Flow Sorting Enrichment and Nanopore Sequencing of Chromosome 1 From a Chinese Individual.
chromosome enrichment
chromosome sequencing
chromosome sorting
flow karyotyping
genome assembly
nanopore sequencing
structural variation
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2019
2019
Historique:
received:
18
09
2019
accepted:
02
12
2019
entrez:
31
1
2020
pubmed:
31
1
2020
medline:
31
1
2020
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 31998370
doi: 10.3389/fgene.2019.01315
pmc: PMC6962354
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1315Informations de copyright
Copyright © 2020 Kuderna, Solís-Moruno, Batlle-Masó, Julià, Lizano, Anglada, Ramírez, Bote, Tormo, Marquès-Bonet, Fornas and Casals.
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