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Sync for Genes Data Project Publishes Use Cases, Launches Pilot Projects


CHICAGO (GenomeWeb) – The nascent Sync for Genes project took two major steps forward this week, with the publication of a list of potential use cases and the launch of a series of pilots demonstrating some of those use cases.

Both new developments are aimed at speeding the transition of genomics from laboratory to clinical practice. They lean on FHIR Genomics, a component of Fast Health Interoperability Resources (FHIR), a fairly new interoperability standard from Health Level Seven International, an Ann Arbor, Michigan-based nonprofit standards development organization.

To this end, HL7 published a domain analysis model on clinical sequencing, a document detailing several dozen use cases from around the world for genomics in clinical practice, naming types of stakeholders, standards, and workflows necessary to share genetic data following FHIR protocols.

"This is a consistent way of sharing genomics using standards," said Gil Alterovitz, director of the Biomedical Cybernetics Laboratory at Harvard Medical School, director of Sync for Genes, and co-chair of the HL7 Clinical Genomics Work Group. "We seek to get labs to try out this standard" to help them to use test results across their organizations in a standard way, added Alterovitz, who led development of FHIR’s genomics component and co-authored the new document.

Scenarios described in the HL7 document include cancer profiling, specimen identification, family history, drug dosage calculators, sequencing for cytogenic marker identification, public health reporting, pharmacogenomics, and human leukocyte antigen typing. HL7 also recommends various nomenclature, reference databases, and vocabulary constraints for these uses.

The document goes into detail in certain areas, notably specimen identification, breaking that broad topic down into sub-areas, including pediatric and prenatal testing, infectious diseases, germline testing, tumor analysis for biomarkers and mutations, and microbiome analysis. Additionally, HL7 discusses alternative workflows for some case studies and mentions use cases that should be in future FHIR implementations, such as newborn screening, rare diseases, and preimplantation testing.

A day after the HL7 document came out, the federal government's Office of the National Coordinator for Health Information Technology announced five pilots among public and private entities, each following one of the dozens of use cases listed by HL7. This is part of a special effort by Sync for Genes is making to pilot FHIR for genomics, Alterovitz said.

According to an ONC blog post, Counsyl and Utah's Intermountain Healthcare will be testing genetics in family health history; the US Food and Drug Administration will be examining sequencing quality and regulatory genomics; Foundation Medicine and Vanderbilt University Medical Center are teaming up to test data exchange for somatic and tumor testing; Illumina is working with next-generation sequencing technologies; and the National Marrow Donor Program's Be The Match effort will apply FHIR genomics to tissue matching.

There is no set timeline for running the pilots, which actually got underway in January, according to Alterovitz. Sync for Genes is helping the pilot sites build a conformance guidance system, he said.

These tests will assist Sync for Genes in the development of open-source validation scripts and implementation guidance documents, ONC said.

"Now is an inflection point in clinical genomics," Alterovitz said, noting that private companies are now investing in a segment that once was the domain of federal government and academic research institutions.

The Sync for Genes project helps drive clinical research and create a feedback loop, Alterovitz explained.

The program started in January but was publicly announced at the end of February at the Healthcare Information and Management Systems Society annual conference in Orlando, Florida. It is an extension of the Sync for Science program, which launched last year to provide open, standardized applications for individuals to contribute their data to research. Sync for Science is under the umbrella of the National Institute of Health’s All of Us research program, formerly called the Precision Medicine Initiative cohort program.

Leaning on the FHIR standard is an attempt to automate sharing of machine-readable data to do away with the decidedly low-tech approach of exchanging records by fax or PDF. Alterovitz has previously said that the pilots will assist in the refinement of the genomics component in future releases of FHIR.