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Phenopackets are certified as ISO standard

Image: A collaboration between the Global Alliance for Genomics and Health (GA4GH) and the Canadian Standards Board led to the publication of GA4GH Phenopackets as an ISO standard.
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Credit: GA4GH / Stephanie Lee

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

The standard was initially developed by the Global Alliance for Genomics and Health (GA4GH) and approved at ISO under the Canadian Mirrors Committee in accordance with ISO/TC215/SC1. genomicsand supported by the Canadian Standards Council.

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

“Having this ISO standard will encourage software developers, infrastructure developers, and healthcare systems to see Phenopackets as a way to share patient-level information – securely and in an unidentified manner – that can be useful for everything from rare to infectious diseases, treating many types of disease.” public health questions,” Heindel said.

standard,”Genomic Informatics ISO 4454 – Phenotype packages: a format for interchange of phenotype dataOn July 6, 2022.

Phenopackets debuted at ISO thanks to the leadership of GA4GH and through the support of Canada’s national member body, the Standards Council of Canada (SCC), and Innovation Initiative.

In addition to promoting the UN’s Sustainable Development Goals for good health and innovation, Phenopackets has the potential to benefit a range of Canadian and global organizations, from Google to the Canadian Institute for Health Research to the Red Cross.

A “Phenopacket” is a packet of data – usually a file – that humans and computers can read. describe the person Phenotypea term that refers to the way our genes appear in our bodies, such as hair color, hormone levels, or a bad reaction to a drug.

For more than a thousand years, clinicians have used the same technology to record and share phenotypes: written observation.

While handwritten scribbling has turned into complex electronic health records, fundamentally, not much has changed. Physicians may record two identical phenotypes of two patients in significantly different ways that are difficult to compare.

For bioinformaticians who study how genes affect the chances of developing cancer, rare diseases, and disease, this free flexibility is a problem.

“If someone gave you a piece of paper with a bunch of things scribbled on and said, ‘Go find that,’ you would go, ‘Well, I don’t know what that is! “You have to read it, understand it, extract all the data and understand it in your head. And that takes a long time,” said Julius Jacobsen, a bioinformatics software developer at Queen Mary University of London who co-led the GA4GH team working on Phenopackets.

“But Phenopacket provides a sense of how all the bits fit together, like a blank form. All anyone has to do is fill in the pre-existing fields, and then it can give you a nice piece of structured information that anyone can understand,” Jacobsen said.

So in 2019, GA4GH – the Global Standards Organization for Genomics – approved Phenopacket standard To store phenotype data in predictable formats that computers everywhere can read.

A few months later, the newly formed ISO Genomic Informatics Subcommittee met in the South Korean city of Daegu. The group chose Phenopackets as one of its first standards for its development, working alongside GA4GH contributors to update the original version of the standard. (Phenopackets v2.0.0.apk It was certified to the ISO standard after it was approved in February.)

To formally propose Phenopackets to ISO, GA4GH Work Stream Director Lindsay Smith, based at the Ontario Institute for Cancer Research in Toronto, collaborated with the Canadian Mirror Commission for ISO/TC215/SC1, with support from SCC.

Through programs such as its Innovation Initiative, SCC helps innovators commercialize technologies and facilitate their participation in national and international standardization committees for the benefit of economic growth and the health and safety of Canadians.

“Finding ways to advance health technologies has been an important area of ​​interest for the innovation initiative,” said Chantal Guay, CEO of SCC. “The development of the ISO standard is fundamental to harmonizing views internationally and promoting shared health information around the world.”

Numerous rounds of reviews from ISO experts in Japan, India, Canada, the United States, and Korea have confirmed that Phenopackets will work in diverse healthcare systems.

“In Japan, a network of 14 major biobanks has implemented Phenopackets, with 920,000 samples and 250,000 genomic and omics data submitted by 490,000 individuals,” said Soichi Ogishima, an ISO project team member who reviewed Phenopackets.

“Researchers can access phenotypic information using GA4GH’s Phenopackets standard to capture clinical data and combine it with genomic data to develop precision medicine,” added Ogishima, professor of genomic informatics at Tohoku University in Sendai, Japan.

The humble Phenopacket has the potential to transform the treatment of common ailments.

Asthma, inflammatory bowel disease, schizophrenia, and other complex conditions are unlikely to be a single disease. But it is difficult to divide these diseases into groups that respond to specific treatments. One reason is that everyone uses their own formats, so you can’t combine the data, said Peter Robinson, a computational biologist at Jackson Lab who co-led the GA4GH Phenopackets development team.

“By using Phenopackets, we will be able to improve precision medicine for individuals by being able to compare and group patients based on their individual characteristics,” he said.

Standard can be improved too Study and diagnosis of rare diseases.

“There should be a tool for patients to share their information like Phenopackets,” Haendel said. “Currently there are rare patients all over social media sharing a free script that can be organized in such a way that we can extract it as data – for example, to identify patients with the same condition worldwide.”

Matching patients will be made easier with a database of cases described in Phenopacket format.

“Many journals in human genetics are willing to consider adulation or ask authors to submit Phenopackets along with case reports. Usually if you find a new disease gene, you will describe ten patients, but none of that information is accessible,” Robinson said. at the patient level.

In June, Robinson, Jacobsen, Haendel, Smith and collaborators published a file article in nature biotechnology Explains how Phenopackets are making available to researchers and clinicians Share patient characteristics more effectively Linking that data to genetic information.

While Phenopacket scheme is still Available for free From GA4GH, the ISO publication significantly expands its scope. Unlike Japanese biobanks, databases such as the widely used BioSamples have already implemented Phenopackets. Electronic health record vendors and national health systems are studying the standard.

As an added benefit, any organization that adopts Phenopackets can easily link to other powerful clinical and research tools from GA4GH Genomic Data Toolkit.

Going forward, there are plans to build Phenopackets into standards for sharing electronic health records, such as Fast Healthcare Interoperability Resources (FHIR) by Health Level 7 (HL7).

Phenopackets selected as one of HL7’s Vulcan accelerator projects. Accelerator projects attempt to improve how clinical studies are designed, conducted, and reported by enhancing the implementation of research-ready standards. A project to represent Phenopackets in the FHIR standard is underway to ensure that this scheme – which is now an ISO standard – can also be used in the context of HL7,” Haendel said.

Phenopackets may be the first GA4GH standard published by ISO, but it won’t be the last. Currently, the ISO Genome Information Subcommittee is reviewing a proposed standard for genetic surveillance systems – such as public health systems that track Covid-19 variants circulating around the world. The GA4GH standards feature prominently in the requirements.

When standards development organizations align their work, everyone benefits.

“The ISO publication for Phenopackets exemplifies the benefits of harmonizing standards. When different standards-setting bodies collaborate, they amplify the impact of all our standards. Global standards truly expand responsible data sharing and bring the benefits of precision medicine to more patients and their families,” said Peter Goodhand, CEO of GA4GH. .

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About the Global Alliance for Genomics and Health (GA4GH)

The Global Alliance for Genomics and Health (GA4GH) is an international, not-for-profit alliance formed in 2013 to accelerate the potential of research and medicine to advance human health. By bringing together more than 600 leading organizations working in healthcare, research, patient advocacy, life sciences, and information technology, the GA4GH community works together to create frameworks and standards to enable responsible, voluntary, and safe sharing of genomic and health-related data.

About the Canadian Standards Council (SCC)

Since 1970, the Canadian Standards Council (SCC) has helped make life safer, healthier, more prosperous and sustainable for individuals, communities and businesses in Canada through the power of standardization. Working with an extensive network of partners nationally and around the world, SCC serves as Canada’s voice on standards and accreditation on the international stage, including as a member of the International Organization for Standardization (ISO) and the International Electrotechnical Commission (IEC). As the nation’s leading accreditation organization, SCC creates market confidence at home and abroad by ensuring conformity assessment bodies meet the highest expectations. In all these ways, SCC opens up a world of possibilities. For more information visit https://www.scc-ccn.ca (link is external)