A clear and standardized way to share patient data responsibly

A clear and standardized way to share patient data responsibly

The International Organization for Standardization (ISO) has published Phenopackets, the first clear computational way to responsibly share individual patient traits, removing a major barrier to research on disease diagnosis, treatment, and mechanism discovery.

A “Phenopacket” is structured text that both humans and computers can read. It describes a person’s phenotype, a term for the way our genes manifest in our bodies, such as hair colour, hormone levels, or a bad reaction to a drug.

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The standard was initially developed by the Global Alliance for Genomics and Health (GA4GH). The CSC is heavily involved in the GA4GH and was also involved in the development of Phenopackets. The GA4GH is a worldwide organisation which, in addition to sharing information and increasing understanding, systematically develops compatible open standards. The CSC takes the information from these developments forward in Finland and builds services that are inherently compatible with international services. 

“We finally have the very first standard for phenotype data available worldwide,” said University of Colorado professor Melissa Haendel, a GA4GH contributor who launched the Phenopacket idea eight years ago.

“Having this ISO standard will encourage software developers, infrastructure developers, healthcare systems to consider Phenopackets as a method for sharing patient-level information — securely and in a deidentified way — that can be useful for everything from rare to infectious diseases, and addressing many kinds of public health questions,” Haendel said.

“Phenopackets is the first open, standards-based exchange format that makes it possible to describe diagnoses, observations and measurements in the same accuracy as genetic components in computational workflows. It will soon become an essential part of all biological research services at CSC,” says Heikki Lehväslaiho, Senior Applications Specialist from CSC.

The GA4GH Phenopacket is featured in the July 2022 Nature Biotechnology article The GA4GH Phenopacket schema defines a computable representation of clinical data. Heikki Lehväslaiho is one of the authors of this article.

While the Phenopacket schema will continue to be available free of cost from GA4GH, ISO publication significantly broadens its reach. As an added benefit, any organisation that adopts Phenopackets can easily link to other powerful clinical and research tools from the GA4GH Genomic Data Toolkit.

More information:

Global Alliance for Genomics and Health: First GA4GH standard published by ISO will reshape how doctors and researchers share phenotypic information

CSC services for sensitive data

Finnish FEGA service 

Jacobsen, J.O.B., Baudis, M., Baynam, G.S. et al. The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol 40, 817–820 (2022). https://doi.org/10.1038/s41587-022-01357-4

Ladewig et al. GA4GH Phenopackets: A Practical Introduction. Advanced Genetics 2022, 2200016
DOI: 10.1002/ggn2.202200016