Whole Genome Sequencing Advances Rare Disease Diagnosis Across Multiple Studies

Whole genome sequencing is increasingly becoming a routine tool for diagnosing rare diseases, with recent initiatives and studies from Scotland, Sweden, and the Netherlands reporting improved diagnostic yields and detection of previously missed genetic variants.

The Scottish Genomes Partnership, a program using genome sequencing to diagnose rare disease patients in the Scottish NHS, previously achieved a 23% diagnostic rate with short-read sequencing in affected families. To increase diagnostic yield, researchers applied Oxford Nanopore Technologies long-read sequencing to 24 families (74 individuals) that remained undiagnosed after short-read-based SNV/indel analysis. Pathogenic or likely pathogenic de novo structural variants were identified in 3 of 24 families: an AUTS2 inversion, a DLX5/6 locus inversion, and an FN1 deletion. All three variants were independently confirmed by retrospective short-read re-analysis.

Rare diseases affect fewer than 1 in 2000 people, and up to 10,000 rare diseases collectively affect 3–6% of the population worldwide. Whole-genome sequencing projects for rare disease diagnosis typically yield a diagnostic rate of 25–41%, depending on patient selection and prior testing.

In Sweden, a collaboration between Karolinska Institutet, Karolinska University Hospital, and SciLifeLab has integrated whole genome sequencing into routine diagnostic investigations for rare diseases. A study published in Genome Medicine summarizes data from 15,644 individuals and reports that a genetic cause was identified in 3,538 individuals, corresponding to 23%. The diagnoses involved variants in more than 1,500 different genes. Many of the diagnosed patients were children, and in cases such as congenital metabolic disorders and severe epilepsies, targeted treatment was offered as a direct result of the diagnosis.

Researchers at Radboud University Medical Center in the Netherlands conducted one of the largest studies to date directly evaluating long-read whole genome sequencing against standard clinical care. They sequenced 832 individuals and 84 trios at 30x coverage using HiFi long-read sequencing and compared results in a blinded manner with standard genetic tests. HiFi whole genome sequencing matched standard-of-care testing with 96.4% concordance across variant types, and only a single low-frequency somatic variant was not detected. When modeled across an annual patient population, HiFi WGS could improve or refine genetic diagnostic findings in an estimated 3.4% of cases. As a potential first-tier test, it could increase the diagnostic rate from 16.4% to 18.9%, improving findings in more than 500 patients per year. The approach also enables full phasing of maternal and paternal haplotypes, and the researchers showed that lowering coverage to 20x resulted in only marginal loss, with a 99.6% recall rate for single nucleotide variants and small insertions and deletions.

A senior co-author of the Radboud study stated that long-read WGS is now sufficiently accurate and comprehensive to substitute medical genetic tests, and has the potential to improve on the current standard of care through phasing and epigenetic analysis.