When you work in rare disease, you recognize the pattern: Test. Wait. Repeat.
For families, that loop is a stretch of time that includes birthdays, school years, and treatment windows passing while searching for answers. But new real-world clinical data is bringing a new hope of providing families with more certain answers sooner.
Rare Disease month is a reminder of the impact of lingering uncertainty on families and how much it matters when science starts closing them faster.
Researchers at Radboud University Medical Center in the Netherlands recently released one of the largest studies to date directly evaluating long-read whole genome sequencing against the standard of care in routine clinical settings. The findings add weight to a shift many researchers have been pushing toward: potentially using HiFi whole genome sequencing as a first-line test. In the study, HiFi sequencing delivered a comprehensive view of the genome with a single assay and the potential to replace a patchwork of tests to get earlier explanations to families.
HiFi WGS is comparable to standard testing across multiple assays
For this study, Radboud researchers evaluated over 1,000 samples, including 832 individuals and 84 trios. Each sample was sequenced at 30x coverage using HiFi long-read whole genome sequencing and compared, in a blinded manner, against the genetic tests typically ordered as part of standard clinical care. A few aspects of how this study was designed makes it really stand out: First, its scale and inclusion of the full range of tests and indications seen in practice reflects how HiFi sequencing would function in a real-world setting. Second, using a prospective study design and being blinded for the outcome truly put it to the test in providing insights for undiagnosed subjects.
Remarkably, HiFi whole genome sequencing matched standard-of-care testing with 96.4 percent concordance across variant types. Since this study reflected real-world practice, many of the comparator tests were targeted assays focused on genes related to suspected diseases, and the study aimed to replicate findings rather than identify novel candidate variants. Although the study was designed to compare against routine clinical tests, when modeled across an annual patient population HiFi WGS could actually improve or refine the genetic diagnosic findings in an estimated 3.4 percent of cases, translating to what could be clearer answers for hundreds of families. Notably, only a single, low-frequency somatic variant was not detected in this study.
Taken together, the findings show that long-read whole genome sequencing can reliably match existing clinical approaches, while also delivering additional findings that would otherwise be missed.
Fewer tests and clearer results with HiFi sequencing
By modeling the use of HiFi whole genome sequencing as a potential first-tier test across their annual patient population, they found that it could help improve diagnostic findings in more than 500 patients per year, amounting to an increase from 16.4 percent to 18.9 percent. This improvement is bolstered by the ability to fully phase maternal and paternal haplotypes, allowing the team to determine whether variants occur on the same allele. This distinction is substantial, particularly for instances, that without phasing, would require sequencing of parent samples for confirmation, which requires additional time, cost, and effort and can prevent a definitive diagnosis when parents are unavailable. This additional increase in findings can have a meaningful impact to each family, as well as to a healthcare system, potentially reducing the uncertainty, time, and costs associated with serial testing.
The study also explored whether sequencing depth could be reduced without compromising potential clinical utility. The authors found that lowering coverage to 20x resulted in only a marginal loss of relevant findings, supported by a 99.6 percent recall rate for single nucleotide variants and small insertions and deletions. This kind of modeling is important for understanding how long-read sequencing could be deployed efficiently at scale within healthcare systems. In related work, the Radboud team showed that even at reduced coverage levels, HiFi sequencing can also reliably detect clinically relevant episignatures across the genome, reinforcing the potential of a single HiFi genome to deliver multiple layers of clinically useful information at scale.
Christian Gilissen, Professor at Radboudumc and senior co-author of the study explains ––
“This study not only shows that long-read WGS is now sufficiently accurate and comprehensive to substitute medical genetic tests, but, more importantly, has the potential to significantly improve on the current standard of care through phasing and epigenetic analysis.”
Another aspect that makes this work particularly meaningful for potential clinical implementation is that the researchers designed the study to reflect how testing is ordered today, allowing for a fair comparison with standard workflows. At the same time, these results hint at something bigger than a singular diagnostic moment. Because of its greater completeness and near haplotype-resolved representation, the data can be reinterpreted in the future as new disease genes are discovered or clinical knowledge evolves. This provides clinicians and families with a stronger foundation than short-read data can provide.
Why long reads matter in rare disease detection
Long-read sequencing changes what clinicians can see and interpret in the genome. Structural variants, repeat expansions, complex rearrangements, and phased variants become easier to detect and understand with a full, more accurate view of their place in the genome. This higher resolution reduces ambiguity and helps connect genetic findings to disease mechanisms with greater confidence.
Clearer genomic answers can help influence how patients are managed, how care is coordinated, and how families plan for the future. Earlier and more accurate findings can open doors to appropriate care pathways, reduce unnecessary testing, and provide a sense of direction after years of uncertainty.
As Lisenka Vissers, Professor of Radboud University Medical Center and senior co-author of the paper emphasizes ––
“This study made promises come true for rare disease diagnostics. Long-read sequencing with PacBio enhances the clinical utility of genomic analysis in rare disease by reducing uncertainty in variant interpretation and revealing pathogenic mechanisms that are inaccessible to short-read methods. This improved resolution supports earlier and more accurate diagnoses, which is critical for guiding patient management and enabling access to appropriate care pathways.”
First-tier HiFi sequencing as the future of rare disease genomics
The Radboud study joins a growing wave of evidence pointing toward a HiFi-first approach to rare disease testing. Recent multi-center findings from the HiFi Solves EMEA consortium showed that HiFi-based methods achieved 100 percent detection of the variants in the study that remained hidden to short-read approaches. Relatedly, a study from the pan-European rare disease research program Solve-RD used HiFi sequencing to identify disease-causing genetic variants that were previously unresolved or unresolvable with existing methods. Another recent study in JAMA Pediatrics from a team at Children’s Mercy Kansas City demonstrated how HiFi sequencing can lead to higher diagnostic findings, fewer assays, and a faster turnaround time, potentially leading to meaningful impact for children with rare disease. These studies point to a future where a single, comprehensive genome assay can replace a patchwork of tests and help families reach answers sooner.
During Rare Disease Month, progress is often measured not just in percentages, but in momentum. Each new study builds confidence that more complete genomic tools can be integrated into routine care, bringing clarity where there was once uncertainty. The outlook for rare disease diagnostics continues to move in a hopeful direction, with better answers arriving faster and with greater confidence.
Learn more about the impact of HiFi sequencing on rare disease research at pacb.com/rare-disease.