How advanced sequencing is transforming rare disease diagnostics for labs and patients

Behind nearly every rare disease is a story of delayed answers. The so-called ‘diagnostic odyssey’ has become a painful rite of passage for many rare disease patients and their families, marked by misdiagnoses, repeated tests and growing emotional and physical toll. Globally, an estimated 300 million people are living with a rare disease, facing an average wait of 4-5 years for diagnosis – a time luxury sadly not all patients can afford.

Beyond the human cost, the current diagnostic process put strain on the clinical laboratories at the heart of research projects trying to solve such complex diseases. Multiple sequential tests consume precious time and resources, often yielding inconclusive or partial answers. The limitations of traditional diagnostic approaches frustrate both clinicians and lab teams alike and highlight a broader problem: existing tools often fail to reveal the full genetic picture. However, new research suggests a path forward, one where a single, comprehensive genetic test could dramatically reduce time to diagnosis, offering clarity for families and greater efficiency for laboratories.

Why current approaches fall short

In many regions, the standard diagnostic pathway typically begins with targeted gene panels or chromosomal microarray analysis (CMA). Targeted gene panels are tailored to known gene sets associated with specific phenotypes, for example, if a patient's symptoms suggest a neuromuscular disorder, a neuromuscular gene panel might be ordered. CMA detects larger chromosomal abnormalities, such as specific deletions or duplications of DNA segments that can be associated with various genetic conditions.

While useful for well-characterised disorders, these methods fall short when faced with the unknown. Many rare disease-causing variants are novel, structural, or located in non-coding regions that existing narrow-view tests cannot capture. Such tests also depend on prior knowledge of the likely culprit genes; if the underlying variant is unfamiliar or falls outside targeted regions, it remains hidden.

When gene panels or CMA don’t reveal a diagnosis, the next step is short-read whole genome sequencing (srWGS), which is now the first-line test in England and Wales. SrWGS breaks DNA into small fragments and reassembles them against a reference genome to detect genetic variants that are potentially causative of disease. Despite giving a much wider view of the genome, srWGS has major limitations. The final genome assembly often contains gaps and errors, particularly in complex or repetitive regions – the very regions where many rare disease-causing variants lie.

Even after srWGS is conducted, more than half (50%) of cases remain undiagnosed. For families and clinicians, this statistic translates to continued uncertainty and missed opportunities for treatment. For laboratories, it means greater resource expenditure on additional rounds of testing, with diminishing returns.

One test to rule them all: Long read sequencing in practice

Long-read sequencing technologies are offering new hope to labs and patients alike. This method captures much longer stretches of DNA at an extremely high degree of accuracy in a single read, producing contiguous genomes and uncovering structural variants, repeat expansions and complex rearrangements that existing technologies often miss.

Recent real-world studies have underlined the transformational potential of long-read sequencing. In the Netherlands, researchers at Radboud University Medical Center demonstrated that the technology could identify 93% of pathogenic variants in a single test in cases that had previously required complex, multi-step genetic analysis. This result demonstrates that moving to single genomic test could increase diagnostic yield and help patients receive answers more quicky. Radboud also hope a single test approach could remove significant overheads for labs, by reducing the need to maintain the additional equipment and trained staff required to conduct a broad range of tests.

Beyond the genome: Moving to multiomics

The most advanced sequencing technologies are now expanding beyond DNA to incorporate insights from other biological layers, such as the epigenome. This offers new diagnostic possibilities for imprinting disorders and conditions with elusive mechanisms. For example, in a pioneering study from the University of Washington, researchers analysed four biological 'omes' simultaneously in a nine-month-old patient with complex symptoms.

The genome revealed a missing NBEA gene explaining developmental delay, while the epigenome uncovered the deactivation of the RB1 cancer suppression gene, explaining the patient's retinoblastomas. Notably, the epigenetic change would have been invisible if only DNA sequence had been considered, demonstrating the diagnostic power of multiomic approaches.

The future is here

The path to faster, more accurate rare disease diagnoses lies in embracing more advanced genomic technologies from the outset. Investing in long-read and multiomic sequencing dramatically improves diagnostic yield, reduces the costly cycle of sequential testing, and most importantly, reclaims time: the most precious resource for patients and families. As these technologies become more accessible and scalable, a future where rare disease patients wait months rather than years for answers is within reach.