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| Item Type: | Article |
|---|---|
| Title: | Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome |
| Creators Name: | Lee, H. and Greer, S.U. and Pavlichin, D.S. and Zhou, B. and Urban, A.E. and Weissman, T. and Ji, H.P. |
| 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. |
| Keywords: | Pangenome, Reference Genome, Structural Variations, Pan-Conserved Segment, Structural Polymorphism, K-Mer |
| Source: | Cell Reports Methods |
| ISSN: | 2667-2375 |
| Publisher: | Elsevier |
| Volume: | 3 |
| Number: | 8 |
| Page Range: | 100543 |
| Date: | 28 August 2023 |
| Additional Information: | Ashley D. Sanders is a member of the Human Pangenome Reference Consortium |
| Official Publication: | https://doi.org/10.1016/j.crmeth.2023.100543 |
| PubMed: | View item in PubMed |
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