2-AIN-506, 2-AIN-252: Seminar in Bioinformatics (2), (4)
Summer 2025
Abstrakt

Chen-Shan Chin, Sairam Behera, Asif Khalak, Fritz J. Sedlazeck, Peter H. Sudmant, Justin Wagner, Justin M. Zook. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nature methods, 20(8):1213-1221. 2023.

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Download from publisher: https://doi.org/10.1038/s41592-023-01914-y PubMed

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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.