ArticleGenome research2025
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.
Article in Genome research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Review
- Population-scale detection of methylation outliers from long-read genome sequencing.medRxiv : the preprint server for health sciences · 2026Article
- Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore.G3 (Bethesda, Md.) · 2026Article
- Genome-wide detection and clinical prioritization of tandem repeat outliers using long-read sequencing.medRxiv : the preprint server for health sciences · 2026Article
- Oxford Nanopore Technologies [ONT] Sequencing: Clinical Validation in Genetically Heterogeneous Disorders.Genes · 2025Article
- GREGoR: accelerating genomics for rare diseases.Nature · 2025Article
- Long-read genome sequencing and multi-omics in aging and neurodegeneration.medRxiv : the preprint server for health sciences · 2025Article
- Exploration of Neurodegenerative Diseases Using Long-Read Sequencing and Optical Genome Mapping Technologies.Movement disorders : official journal of the Movement Disorder Society · 2025Review
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection.American journal of human genetics · 2025Article
- Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity.bioRxiv : the preprint server for biology · 2025Article
- GREGoR: Accelerating Genomics for Rare Diseases.ArXiv · 2024Article
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18 authors.
Funding
Abstract
Rare structural variants (SVs)-insertions, deletions, and complex rearrangements-can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore Technologies long-read genomes of 68 individuals from the undiagnosed disease network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4× increase from short reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably, these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that do not incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in
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