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

J 2023

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 et. al.

Základní údaje

Originální název

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

Autoři

WEISSENSTEINER, Matthias H, Marzia A CREMONA, Wilfried M GUIBLET, Nicholas STOLER, Robert S HARRIS, Monika ČECHOVÁ (203 Česká republika, garant, domácí), Kristin A ECKERT, Francesca CHIAROMONTE, Yi-Fei HUANG a Kateryna D MAKOVA

Vydání

Genome research, COLD SPRING HARBOR, COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2023, 1088-9051

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 7.000 v roce 2022

Kód RIV

RIV/00216224:14330/23:00133333

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1101/gr.277490.122

UT WoS

001056384700001

Klíčová slova anglicky

DNA sequencing

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 8. 4. 2024 03:45, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

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.

Citovat

WEISSENSTEINER, Matthias H, Marzia A CREMONA, Wilfried M GUIBLET, Nicholas STOLER, Robert S HARRIS, Monika ČECHOVÁ, Kristin A ECKERT, Francesca CHIAROMONTE, Yi-Fei HUANG a 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, roč. 33, č. 6, s. 907-922. ISSN 1088-9051. Dostupné z: https://dx.doi.org/10.1101/gr.277490.122.

@article{2367938,
   author = {Weissensteiner, Matthias H and Cremona, Marzia A and Guiblet, Wilfried M and Stoler, Nicholas and Harris, Robert S and Čechová, Monika and Eckert, Kristin A and Chiaromonte, Francesca and Huang, YiandFei and Makova, Kateryna D},
   article_location = {COLD SPRING HARBOR},
   article_number = {6},
   doi = {http://dx.doi.org/10.1101/gr.277490.122},
   keywords = {DNA sequencing},
   language = {eng},
   issn = {1088-9051},
   journal = {Genome research},
   title = {Accurate sequencing of DNA motifs able to form alternative (non-B) structures},
   url = {http://dx.doi.org/10.1101/gr.277490.122},
   volume = {33},
   year = {2023}
}

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  -

WEISSENSTEINER, Matthias H, Marzia A CREMONA, Wilfried M GUIBLET, Nicholas STOLER, Robert S HARRIS, Monika ČECHOVÁ, Kristin A ECKERT, Francesca CHIAROMONTE, Yi-Fei HUANG a Kateryna D MAKOVA. Accurate sequencing of DNA motifs able to form alternative (non-B) structures. \textit{Genome research}. COLD SPRING HARBOR: COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2023, roč.~33, č.~6, s.~907-922. ISSN~1088-9051. Dostupné z: https://dx.doi.org/10.1101/gr.277490.122.

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