ArticleGenome research2023
Accurate sequencing of DNA motifs able to form alternative (non-B) structures.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 23 citations in OpenAlex.
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Z-DNA-induced genomic instability in the human pangenome.Research square · 2026Article
- Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches.bioRxiv : the preprint server for biology · 2026Article
- Exploring per-base quality scores as a surrogate marker of cell-free DNA fragmentome.Briefings in bioinformatics · 2026Article
- Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.NAR genomics and bioinformatics · 2026Article
- G-Quadruplex Unwinding Molecular Mechanisms by Helicases and Their Applications.International journal of molecular sciences · 2026Review
- Strong bias in long-read sequencing prevents assembly ofGenome research · 2026Article
- Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes.bioRxiv : the preprint server for biology · 2025Article
- High-Resolution Assembly of the Human Y Chromosome Identifies a Vast Landscape of Inverted Repeats Associated with Structural and Functional Genomic Features.International journal of molecular sciences · 2025Article
- Genetic analysis using long-read sequencing to overcome the difficulties inResearch and practice in thrombosis and haemostasis · 2025Article
- Complete sequencing of ape genomes.Nature · 2025Article
- Centromere-size reduction and chromatin state dynamics following intergenomic hybridization in cotton.PLoS genetics · 2025Article
- Non-canonical DNA in human and other ape telomere-to-telomere genomes.Nucleic acids research · 2025Article
- Non-canonical DNA in human and other ape telomere-to-telomere genomes.bioRxiv : the preprint server for biology · 2025Article
- Article
- Comparative analysis of predicted DNA secondary structures infers complex human centromere topology.American journal of human genetics · 2024Article
- Complete sequencing of ape genomes.bioRxiv : the preprint server for biology · 2024Article
- Non-B-form DNA is associated with centromere stability in newly-formed polyploid wheat.Science China. Life sciences · 2024Article
- Article
- Special Issue "Bioinformatics of Unusual DNA and RNA Structures".International journal of molecular sciences · 2024Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 4 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.