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


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.

SUBMITTER: Chin CS 

PROVIDER: S-EPMC10406601 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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

Chin Chen-Shan CS   Behera Sairam S   Khalak Asif A   Sedlazeck Fritz J FJ   Sudmant Peter H PH   Wagner Justin J   Zook Justin M JM  

Nature methods 20230626 8


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  ...[more]

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