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

Published

Author(s)

Chen-Shan Chin, Sairam Behera, Asif Khalak, Fritz Sedlazeck, Justin Wagner, Justin Zook

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.
Citation
Nature Methods
Volume
20

Keywords

genomics, pangenome graph, structural variation, de novo assembly

Citation

Chin, C. , Behera, S. , Khalak, A. , Sedlazeck, F. , Wagner, J. and Zook, J. (2023), Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes, Nature Methods, [online], https://doi.org/10.1038/s41592-023-01914-y, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=935376 (Accessed May 22, 2024)

Issues

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Created June 26, 2023, Updated September 18, 2023