Helmholtz Gemeinschaft


Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

PDF (Original Article) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
[img] Other (Supplemental Information)

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
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

Repository Staff Only: item control page


Downloads per month over past year

Open Access
MDC Library