Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes

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dc.citation.firstpage1213en_US
dc.citation.journalTitleNature Methodsen_US
dc.citation.lastpage1221en_US
dc.citation.volumeNumber20en_US
dc.contributor.authorChin, Chen-Shanen_US
dc.contributor.authorBehera, Sairamen_US
dc.contributor.authorKhalak, Asifen_US
dc.contributor.authorSedlazeck, Fritz J.en_US
dc.contributor.authorSudmant, Peter H.en_US
dc.contributor.authorWagner, Justinen_US
dc.contributor.authorZook, Justin M.en_US
dc.date.accessioned2024-05-03T15:51:19Zen_US
dc.date.available2024-05-03T15:51:19Zen_US
dc.date.issued2023en_US
dc.description.abstractAdvancements 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.en_US
dc.identifier.citationChin, C.-S., Behera, S., Khalak, A., Sedlazeck, F. J., Sudmant, P. H., Wagner, J., & Zook, J. M. (2023). Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nature Methods, 20(8), 1213–1221. https://doi.org/10.1038/s41592-023-01914-yen_US
dc.identifier.digitals41592-023-01914-yen_US
dc.identifier.doihttps://doi.org/10.1038/s41592-023-01914-yen_US
dc.identifier.urihttps://hdl.handle.net/1911/115621en_US
dc.language.isoengen_US
dc.publisherSpringer Natureen_US
dc.rightsExcept where otherwise noted, this work is licensed under a Creative Commons Attribution (CC BY) license. Permission to reuse, publish, or reproduce the work beyond the terms of the license or beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleMultiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genesen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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