Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
21 05 2020
21 05 2020
Historique:
accepted:
03
04
2020
revised:
14
03
2020
received:
25
11
2019
pubmed:
8
4
2020
medline:
9
9
2020
entrez:
8
4
2020
Statut:
ppublish
Résumé
Inverted duplicated DNA sequences are a common feature of structural variants (SVs) and copy number variants (CNVs). Analysis of CNVs containing inverted duplicated DNA sequences using nanopore sequencing identified recurrent aberrant behavior characterized by low confidence, incorrect and missed base calls. Inverted duplicate DNA sequences in both yeast and human samples were observed to have systematic elevation in the electrical current detected at the nanopore, increased translocation rates and decreased sampling rates. The coincidence of inverted duplicated DNA sequences with dramatically reduced sequencing accuracy and an increased translocation rate suggests that secondary DNA structures may interfere with the dynamics of transit of the DNA through the nanopore.
Identifiants
pubmed: 32255181
pii: 5816855
doi: 10.1093/nar/gkaa206
pmc: PMC7229812
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
4940-4945Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM107466
Pays : United States
Organisme : NIGMS NIH HHS
ID : F32 GM131573
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Nat Rev Genet. 2016 Apr;17(4):224-38
pubmed: 26924765
PLoS Biol. 2018 Dec 18;16(12):e3000069
pubmed: 30562346
Biophys J. 1999 Dec;77(6):3227-33
pubmed: 10585944
Genome Biol. 2016 Nov 25;17(1):239
pubmed: 27887629
Curr Genet. 2019 Dec;65(6):1287-1295
pubmed: 31076843
Bioinformatics. 2019 Dec 15;35(24):5372-5373
pubmed: 31332428
PLoS Genet. 2011 Mar;7(3):e1002016
pubmed: 21437266
Nat Commun. 2019 Apr 16;10(1):1784
pubmed: 30992455
PLoS Genet. 2015 Dec 23;11(12):e1005699
pubmed: 26700858
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
PLoS Genet. 2014 Jan 30;10(1):e1004139
pubmed: 24497845
Nat Rev Genet. 2013 Feb;14(2):125-38
pubmed: 23329113
Nat Methods. 2019 Dec;16(12):1297-1305
pubmed: 31740818
PLoS One. 2017 Jul 27;12(7):e0181599
pubmed: 28749972
Genome Res. 2019 Jul;29(7):1178-1187
pubmed: 31186302
Genome Res. 2017 May;27(5):677-685
pubmed: 27895111
Genome Biol. 2018 Jul 13;19(1):90
pubmed: 30005597
Nature. 2015 Oct 1;526(7571):75-81
pubmed: 26432246
Nat Methods. 2018 Jun;15(6):461-468
pubmed: 29713083
Nat Biotechnol. 2008 Oct;26(10):1146-53
pubmed: 18846088
Am J Hum Genet. 2015 Feb 5;96(2):208-20
pubmed: 25640679
Nat Biotechnol. 2018 Apr;36(4):338-345
pubmed: 29431738
Bioinformatics. 2012 Nov 1;28(21):2711-8
pubmed: 22942022
Genome Biol. 2019 Jun 24;20(1):129
pubmed: 31234903
Nat Biotechnol. 2016 May 6;34(5):518-24
pubmed: 27153285
Trends Genet. 2015 Oct;31(10):587-599
pubmed: 26209074
RNA. 2019 Oct;25(10):1229-1241
pubmed: 31266821