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Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome. Cell reports methods Lee, H., Greer, S. U., Pavlichin, D. S., Zhou, B., Urban, A. E., Weissman, T., Ji, H. P. 2023; 3 (8): 100543

Abstract

The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer indexing strategy for comparative analysis across multiple assemblies, including the pangenome reference, GRCh38, and CHM13, a telomere-to-telomere reference assembly. Our k-mer indexing approach enabled us to identify a valuable collection of universally conserved sequences across all assemblies, referred to as "pan-conserved segment tags" (PSTs). By examining intervals between these segments, we discerned highly conserved genomic segments and those with structurally related polymorphisms. We found 60,764 polymorphic intervals with unique geo-ethnic features in the pangenome reference. In this study, we utilized ultra-conserved sequences (PSTs) to forge a link between human pangenome assemblies and reference genomes. This methodology enables the examination of any sequence of interest within the pangenome, using the reference genome as a comparative framework.

View details for DOI 10.1016/j.crmeth.2023.100543

View details for PubMedID 37671027

View details for PubMedCentralID PMC10475782