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  1. Article ; Online: Dysgu: efficient structural variant calling using short or long reads.

    Cleal, Kez / Baird, Duncan M

    Nucleic acids research

    2022  Volume 50, Issue 9, Page(s) e53

    Abstract: Structural variation (SV) plays a fundamental role in genome evolution and can underlie inherited or acquired diseases such as cancer. Long-read sequencing technologies have led to improvements in the characterization of structural variants (SVs), ... ...

    Abstract Structural variation (SV) plays a fundamental role in genome evolution and can underlie inherited or acquired diseases such as cancer. Long-read sequencing technologies have led to improvements in the characterization of structural variants (SVs), although paired-end sequencing offers better scalability. Here, we present dysgu, which calls SVs or indels using paired-end or long reads. Dysgu detects signals from alignment gaps, discordant and supplementary mappings, and generates consensus contigs, before classifying events using machine learning. Additional SVs are identified by remapping of anomalous sequences. Dysgu outperforms existing state-of-the-art tools using paired-end or long-reads, offering high sensitivity and precision whilst being among the fastest tools to run. We find that combining low coverage paired-end and long-reads is competitive in terms of performance with long-reads at higher coverage values.
    MeSH term(s) Genomic Structural Variation ; High-Throughput Nucleotide Sequencing ; INDEL Mutation ; Sequence Analysis, DNA ; Software
    Language English
    Publishing date 2022-01-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkac039
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  2. Article ; Online: Editorial overview: The instability of the cancer genome: it starts at the end.

    Harrington, Lea / Baird, Duncan M

    Current opinion in genetics & development

    2020  Volume 60, Page(s) iii–vi

    MeSH term(s) Genome, Human ; Genomic Instability ; Humans ; Neoplasms/genetics ; Neoplasms/pathology
    Language English
    Publishing date 2020-03-30
    Publishing country England
    Document type Editorial
    ZDB-ID 1077312-5
    ISSN 1879-0380 ; 0959-437X
    ISSN (online) 1879-0380
    ISSN 0959-437X
    DOI 10.1016/j.gde.2020.02.020
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  3. Article ; Online: Telomeres and genomic evolution.

    Baird, Duncan M

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2018  Volume 373, Issue 1741

    Abstract: The terminal regions of eukaryotic chromosomes, composed of telomere repeat sequences and sub-telomeric sequences, represent some of the most variable and rapidly evolving regions of the genome. The sub-telomeric regions are characterized by segmentally ... ...

    Abstract The terminal regions of eukaryotic chromosomes, composed of telomere repeat sequences and sub-telomeric sequences, represent some of the most variable and rapidly evolving regions of the genome. The sub-telomeric regions are characterized by segmentally duplicated repetitive DNA elements, interstitial telomere repeat sequences and families of variable genes. Sub-telomeric repeat sequence families are shared among multiple chromosome ends, often rendering detailed sequence characterization difficult. These regions are composed of constitutive heterochromatin and are subjected to high levels of meiotic recombination. Dysfunction within telomere repeat arrays, either due to disruption in the chromatin structure or because of telomere shortening, can lead to chromosomal fusion and the generation of large-scale genomic rearrangements across the genome. The dynamic nature of telomeric regions, therefore, provides functionally useful variation to create genetic diversity, but also provides a mechanism for rapid genomic evolution that can lead to reproductive isolation and speciation. This article is part of the theme issue 'Understanding diversity in telomere dynamics'.This article is part of the theme issue 'Understanding diversity in telomere dynamics'.
    MeSH term(s) Chromosomal Instability ; Chromosomes/genetics ; Evolution, Molecular ; Genetic Variation ; Humans ; Neoplasms/genetics ; Recombinational DNA Repair ; Telomere/genetics ; Telomere Homeostasis
    Language English
    Publishing date 2018-01-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2016.0437
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  4. Article: Catastrophic Endgames: Emerging Mechanisms of Telomere-Driven Genomic Instability.

    Cleal, Kez / Baird, Duncan M

    Trends in genetics : TIG

    2020  Volume 36, Issue 5, Page(s) 347–359

    Abstract: When cells progress to malignancy, they must overcome a final telomere-mediated proliferative lifespan barrier called replicative crisis. Crisis is characterized by extensive telomere fusion that drives widespread genomic instability, mitotic arrest, ... ...

    Abstract When cells progress to malignancy, they must overcome a final telomere-mediated proliferative lifespan barrier called replicative crisis. Crisis is characterized by extensive telomere fusion that drives widespread genomic instability, mitotic arrest, hyperactivation of autophagy, and cell death. Recently, it has become apparent that that the resolution of dicentric chromosomes, which arise from telomere fusions during crisis, can initiate a sequence of events that leads to chromothripsis, a form of extreme genomic catastrophe. Chromothripsis is characterized by localized genomic regions containing tens to thousands of rearrangements and it is becoming increasingly apparent that chromothripsis occurs widely across tumor types and has a clinical impact. Here we discuss how telomere dysfunction can initiate genomic complexity and the emerging mechanisms of chromothripsis.
    MeSH term(s) Chromosome Disorders/genetics ; Chromosome Disorders/pathology ; Chromothripsis ; DNA Replication/genetics ; Genomic Instability/genetics ; Genomics ; Humans ; Mutation ; Neoplasms/genetics ; Neoplasms/pathology ; Telomere/genetics
    Language English
    Publishing date 2020-03-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2020.02.001
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  5. Article ; Online: UPF1 promotes the formation of R loops to stimulate DNA double-strand break repair.

    Ngo, Greg H P / Grimstead, Julia W / Baird, Duncan M

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 3849

    Abstract: DNA-RNA hybrid structures have been detected at the vicinity of DNA double-strand breaks (DSBs) occurring within transcriptional active regions of the genome. The induction of DNA-RNA hybrids strongly affects the repair of these DSBs, but the nature of ... ...

    Abstract DNA-RNA hybrid structures have been detected at the vicinity of DNA double-strand breaks (DSBs) occurring within transcriptional active regions of the genome. The induction of DNA-RNA hybrids strongly affects the repair of these DSBs, but the nature of these structures and how they are formed remain poorly understood. Here we provide evidence that R loops, three-stranded structures containing DNA-RNA hybrids and the displaced single-stranded DNA (ssDNA) can form at sub-telomeric DSBs. These R loops are generated independently of DNA resection but are induced alongside two-stranded DNA-RNA hybrids that form on ssDNA generated by DNA resection. We further identified UPF1, an RNA/DNA helicase, as a crucial factor that drives the formation of these R loops and DNA-RNA hybrids to stimulate DNA resection, homologous recombination, microhomology-mediated end joining and DNA damage checkpoint activation. Our data show that R loops and DNA-RNA hybrids are actively generated at DSBs to facilitate DNA repair.
    MeSH term(s) Base Sequence ; Cell Line ; Cell Line, Tumor ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Breaks, Double-Stranded ; DNA Repair ; DNA, Single-Stranded/chemistry ; DNA, Single-Stranded/genetics ; DNA, Single-Stranded/metabolism ; HCT116 Cells ; Humans ; Nucleic Acid Hybridization ; R-Loop Structures ; RNA/genetics ; RNA/metabolism ; RNA Helicases/genetics ; RNA Helicases/metabolism ; RNA Interference ; Telomere/genetics ; Telomere/metabolism ; Trans-Activators/genetics ; Trans-Activators/metabolism
    Chemical Substances DNA, Single-Stranded ; Trans-Activators ; RNA (63231-63-0) ; DNA (9007-49-2) ; RNA Helicases (EC 3.6.4.13) ; UPF1 protein, human (EC 3.6.4.13)
    Language English
    Publishing date 2021-06-22
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-24201-w
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  6. Article ; Online: POLQ suppresses genome instability and alterations in DNA repeat tract lengths.

    Liddiard, Kate / Aston-Evans, Alys N / Cleal, Kez / Hendrickson, Eric A / Baird, Duncan M

    NAR cancer

    2022  Volume 4, Issue 3, Page(s) zcac020

    Abstract: DNA polymerase theta (POLQ) is a principal component of the alternative non-homologous end-joining (ANHEJ) DNA repair pathway that ligates DNA double-strand breaks. Utilizing independent models of POLQ insufficiency during telomere-driven crisis, we ... ...

    Abstract DNA polymerase theta (POLQ) is a principal component of the alternative non-homologous end-joining (ANHEJ) DNA repair pathway that ligates DNA double-strand breaks. Utilizing independent models of POLQ insufficiency during telomere-driven crisis, we found that
    Language English
    Publishing date 2022-06-29
    Publishing country England
    Document type Journal Article
    ISSN 2632-8674
    ISSN (online) 2632-8674
    DOI 10.1093/narcan/zcac020
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  7. Article ; Online: T cell memory revisited using single telomere length analysis.

    Roger, Laureline / Miners, Kelly L / Leonard, Louise / Grimstead, Julia W / Price, David A / Baird, Duncan M / Ladell, Kristin

    Frontiers in immunology

    2023  Volume 14, Page(s) 1100535

    Abstract: The fundamental basis of T cell memory remains elusive. It is established that antigen stimulation drives clonal proliferation and differentiation, but the relationship between cellular phenotype, replicative history, and longevity, which is likely ... ...

    Abstract The fundamental basis of T cell memory remains elusive. It is established that antigen stimulation drives clonal proliferation and differentiation, but the relationship between cellular phenotype, replicative history, and longevity, which is likely essential for durable memory, has proven difficult to elucidate. To address these issues, we used conventional markers of differentiation to identify and isolate various subsets of CD8
    MeSH term(s) Memory T Cells ; Cell Differentiation ; Leukocyte Common Antigens/metabolism ; Lymphocyte Activation ; Telomere/genetics
    Chemical Substances Leukocyte Common Antigens (EC 3.1.3.48)
    Language English
    Publishing date 2023-09-14
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2023.1100535
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  8. Article: Telomeres and Chromosomal Translocations : There's a Ligase at the End of the Translocation.

    Baird, Duncan M / Hendrickson, Eric A

    Advances in experimental medicine and biology

    2018  Volume 1044, Page(s) 89–112

    Abstract: Chromosomal translocations are now well understood to not only constitute signature molecular markers for certain human cancers but often also to be causative in the genesis of that tumor. Despite the obvious importance of such events, the molecular ... ...

    Abstract Chromosomal translocations are now well understood to not only constitute signature molecular markers for certain human cancers but often also to be causative in the genesis of that tumor. Despite the obvious importance of such events, the molecular mechanism of chromosomal translocations in human cells remains poorly understood. Part of the explanation for this dearth of knowledge is due to the complexity of the reaction and the need to archaeologically work backwards from the final product (a translocation) to the original unrearranged chromosomes to infer mechanism. Although not definitive, these studies have indicated that the aberrant usage of endogenous DNA repair pathways likely lies at the heart of the problem. An equally obfuscating aspect of this field, however, has also originated from the unfortunate species-specific differences that appear to exist in the relevant model systems that have been utilized to investigate this process. Specifically, yeast and murine systems (which are often used by basic science investigators) rely on different DNA repair pathways to promote chromosomal translocations than human somatic cells. In this chapter, we will review some of the basic concepts of chromosomal translocations and the DNA repair systems thought to be responsible for their genesis with an emphasis on underscoring the differences between other species and human cells. In addition, we will focus on a specific subset of translocations that involve the very end of a chromosome (a telomere). A better understanding of the relationship between DNA repair pathways and chromosomal translocations is guaranteed to lead to improved therapeutic treatments for cancer.
    MeSH term(s) Animals ; DNA Damage ; DNA Ligases/physiology ; DNA Repair ; Humans ; Mice ; Telomere ; Translocation, Genetic
    Chemical Substances DNA Ligases (EC 6.5.1.-)
    Language English
    Publishing date 2018-06-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 410187-X
    ISSN 0065-2598
    ISSN 0065-2598
    DOI 10.1007/978-981-13-0593-1_7
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  9. Article ; Online: UPF1 promotes the formation of R loops to stimulate DNA double-strand break repair

    Greg H. P. Ngo / Julia W. Grimstead / Duncan M. Baird

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 15

    Abstract: R loops are formed when single-stranded RNA anneals to one strand of DNA, forming three-stranded structures containing DNA-RNA hybrids and the displaced non-template single-stranded DNA. Here the authors reveal that the DNA:RNA helicase UPF1 plays a role ...

    Abstract R loops are formed when single-stranded RNA anneals to one strand of DNA, forming three-stranded structures containing DNA-RNA hybrids and the displaced non-template single-stranded DNA. Here the authors reveal that the DNA:RNA helicase UPF1 plays a role in promoting R loops formation at telomeric double strand breaks to stimulate DNA resection and repair.
    Keywords Science ; Q
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Tracking telomere fusions through crisis reveals conflict between DNA transcription and the DNA damage response.

    Liddiard, Kate / Grimstead, Julia W / Cleal, Kez / Evans, Anna / Baird, Duncan M

    NAR cancer

    2021  Volume 3, Issue 1, Page(s) zcaa044

    Abstract: Identifying attributes that distinguish pre-malignant from senescent cells provides opportunities for targeted disease eradication and revival of anti-tumour immunity. We modelled a telomere-driven crisis in four human fibroblast lines, sampling at ... ...

    Abstract Identifying attributes that distinguish pre-malignant from senescent cells provides opportunities for targeted disease eradication and revival of anti-tumour immunity. We modelled a telomere-driven crisis in four human fibroblast lines, sampling at multiple time points to delineate genomic rearrangements and transcriptome developments that characterize the transition from dynamic proliferation into replicative crisis. Progression through crisis was associated with abundant intra-chromosomal telomere fusions with increasing asymmetry and reduced microhomology usage, suggesting shifts in DNA repair capacity. Eroded telomeres also fused with genomic loci actively engaged in transcription, with particular enrichment in long genes. Both gross copy number alterations and transcriptional responses to crisis likely underpin the elevated frequencies of telomere fusion with chromosomes 9, 16, 17, 19 and most exceptionally, chromosome 12. Juxtaposition of crisis-regulated genes with loci undergoing
    Language English
    Publishing date 2021-01-06
    Publishing country England
    Document type Journal Article
    ISSN 2632-8674
    ISSN (online) 2632-8674
    DOI 10.1093/narcan/zcaa044
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