ArticleNature methods2023
Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
43 citing papers in PubMed, 52 citations in OpenAlex.
- Article
- gaftools: a toolkit for analyzing and manipulating pangenome alignments.Bioinformatics (Oxford, England) · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Recurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes.Nature communications · 2026Article
- Recent advances in understanding the spectrum of genetic determinants of lipoprotein(a) levels.Current opinion in lipidology · 2026Review
- Scalable and comprehensive mosaic variant calling using DRAGEN.medRxiv : the preprint server for health sciences · 2026Article
- The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations.Cell genomics · 2026Article
- On the optimization of copy number variations representation in pangenome graphs.Frontiers in bioinformatics · 2026Article
- Recurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes.bioRxiv : the preprint server for biology · 2025Article
- A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025Article
- The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations.bioRxiv : the preprint server for biology · 2025Article
- PangenomeX: a graph convolutional network-based pangenome framework for unbiased population-scale genomic variation analysis.Briefings in bioinformatics · 2025Article
- Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia.Scientific data · 2025Article
- Article
- Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.Molecular biology and evolution · 2025Article
- Taurine pangenome uncovers a segmental duplication upstream ofGenome research · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- The long and short of hyperdivergent regions.Trends in genetics : TIG · 2025Review
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
Advancements in sequencing technologies and assembly methods enable the regular production of high-quality genome assemblies characterizing complex regions. However, challenges remain in efficiently interpreting variation at various scales, from smaller tandem repeats to megabase rearrangements, across many human genomes. We present a PanGenome Research Tool Kit (PGR-TK) enabling analyses of complex pangenome structural and haplotype variation at multiple scales. We apply the graph decomposition methods in PGR-TK to the class II major histocompatibility complex demonstrating the importance of the human pangenome for analyzing complicated regions. Moreover, we investigate the Y-chromosome genes, DAZ1/DAZ2/DAZ3/DAZ4, of which structural variants have been linked to male infertility, and X-chromosome genes OPN1LW and OPN1MW linked to eye disorders. We further showcase PGR-TK across 395 complex repetitive medically important genes. This highlights the power of PGR-TK to resolve complex variation in regions of the genome that were previously too complex to analyze.
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Registered trials
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.