Open standards for a genomics ecosystem

2025-11-27

The paper related to our database has been accepted by Oxford University Press, Bioinformatics, today. QV: Lawless, Dylan, et al. “Application of qualifying variants for genomic analysis” medRxiv preprint (2025) DOI | PDF | Video | Database. Here is the response email to colleagues on that paper:

On 27 Nov 2025, at 13:41, Lawless Dylan wrote:

Thanks everyone for your involvement.

These papers are not flashy but in simple terms, this first pillar gives us a clean way to separate genetic analysis variables from the software that uses them. This brings two practical benefits:

1. Experts and patients can see clear and exact information about what analysis was done.
2. Public institutions and private companies can agree on analysis protocols without exposing IP, which strengthens trust and supports accreditation.

A second pillar is under way; a national scale standard for minimal, verifiable evidence necessary for automated clinical genetics. Analysis providers can use it to deliver verifiable outputs to hospitals and users, separate from their IP and without repeating the manual checks that hinder collaboration. Many institutions avoid this problem, which shows how far the field can progress and why removing these barriers will be valuable (PDF link BSMD 2025) ¹. Initial validation tests show that this can deliver results in SPHN compliant format for PostgreSQL and RDF to integrate cleanly with Swiss hospitals (our overview documents).

Many thanks,
Dylan

We develop genomic systems for industry and for research, and we publish the resulting designs so they can be reused in scientific work rather than remain internal. These open standards are translated by academic work, such as the paper accepted today. We release these standards in an open, reusable form because genomics becomes reliable only when the field shares formats and evidence frameworks. This is also why we contribute voluntary work to the Swiss Genomics Association to support national collaboration.

The long term aim is to make genomics a mainstream part of life so that its benefits are available to everyone, independent of any direct commercial gain.

Leading institutions lag

The linked PDF is from the British Society for Genetic Medicine, Direct to consumer genomic testing, Position statement, September 2025. It includes the following recommendations. We aim to overcome this hurdle so that such recommendations are no longer necessary, and so that verified standards can be trusted across clinical and public settings.