Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
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 assemb...
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| Veröffentlicht in: | Cell reports methods 2023-08, Vol.3 (8), p.100543-100543, Article 100543 |
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| creator | Lee, HoJoon Greer, Stephanie U Pavlichin, Dmitri S Zhou, Bo Urban, Alexander E Weissman, Tsachy Ji, Hanlee P |
| description | 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. |
| doi_str_mv | 10.1016/j.crmeth.2023.100543 |
| format | Article |
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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.</description><identifier>ISSN: 2667-2375</identifier><identifier>EISSN: 2667-2375</identifier><identifier>DOI: 10.1016/j.crmeth.2023.100543</identifier><identifier>PMID: 37671027</identifier><language>eng</language><publisher>United States: Elsevier</publisher><subject>Conserved Sequence ; Haploidy ; Humans ; Neoplasms, Squamous Cell ; Polymorphism, Genetic ; Skin Neoplasms</subject><ispartof>Cell reports methods, 2023-08, Vol.3 (8), p.100543-100543, Article 100543</ispartof><rights>2023 The Authors.</rights><rights>2023 The Authors 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c409t-16f29049ab6040e491f3d25d4cc94b616ea48fae90169e0ec3f499f4f740c1253</citedby><cites>FETCH-LOGICAL-c409t-16f29049ab6040e491f3d25d4cc94b616ea48fae90169e0ec3f499f4f740c1253</cites><orcidid>0000-0003-3772-3424</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10475782/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10475782/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37671027$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee, HoJoon</creatorcontrib><creatorcontrib>Greer, Stephanie U</creatorcontrib><creatorcontrib>Pavlichin, Dmitri S</creatorcontrib><creatorcontrib>Zhou, Bo</creatorcontrib><creatorcontrib>Urban, Alexander E</creatorcontrib><creatorcontrib>Weissman, Tsachy</creatorcontrib><creatorcontrib>Ji, Hanlee P</creatorcontrib><creatorcontrib>Human Pangenome Reference Consortium</creatorcontrib><title>Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome</title><title>Cell reports methods</title><addtitle>Cell Rep Methods</addtitle><description>The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. 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This methodology enables the examination of any sequence of interest within the pangenome, using the reference genome as a comparative framework.</description><subject>Conserved Sequence</subject><subject>Haploidy</subject><subject>Humans</subject><subject>Neoplasms, Squamous Cell</subject><subject>Polymorphism, Genetic</subject><subject>Skin Neoplasms</subject><issn>2667-2375</issn><issn>2667-2375</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkU1PwzAMhiMEYtPYP0CoRy4d-WqznBCa-JImwQHOUZY6W6c2HUk7af-ejI5pO9lyXr-x_SB0S_CEYJI_rCfG19CuJhRTFks44-wCDWmei5QykV2e5AM0DmGNMaYZYUySazRgIhcEUzFE9lO71DQugN9CkQRY1uDapNXLkJRFTEu7S7qq9fpM9dOBMxASbXwTYggB6kVVxkrpknYFyaqrtUs22i3BNTXcoCurqwDjQxyh75fnr9lbOv94fZ89zVPDsWxTklsqMZd6kWOOgUtiWUGzghsj-SInOWg-tRpkvIEEDIZZLqXlVnBsCM3YCD32vptuUUNh4gJeV2rjy1r7nWp0qc5fXLlSy2arCOYiE1MaHe4PDr6JW4ZW1WUwUFXaQdMFRadxDJ5NBY9S3kv_juDBHv8hWO0xqbXqMak9JtVjim13pzMem_6hsF-M8pLO</recordid><startdate>20230828</startdate><enddate>20230828</enddate><creator>Lee, HoJoon</creator><creator>Greer, Stephanie U</creator><creator>Pavlichin, Dmitri S</creator><creator>Zhou, Bo</creator><creator>Urban, Alexander E</creator><creator>Weissman, Tsachy</creator><creator>Ji, Hanlee P</creator><general>Elsevier</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-3772-3424</orcidid></search><sort><creationdate>20230828</creationdate><title>Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome</title><author>Lee, HoJoon ; Greer, Stephanie U ; Pavlichin, Dmitri S ; Zhou, Bo ; Urban, Alexander E ; Weissman, Tsachy ; Ji, Hanlee P</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c409t-16f29049ab6040e491f3d25d4cc94b616ea48fae90169e0ec3f499f4f740c1253</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Conserved Sequence</topic><topic>Haploidy</topic><topic>Humans</topic><topic>Neoplasms, Squamous Cell</topic><topic>Polymorphism, Genetic</topic><topic>Skin Neoplasms</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lee, HoJoon</creatorcontrib><creatorcontrib>Greer, Stephanie U</creatorcontrib><creatorcontrib>Pavlichin, Dmitri S</creatorcontrib><creatorcontrib>Zhou, Bo</creatorcontrib><creatorcontrib>Urban, Alexander E</creatorcontrib><creatorcontrib>Weissman, Tsachy</creatorcontrib><creatorcontrib>Ji, Hanlee P</creatorcontrib><creatorcontrib>Human Pangenome Reference Consortium</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Cell reports methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lee, HoJoon</au><au>Greer, Stephanie U</au><au>Pavlichin, Dmitri S</au><au>Zhou, Bo</au><au>Urban, Alexander E</au><au>Weissman, Tsachy</au><au>Ji, Hanlee P</au><aucorp>Human Pangenome Reference Consortium</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome</atitle><jtitle>Cell reports methods</jtitle><addtitle>Cell Rep Methods</addtitle><date>2023-08-28</date><risdate>2023</risdate><volume>3</volume><issue>8</issue><spage>100543</spage><epage>100543</epage><pages>100543-100543</pages><artnum>100543</artnum><issn>2667-2375</issn><eissn>2667-2375</eissn><abstract>The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. 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| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Conserved Sequence Haploidy Humans Neoplasms, Squamous Cell Polymorphism, Genetic Skin Neoplasms |
| title | Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome |
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