Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual

Kuderna, Lukas, 1989-; Solís Moruno, Manuel, 1993-; Batlle Masó, Laura, 1993-; Julià, Eva; Lizano González, Esther, 1974-; Anglada Busquets, Roger; Ramírez Bautista, Eva; Bote, Alex; Tormo, Marc; Marquès i Bonet, Tomàs, 1975-; Fornas Carreño, Oscar; Casals López, Ferran

Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual

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dc.contributor.author Kuderna, Lukas, 1989-
dc.contributor.author Solís Moruno, Manuel, 1993-
dc.contributor.author Batlle Masó, Laura, 1993-
dc.contributor.author Julià, Eva
dc.contributor.author Lizano González, Esther, 1974-
dc.contributor.author Anglada Busquets, Roger
dc.contributor.author Ramírez Bautista, Eva
dc.contributor.author Bote, Alex
dc.contributor.author Tormo, Marc
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.contributor.author Fornas Carreño, Oscar
dc.contributor.author Casals López, Ferran
dc.date.accessioned 2020-03-23T10:53:40Z
dc.date.available 2020-03-23T10:53:40Z
dc.date.issued 2020
dc.description.abstract Sorting of individual chromosomes by Flow Cytometry (flow-sorting) is an enrichment method to potentially simplify genome assembly by isolating chromosomes from the context of the genome. We have recently developed a workflow to sequence native, unamplified DNA and applied it to the smallest human chromosome, the Y chromosome. Here, we modify improve upon that workflow to increase DNA recovery from chromosome sorting as well as sequencing yield. We apply it to sequence and assemble the largest human chromosome - chromosome 1 - of a Chinese individual using a single Oxford Nanopore MinION flow cell. We generate a selective and highly continuous assembly whose continuity reaches into the order of magnitude of the human reference GRCh38. We then use this assembly to call candidate structural variants against the reference and find 685 putative novel SV candidates. We propose this workflow as a potential solution to assemble structurally complex chromosomes, or the study of very large plant or animal genomes that might challenge traditional assembly strategies.
dc.description.sponsorship This study was funded by grants RTI2018-096824-B-C22 from the Agencia Estatal de Investigación-Ministerio de Ciencia, Innovación y Universidades (Spain) and FEDER (EU) to OF and FC, SAF2015-68472-C2-2-R from the Ministerio de Economía y Competitividad (Spain) and FEDER (EU) to FC, the Centro de Excelencia Severo Ochoa, and by Direcció General de Recerca, Generalitat de Catalunya (2017SGR-702). TM-B is supported by BFU2017-86471-P (MINECO/FEDER, UE), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). LK is supported by an FPI fellowship associated with BFU2014-55090-P (MINECO/FEDER, UE) and by an EMBO Short-Term Fellowship STF-8286. LB-M is supported by a Formació de personal Investigador fellowship from Generalitat de Catalunya (2018_FI_B00072). MS-M is supported by the María de Maetzu Programme (MDM-2014-0370-16-3)
dc.format.mimetype application/pdf
dc.identifier.citation Kuderna LFK, Solís-Moruno M, Batlle-Masó L, Julià E, Lizano E, Anglada R et al. Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual. Front Genet. 2020 Jan 9; 10: 1315. DOI: 10.3389/fgene.2019.01315
dc.identifier.doi http://dx.doi.org/10.3389/fgene.2019.01315
dc.identifier.issn 1664-8021
dc.identifier.uri http://hdl.handle.net/10230/43993
dc.language.iso eng
dc.publisher Frontiers Media
dc.relation.ispartof Frontiers in Genetics. 2020 Jan 9;10:1315
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/RTI2018-096824-B-C22
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SAF2015-68472-C2-2-R
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86471-P
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55090-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Cromosomes
dc.subject.other Genomes
dc.subject.other ADN
dc.title Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

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