Accès ouvert déclaré
2023
article
Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
HoJoon Lee, Stephanie Greer, Dmitri S. Pavlichin, Bo Zhou, Alexander E. Urban, Tsachy Weissman, Wen‐Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian Lucas, Jean Monlong, Haley Abel, Silvia Buonaiuto, Xian Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubskỳ, Pjotr Prins, Jonas A. Sibbesen, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda Antonacci-Fulton, Gunjan Baid, Carl Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fédrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Carlos García Girón, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco‐Sola, Pierre Marijon, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Nathan D. Olson, Daniela Puiu, Allison Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valérie Schneider, Baergen I. Schultz, Kishwar Shafin, Jouni Sirén, Michael W. Smith, Heidi J. Sofia, Ahmad Abou Tayoun, Françoise Thibaud‐Nissen, Francesca Floriana Tricomi, Justin Wagner, Jonathan Wood, Aleksey V. Zimin, Alice B. Popejoy, Guillaume Bourque, Mark Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Erich D. Jarvis, Karen H. Miga, Ting Wang, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, Benedict Paten
6Citations signalées — pas une note de qualité
2Institutions déclarées
1Pays d’affiliation déclarés
Résumé fourni par la source
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.
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Contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
- Date Crossref
- 01/08/2023
- Éditeur
- Elsevier BV
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude et ne compte pas comme une seconde source scientifique indépendante.
Institutions déclarées
Une affiliation ne permet pas de déduire la nationalité d’un auteur.
Sujets associés
Chromosomal and Genetic VariationsCRISPR and Genetic EngineeringGenomics and Phylogenetic Studies