Phenopackets Version 2.0

New release of the Phenopackets standard captures a more complete medical picture

Illustration by GA4GH

The Global Alliance for Genomics and Health (GA4GH) Phenopacket standard provides a human- and machine-readable way to structure phenotypic data about a patient and share it across clinical and research environments to support translational research, diagnostics, and personalized healthcare. The Phenopacket standard is a product of the NIH-funded Phenomics First Center of Excellence, led by Melissa Haendel (CU Anschutz), Chris Mungall (LBNL) and Peter Robinson (Jackson Laboratory).

The Phenopacket standard has been in development for several years; v1 was approved by GA4GH in 2019. Phenopackets v1 focused on the rare disease use case; the newly approved Phenopacket schema v2.0 builds and expands on this, now enabling representation of cancer and common disease phenotypes as well. Three new elements in v2.0 help to capture a more complete medical picture:

  • The Measurements property captures quantitative or categorical measurements such as platelet count in a blood sample or body temperature.

These new elements were added in collaboration with community members. For example, the Measurements element was initially proposed by Núria Queralt Rosinach, a member of the European Joint Programme on Rare Diseases Driver Project and GA4GH and a researcher at Leiden University Medical Center, during a COVID-19 BioHackathon. To better capture cancer-relevant information, the Phenopackets team collaborated with ICGC-ARGO, which leverages genomics to accelerate cancer research, and mCODE, an initiative aiming to create a common cancer data model.

Phenopackets Version 2.0 is better aligned with other relevant standards such as the Fast Healthcare Interoperability Resource (FHIR) HL7 — a widely-adopted standard for exchanging electronic health records — as well as the GA4GH-developed Variation Representation Specification (VRS) and VRSATILE, which aim to standardize the exchange of genetic variation data.

More information:

Preprint: The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

GA4GH press release: Phenopackets v2 expands utility to provide a more complete medical picture

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