ArticleNature communications2024
Pangenome graphs improve the analysis of structural variants in rare genetic diseases.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it, 33 citations in OpenAlex.
- A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools.Nature protocols · 2026Guideline
- A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.Genome research · 2026Article
- Pangenomes aid accurate detection of large insertions and deletions from targeted sequencing: the case of cardiomyopathies.Genome medicine · 2026Article
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Diagnostic utility of clinical genome reanalysis in rare pediatric disorders using long-read sequencing.HGG advances · 2026Article
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Graph-based pan-genome reveals structural and functional diversity across oil palm domestication gradients.BMC plant biology · 2026Article
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- African Pan Genome Contigs Expose Biologically Relevant Sequence Still Hidden from Human Reference Frameworks.bioRxiv : the preprint server for biology · 2026Article
- Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon.Nature genetics · 2026Article
- Reference-Guided Chromosome-by-Chromosome de novo Assembly at Scale Using Low-Coverage High-Fidelity Long-Reads with HiFiCCL.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Population-level structural variant characterization using pangenome graphs.Nature genetics · 2026Article
- Charcot-Marie-Tooth disease and related neuropathies.Nature reviews. Disease primers · 2026Review
- Puzzler: scalable one-command platinum-quality genome assembly from HiFi and Hi-C.Bioinformatics advances · 2026Article
- Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.Journal of advanced research · 2026Article
- Insights into natural neocentromere evolution from a cattle T2T X chromosome.Nature communications · 2025Article
- Genome analyses and breeding of polyploid crops.Nature plants · 2025Review
- Agptools: a utility suite for editing genome assemblies.Bioinformatics (Oxford, England) · 2025Article
- Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA.Genome research · 2025Article
Corrections and comments
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Authors and funding
11 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rare DNA alterations that cause heritable diseases are only partially resolvable by clinical next-generation sequencing due to the difficulty of detecting structural variation (SV) in all genomic contexts. Long-read, high fidelity genome sequencing (HiFi-GS) detects SVs with increased sensitivity and enables assembling personal and graph genomes. We leverage standard reference genomes, public assemblies (n = 94) and a large collection of HiFi-GS data from a rare disease program (Genomic Answers for Kids, GA4K, n = 574 assemblies) to build a graph genome representing a unified SV callset in GA4K, identify common variation and prioritize SVs that are more likely to cause genetic disease (MAF < 0.01). Using graphs, we obtain a higher level of reproducibility than the standard reference approach. We observe over 200,000 SV alleles unique to GA4K, including nearly 1000 rare variants that impact coding sequence. With improved specificity for rare SVs, we isolate 30 candidate SVs in phenotypically prioritized genes, including known disease SVs. We isolate a novel diagnostic SV in KMT2E, demonstrating use of personal assemblies coupled with pangenome graphs for rare disease genomics. The community may interrogate our pangenome with additional assemblies to discover new SVs within the allele frequency spectrum relevant to genetic diseases.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.