification currently consists of 99 defined healthcare resources. These resources are relatively generic and can then have profiles attached to them to give the resources more meaning. For example, the Observation resource can represent lab results or smoking status depending on what profile is attached. The profile doesn’t change the underlying resource; it just gives it meaning. Because of this, even applications that do not understand the profiles can still see the resource content.

FHIR Genomics

Gil Alterovitz from Harvard Medical School and the SMART on FHIR Genomics team have created a set of genetic specific profiles on top of the FHIR resources; Observation, Diagnostic Report, Diagnostic Order, FamilyMemberHistory, and Sequence. This allows applications that understand FHIR and the Genetics profiles, like the SMART Genomics apps to simply point to any FHIR servers that also implement the FHIR Genetics profiles to query and retrieve the data they need to embed it in EMRs and other applications. Below is an illustration of how these FHIR resources are related when used in conjunction with the Genetic Profiles.

FHIR Genetic Profile

Slide from the HL7 TH20 Tutorial

During the tutorial, Dr. Jeremy Warner demonstrated the apps that are being developed in the SMART App Gallery under Precision Cancer Medicine, These apps help clinicians and patients better understand how their genomes affect their diagnoses. You can view the apps here:


Slide from the FHIR Clinical Genomics tutorial TH20

Building Your FHIR Genomic Server

Akana can help you establish an enterprise scalable secure FHIR server based on the HAPI open source project that can implement the FHIR Genetics Profiles. The Akana HAPI FHIR server is a part of the Akana Healthcare API Platform. The Akana Healthcare API platform can increase the mobility of the data in your healthcare organization to get the right information to the right person at the right time securely.

The Akana Healthcare API Platform provides the latest security technology from OAuth to OpenID and JWT to secure the HAPI FHIR server or your own FHIR server. The Akana Healthcare API Platform protects your sensitive data from threats and attacks such as denial of service, SQL injections and JavaScript injections. It also provides extensive auditing capabilities for the healthcare industry, which is heavily regulated and must be able to produce audit records at any moment in time. Part of increasing the mobility of data is making the community aware of its availability and control what apps are consuming the data. The Akana Healthcare API platform provides an API Developer Portal and socializes the available APIs to be consumed in application such as the FHIR Restful APIs and other APIs.

Innovative Healthcare

Giving and receiving a diagnosis is tough on both the clinicians and patients, especially when information and time is not available. The advances of healthcare interoperability with HL7 FHIR gives us the ability to analysis data such as genomic data and put it in the hands of clinicians and patients at right time and place to determine treatments, outcomes of treatments, trial eligibility, and most importantly, being able to give more data back answers instead of “wait and see.” We will see service offering differentiation amongst healthcare providers in the next few years with those that choose to mobilize their data and get it into their clinicians and patients hands. Having more information at my fingertips at the time of my diagnosis would have helped my family and I greatly during a time of uncertainty. I am excited for the future of healthcare with clinical genomics on FHIR.