Accurate sequencing of DNA motifs able to form alternative
(non-B) structures

WEISSENSTEINER, Matthias H, Marzia A CREMONA, Wilfried M GUIBLET, Nicholas STOLER, Robert S HARRIS, Monika ČECHOVÁ, Kristin A ECKERT, Francesca CHIAROMONTE, Yi-Fei HUANG and Kateryna D MAKOVA. Accurate sequencing of DNA motifs able to form alternative (non-B) structures. Genome research. COLD SPRING HARBOR: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2023, vol. 33, No 6, p. 907-922. ISSN 1088-9051. Available from: https://dx.doi.org/10.1101/gr.277490.122.

Other formats: BibTeX LaTeX RIS

TY  - JOUR
ID  - 2367938
AU  - Weissensteiner, Matthias H - Cremona, Marzia A - Guiblet, Wilfried M - Stoler, Nicholas - Harris, Robert S - Čechová, Monika - Eckert, Kristin A - Chiaromonte, Francesca - Huang, Yi-Fei - Makova, Kateryna D
PY  - 2023
TI  - Accurate sequencing of DNA motifs able to form alternative (non-B) structures
JF  - Genome research
VL  - 33
IS  - 6
SP  - 907-922
EP  - 907-922
PB  - COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
SN  - 10889051
KW  - DNA sequencing
UR  - http://dx.doi.org/10.1101/gr.277490.122
N2  - Approximately 13% of the human genome at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity of polymerases and helicases. Because sequencing technologies use these enzymes, they might possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif types but were increased for G-quadruplexes and Z-DNA in all three technologies. Deletion errors were increased for all non-B types but Z-DNA in Illumina and HiFi, as well as only for G-quadruplexes in ONT. Insertion errors for non-B motifs were highly, moderately, and slightly elevated in Illumina, HiFi, and ONT, respectively. Additionally, we developed a probabilistic approach to determine the number of false positives at non-B motifs depending on sample size and variant frequency, and applied it to publicly available data sets (1000 Genomes, Simons Genome Diversity Project, and gnomAD). We conclude that elevated sequencing errors at non-B DNA motifs should be considered in low-read-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA.
ER  -

Basic information
Original name	Accurate sequencing of DNA motifs able to form alternative (non-B) structures
Authors	WEISSENSTEINER, Matthias H, Marzia A CREMONA, Wilfried M GUIBLET, Nicholas STOLER, Robert S HARRIS, Monika ČECHOVÁ (203 Czech Republic, guarantor, belonging to the institution), Kristin A ECKERT, Francesca CHIAROMONTE, Yi-Fei HUANG and Kateryna D MAKOVA.
Edition	Genome research, COLD SPRING HARBOR, COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2023, 1088-9051.

Other information
Original language	English
Type of outcome	Article in a journal
Field of Study	10201 Computer sciences, information science, bioinformatics
Country of publisher	United States of America
Confidentiality degree	is not subject to a state or trade secret
WWW	URL
Impact factor	Impact factor: 7.000 in 2022
RIV identification code	RIV/00216224:14330/23:00133333
Organization unit	Faculty of Informatics
Doi	http://dx.doi.org/10.1101/gr.277490.122
UT WoS	001056384700001
Keywords in English	DNA sequencing
Tags	International impact, Reviewed
Changed by	Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 8/4/2024 03:45.

Abstract

Approximately 13% of the human genome at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity of polymerases and helicases. Because sequencing technologies use these enzymes, they might possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif types but were increased for G-quadruplexes and Z-DNA in all three technologies. Deletion errors were increased for all non-B types but Z-DNA in Illumina and HiFi, as well as only for G-quadruplexes in ONT. Insertion errors for non-B motifs were highly, moderately, and slightly elevated in Illumina, HiFi, and ONT, respectively. Additionally, we developed a probabilistic approach to determine the number of false positives at non-B motifs depending on sample size and variant frequency, and applied it to publicly available data sets (1000 Genomes, Simons Genome Diversity Project, and gnomAD). We conclude that elevated sequencing errors at non-B DNA motifs should be considered in low-read-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA.

PrintDisplayed: 24/8/2024 12:20

Accurate sequencing of DNA motifs able to form alternative (non-B) structures

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