Introduction to HL7 Clinical Genomics

1. Introduction to HL7 Clinical Genomics Intermountain Healthcare Clinical Genetics Institute Marc S. Williams, M.D.DirectorGrant M. WoodSenior IT Strategist

2. Informatics Line in our Brochure • Link genomic/family medical history data to the electronic medical record to provide advanced genetics-based tools for the clinician.

3. Genomics and Informatics • Clinical genomics data could dwarf the data storage and management challenges posed by genome sequencing projects. • Personalized medicine will require an increased integration of clinical and research databases.

4. Health Level Seven (HL7) Overview • HL7 is an international community of healthcare clinical and informatics experts collaborating to create standards of electronic healthcare information • The organization is comprised of Technical Committees (like Clinical Decision Support, Electronic Health Records, Medical Records, etc) and Special Interest Groups (like Clinical Genomics) • Develop standards that permit structured, encoded health care information, to be exchanged between computer applications • Collaborate with other standards development organizations • Encourage organizations to participate in HL7 to develop healthcare information standards in their area of expertise • Collaborate with healthcare information technology users to ensure that HL7 standards meet real-world requirements

5. HL7 Clinical Genomics • Lead model developer is Amnon Shabo from the IBM Haifa Research Lab • Other participants include representatives from healthcare provider, pharmaceutical, software vendor, professional services, and Veterans Administration • Genetic Locus, Genetic Loci, and Family History models approved via ballot as Draft Standard for Trial Use • Model is designed to store genomic data in the EHR for use by clinical decision support applications • Waiting for implementation by early adopters and partners to test the exchange of clinical genomic and family history data

6. The GeneticLocus Model - Focal Areas: Expression Data The Locus and its Alleles Sequence and Proteomics Sequence Variations Clinical Phenotypes

7. Incorporation of CG data into the EHR Don’t leave behind the raw genomic data… bring it into the EHR! A Clinical Genomics Instance Longitudinal Patient EHR (RIM-based CEN 13606 EHR) Amnon Shabo, IBM Haifa Research Lab

8. The Underlying Paradigm:Encapsulate & Bubble-up Patient Genotype Clinical Guidance Bridging is the challenge… HL7 CG messages associated with HL7 clinical objects (phenotypes – Warfarin metabolism) Knowledge (KBs, Ontologies, registries, reference DBs, Papers, etc.) HL7 CG Messages Encapsulating HL7 Objects Encapsulation of CYP2C9 and VKORC1 sequence data EHR System Evidence-based algorithm to determine starting dose Decision Support Applications Bubble up the most clinically-significant raw genomic data into specialized HL7 objects and link them with clinical data from the patient EHR Amnon Shabo, IBM Haifa Research Lab

9. American Health Information Community Workgroups The EHR Workgroup has identified ten priorities that represent essential minimum features or functions of EHRs. These features or functions are the utilities identified as the most important clinical data elements by clinicians who are either considering adoption of EHRs, or those who have adopted but desire interoperability in these areas. These utilities are noted in priority order as determined by the EHR Workgroup, and are all considered critical for comprehensive patient care. • Patient Identification • Medication List / Allergy • Laboratory Results • Problem List • Clinical / Encounter Notes • Anatomic Pathology Results • Vital Signs • Family History/ Health Factors • Radiology Reports: Not including images • Immunizations 8. Family History/ Health Factors:May contain a detailed problem list and health history of a patient’s family members. Typically used by providers when assessing familial risk and planning care.

10. Ontologies: Clinical Genomics Knowledge EHR: Patient data & care goals Partners FH CaGene Search Query transform transform HL7 Clinical Genomics Family History Interoperability CDC/ Surgeon General Any pedigree program transform transform HL7 Lab Message Raw genomic data user Clinical Lab Genetic Lab Amnon Shabo, IBM Haifa Research Lab

11. Implementations • Family History • Massachusetts General Hospital • Fully based on the v3 models • Incorporating genomic information into the patient EHR • Partners HealthCare – Structured reporting of sequencing based genetic tests • Clinical decision support rules to leverage genetic tests results • Genetic testing information exchange • Harvard HPCGG and Intermountain Health Care • Map to HL7 v2 lab messages that are currently supported by existing lab systems on both sides

12. For More Information • For the Genetic Locus, Genetic Loci, and Family History model walkthroughs and XML Schemas, go to http://hl7.org/Special/committees/clingenomics/docs.cfm • We encourage organizations to participate in HL7 to test the clinical genomic models (including AHIC to help advance implementation!) • Send any further questions to Amnon Shabo, Co-Chair HL7 Clinical Genomics Special Interest Group, IBM Research Lab in HaifaE-mail: shabo@il.ibm.com • Find HL7 website at www.hl7.org • Contact me at via e-mail at grant.wood@intermountainmail.org