Long-read genome sequencing (lrGS) has opened avenues across scientific fields, allowing researchers to map complex DNA regions and identify structural variants otherwise hidden to the human eye. But could lrGS support rare disease diagnostics? A recently published paper in The New England Journal of Medicine aimed to explore the possibilities.
We connected with Tessa J.J. de Bitter, co-first researcher of this study, to learn more about what the future of rare disease diagnostics could look like.
What clinical need or diagnostic challenge prompted this study?
Diagnosing rare genetic diseases often requires multiple sequential tests, including chromosomal microarrays, targeted gene panels, exome or short-read genome sequencing, and specialized assays to detect structural variants or repeat expansions. This stepwise approach can be time-consuming and costly, and many patients still remain without a molecular diagnosis.
lrGS has the potential to detect almost all major classes of genetic variation in a single test. However, before it can be adopted into routine clinical practice, robust evidence is needed to show that it can match or outperform current diagnostic pathways at scale. Our study directly compared the diagnostic performance of lrGS with standard-of-care testing in a real-world clinical setting and evaluated the potential benefits of using lrGS as a first-line diagnostic approach.
What were the main findings of the study, and how did long-read sequencing affect diagnostic yield?
The study included 832 patients referred for rare disease genetic testing over one year at two Dutch diagnostic centers: Radboud University Medical Center and Maastricht UMC+. lrGS produced results that agreed with standard testing in 96.4 percent of cases, while also identifying additional clinically important genetic findings in 28 patients (3.4 percent) that standard testing had missed or could not fully explain.
Using lrGS, we reached a definitive genetic diagnosis in 160 patients (19.2 percent), compared with 137 patients (16.5 percent) using the current testing approach. The improved diagnostic yield was largely due to lrGS's ability to detect complex genetic changes, including structural variants and difficult-to-identify disease-causing variants.
We also modelled what would happen if lrGS were used as the first test instead of the current stepwise approach. Our analysis predicted that a single lrGS test would increase the diagnostic yield by 2.5 percentage points – a 15.2 percent improvement over current practice – while potentially reducing the need for multiple sequential tests.
How could long-read sequencing improve the diagnosis and management of patients with rare diseases?
For patients and their families, receiving a genetic diagnosis can end years of uncertainty – often called the "diagnostic odyssey" – while providing valuable information about prognosis, recurrence risk, treatment options, and eligibility for clinical trials or emerging therapies.
lrGS has the potential to replace multiple separate genetic tests with a single comprehensive assay. This could shorten the time to diagnosis and increase the chances of identifying the underlying genetic cause of disease. As researchers continue to learn more from lrGS data, its diagnostic value is also expected to improve over time.
What does this study tell us about the importance of continuing to explore the complexity of human DNA and genetic variation?
As sequencing technologies advance, we are gaining a more complete understanding of the human genome and uncovering genetic changes that were previously difficult or impossible to detect. Our findings show that this more comprehensive approach can improve diagnostic yield, highlighting the value of capturing the full range of disease-causing genetic variation.
Many clinically important genetic changes lie beyond the reach of conventional sequencing methods. These include structural variants, complex genomic rearrangements, repeat expansions, variants in gene–pseudogene regions, and epigenetic changes such as DNA methylation abnormalities. lrGS can detect all of these variant types in a single test while also determining whether disease-causing variants are inherited together or separately – a key factor in diagnosing many recessive disorders.
In addition, lrGS can identify DNA methylation patterns that help interpret uncertain genetic findings by revealing disease-specific signatures. Together, these capabilities improve our ability to identify the genetic causes of rare diseases and are expected to further increase diagnostic rates as research discoveries continue to be translated into clinical practice.
What are the main barriers to implementing long-read genome sequencing in routine clinical laboratories?
The biggest challenges are no longer technical but practical. Scaling lrGS for routine clinical use requires laboratories to validate the technology, establish robust bioinformatics pipelines, train staff, and integrate lrGS into existing diagnostic workflows. Replacing multiple established tests with a single comprehensive assay is a significant change for any healthcare system.
Cost has also been an important barrier, but the price of clinical-grade lrGS has fallen substantially in recent years and is now approaching that of conventional short-read genome sequencing. More importantly, the discussion should extend beyond the cost of sequencing itself. The real question is whether a single lrGS test can replace multiple existing assays, simplifying the diagnostic pathway while improving diagnostic yield.
The cost-effectiveness of this approach will vary between healthcare systems depending on testing volume, infrastructure, reimbursement, and workforce requirements. However, as evidence continues to show that lrGS can consolidate multiple tests and improve diagnosis, wider adoption is likely to follow. The question is becoming less whether the technology works and more how quickly healthcare systems can implement it for patients.
Looking ahead, what future applications do you see for long-read sequencing in diagnostics and precision medicine?
Based on our findings, we believe lrGS should be considered as a first-line test for patients with suspected rare genetic diseases. By detecting all major classes of genetic variation in a single assay, lrGS has the potential to replace multiple sequential tests, improve diagnostic yield, and simplify the diagnostic pathway.
The technology also has applications beyond rare disease diagnostics, including oncology, reproductive medicine, pharmacogenomics, and population genomics. Its ability to detect complex genetic variants, resolve difficult regions of the genome, generate phased genomes, and assess epigenetic changes makes it a versatile tool for genomic medicine.
As analytical methods continue to advance, lrGS is expected to provide an increasingly complete picture of human genetic variation. This should improve our understanding of disease mechanisms and increase the number of patients who receive an accurate molecular diagnosis.
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