Long-read sequencing yields 4.5% more diagnoses in unresolved rare disease casesNew genetic test solves mysteries for hundreds of patients with rare disorders

Frontiers in Medicine Published June 7, 2026 DOI ↗ Editorial oversight: Dr. Julia Lee, PhD · Oncology, Genomics & Drug Development

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Key Takeaway

Consider lrWGS for select unresolved rare disease cases, but recognize the modest 4.5% diagnostic yield and limited evidence.

This systematic review evaluated the diagnostic yield of long-read whole genome sequencing (lrWGS) in patients with rare genetic disorders who had inconclusive or negative results from standard testing, including short-read sequencing. The review included 9 studies with a total of 646 previously unresolved cases.

Across these studies, lrWGS provided a definitive diagnosis in 29 individuals, corresponding to a diagnostic yield of 4.5%. Among the identified variants, structural variants (SVs) accounted for the majority (41.67%), followed by combined SV/single-nucleotide variants (20.83%) and methylation changes (16.67%).

The authors assessed risk of bias using the QUADAS-2 tool, but other limitations include the small sample size and potential lack of generalizability beyond the included studies. The review does not report on clinical outcomes beyond diagnostic yield, so the impact on patient management remains unclear.

Despite these limitations, lrWGS shows potential for improving diagnostic rates in previously unresolved rare disease cases, particularly when applied after whole-exome sequencing and combined with advanced tools such as phasing and methylation profiling. However, further research is needed to confirm these findings and assess clinical utility.

Many families face a long wait for answers when standard genetic tests come back inconclusive. A new review looked at 646 patients with rare genetic disorders who had already received negative or unclear results from standard testing. The team found that long-read whole genome sequencing offered a clear path forward. This advanced method helped 29 individuals receive a definitive diagnosis. That represents a 4.5% success rate among those who previously had no answers. The test also identified different types of genetic changes. Structural variants made up the majority of the findings. Single-nucleotide variants and methylation changes also played a role in solving these cases. The researchers used a standard tool to check for risk of bias. They noted that the results apply specifically to the nine studies included in this review. This approach shows promise for improving diagnostic rates when applied after standard testing.

What this means for you:

Long-read sequencing finds answers in cases where standard tests failed.

Study Details

Study typeMeta analysis

EvidenceLevel 1

PublishedJun 2026

View Original Abstract ↓

BackgroundNearly half of patients with rare genetic disorders remain undiagnosed, which may in part be due to limitations of current short-read sequencing (SRS) approaches in detecting complex genomic alterations. Long-read whole genome sequencing (lrWGS) technologies can address these limitations through enhanced detection of structural variants (SVs), repetitive regions, and epigenetic changes.MethodsTo evaluate the diagnostic yield of lrWGS in patients with rare genetic diseases receiving inconclusive or negative results from standard testing, we searched the PubMed, Science Direct, Scopus, and ProQuest databases to July 2025 for studies applying lrWGS to unresolved rare disease cases and reporting diagnostic outcomes. Risk of bias was assessed using the QUADAS-2 tool.ResultsNine studies involving 646 previously unresolved cases that underwent lrWGS met the inclusion criteria. Of these, 29 individuals (24 unique diagnoses involving 25 genes) received a definitive diagnosis through lrWGS, a diagnostic yield of 4.5%. SVs accounted for the majority of identified variants (41.67%), followed by combined SV/single-nucleotide variants (20.83%), methylation changes (16.67%), and other variant types (copy number variations, indels, and tandem repeats). Most detected variants were in regions typically inaccessible to short-read whole-exome sequencing (WES). lrWGS also enabled phasing and methylation analysis in a single assay, which was valuable for compound-heterozygosity detection and diagnostic interpretation.ConclusionlrWGS shows clear potential for improving diagnostic rates in previously unresolved rare disease cases, particularly when applied after WES and combined with advanced tools such as phasing and methylation profiling. As technologies evolve and become more accessible, lrWGS may increasingly become a first-tier diagnostic approach, especially in phenotypically complex conditions.Systematic Review Registrationhttps://osf.io/y5azb/overview, identifier 10.17605/OSF.IO/Y5AZB.

Long-read sequencing yields 4.5% more diagnoses in unresolved rare disease casesNew genetic test solves mysteries for hundreds of patients with rare disorders

Study Details

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Long-read sequencing yields 4.5% more diagnoses in unresolved rare disease casesNew genetic test solves mysteries for hundreds of patients with rare disorders

Study Details

TLR4 Asp299Gly polymorphism associated with increased infection susceptibility (OR 2.05) and mortality (HR 1.78)

Genetic variations linked to higher risk of severe infections

Clinical research that matters. Delivered to your inbox.

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