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.

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

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Impact factor

Impact factor: 7.000 in 2022

RIV identification code

RIV/00216224:14330/23:00133333

Organization unit

Faculty of Informatics

DOI

UT WoS

001056384700001

Keywords in English

DNA sequencing

Tags

International impact, Reviewed
Změněno: 8/4/2024 03:45, RNDr. Pavel Šmerk, Ph.D.

Abstract

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.