Gene Therapy

Long-read whole genome sequencing to transform diagnosticsLong-read whole genome sequencing to transform diagnostics

For diagnosing rare diseases, the long-read approach will have several major advantages.

February 9, 2024

4 Min Read

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In May 2023, long-read whole-genome sequencing (WGS), based on Pacific Bioscience’s Revio platform, was established at the Human Genetics Department of Bioscientia in Ingelheim, Germany. The Revio produces highly accurate so-called HiFi reads of 15,000-20,000 bases (15-20 kb). For comparison, the currently widely used short-read next-generation sequencing (NGS) tests, applied as gene-panel or whole-exome (WES) analysis, are based on reads of only 250 base pairs.

The addition of two – and soon a third – Revio platforms complements the portfolio at Bioscientia Human Genetics, which covers all areas and current methodologies in human genetics. These include:

Cytogenetics for prenatal indications and congenital conditions.
Tumour cytogenetics, e.g. for therapeutic guidance in haematological malignancies.
Array of comparative genomic hybridization (aCGH) for submicroscopic detection of structural aberrations.
Optical Genome Mapping (OGM), a recently introduced method for diagnosing even balanced structural aberrations at very high resolution.
NGS on several high-capacity short-read sequencing platforms for WES and WGS.
Genetic counselling, conducted by a highly experienced team of specialized MDs.

Finally unlocked: The dark matter of the human genome

For diagnosing rare diseases, the long-read approach will have several major advantages because it may uncover previously “hidden” mutations:

Variants residing outside the protein-coding gene regions (approximately 15 per cent): These dead angles are not covered by current NGS tests and have thus far escaped detection. Many of these disease-causing aberrations will be deep-intronic and could soon be particularly amenable to splice-correcting therapy approaches.
Complex regions overshadowed by highly homologous and pseudogene regions elsewhere in the genome become readable. This eliminates a major diagnostic gap: Some of these genome areas are mutational hotspots for conditions like blindness (the ORF15 exon of the retinal degeneration gene RPGR) and deafness (the STRC gene).
Large structural variants have often been missed by sequencing because their range exceeds the size of “traditional” short reads. Long reads do uncover them, including balanced aberrations.
Large repeat regions, whose expansions may cause neurological disorders such as Huntington’s disease and ataxia, can precisely be retrieved from the long reads.
Methylation defects which may cause imprinting disorders like Angelman syndrome can be visualised on HiFi reads.

After the advent of NGS and its first introduction into routine diagnostics about a decade ago, this will be the next real quantum leap in human genetics

After in-depth validation with positive control samples for the above aberrations, the Bioscientia Human Genetics team has now shifted their tests for inherited sensory disorders (eye diseases, deafness – both representing conditions with high genetic heterogeneity) and cancer syndromes from short-read exome sequencing onto their two Revio platforms. Additional diagnostically challenging conditions like developmental delay represent prime candidates for this novel approach. As in 2011, when Bioscientia was among the first to apply NGS diagnostically, the company is again pioneering the diagnostic introduction of a novel ground-breaking methodology. This next quantum leap in human genetics enables scientists and medical geneticists at Bioscientia to unlock the remaining dead corners of the genome in one go – by a single test.

Long reads of “half-solved” cases with recessive disorders, that is patients with only one mutant copy of a respective gene, held surprises: In some, the “missing hit” was indeed in protein-coding regions – exons that had been well covered, but missed, by previous short-read sequencing. The lesson learned is: Long-read genomes provide better exomes – and in addition shed light on the dark corners.

Bioscientia has a long-standing cooperation with hospitals and healthcare providers in the Middle East. By offering long-read sequencing in this region, many patients with difficult-to-detect mutations will finally receive a genetic diagnosis, with important implications for their prognosis, recurrence risks and personalised medical management and therapy. First gene therapies have become available for retinal degeneration, and tumour patients are increasingly being treated based on their causative mutations. Both entities represent fields of particular scientific excellence at Bioscientia, reflected by two recent high-level publications on novel disease genes (Abdel-Salam et al., 2023; Nuzhat et al., 2023). The wealth of data from HiFi long-reads allows for deep dives where necessary – this may lead to the identification of novel genes not previously associated with a genetic condition.

Close cooperation between clinicians who initiate genetic analyses and staff at Bioscientia is considered very important. This ensures the best results because information on symptoms and/ or family history may make a major difference when it comes to interpreting complex genetic data. Bioscientia´s geneticists look forward to their Middle East cooperation partners joining them in entering new genetic territories.

References available on request.