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Cited by 178Genomic variations and chromosomal abnormalitiesGenome Rearrangement AlgorithmsGenomics and Chromatin Dynamics

Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours

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Harewood, Louise, Kishore, Kamal, Eldridge, Matthew D., Wingett, Steven, Pearson, Danita, Schoenfelder, Stefan, Collins, V. Peter, Fraser, Peter·2017·Genome Biology
DOI 10.1186/s13059-017-1253-8PMC PMC5488307
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Abstract

Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles. Here we describe the use of Hi-C as a tool for detection of both balanced and unbalanced chromosomal rearrangements in primary human tumour samples, with the potential to define chromosome breakpoints to bp resolution. In addition, we show copy number profiles can also be obtained from the same data, all at a significantly lower cost than standard sequencing approaches.

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  • SVs can now be detected alongside SNVs using cost-effective methods such as single-enzyme Hi-C with short-read sequencing.

    “Importantly, SVs can now be detected alongside SNVs using cost-effective methods such as single-enzyme Hi-C with short-read sequencing, making their integration into conservation genomics protocols both feasible and scalable (196, 197).”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [197]

    The Conclusions report that Hi-C detects chromosomal rearrangements without deep sequencing, and the Discussion says it costs significantly less than deep whole-genome sequencing. Methods describe short paired-end reads and corrections for HindIII sites. Our copy does not show SNVs being detected alongside SVs from the same Hi-C data; the cited evidence therefore supports only part of the attributed claim. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

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Cited by

Sorted by citations

Authors
Harewood, L., Kishore, K., Eldridge, M. D., Wingett, S., Pearson, D., Schoenfelder, S., Collins, V. P., & Fraser, P.
Affiliations
  • Babraham Institute (GB)
  • University of Cambridge (GB)
Corresponding author
  • Harewood, Louise
  • Fraser, Peter
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2017-06-27
Volume
18
Issue
1
Pages
125-125
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-017-1253-8
PMC
PMC5488307
OpenAlex
W2729264945
Cited by
178
References
1
Citations by year
2026: 7 · 2025: 21 · 2024: 19 · 2023: 19 · 2022: 12 · 2021: 29 · 2020: 21 · 2019: 20 · 2018: 23 · 2017: 5 · 2014: 1
FWCI
12.23
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Genome biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • UCL Discovery (University College London) (submittedVersion)
  • Research Portal (Queen's University Belfast) (submittedVersion, cc-by)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • Apollo
  • Apollo (cc-by)
Funders
  • Biotechnology and Biological Sciences Research Council
  • Cancer Research UK (GB)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
Hi-C, chromosomal rearrangements, copy number variation, reciprocal translocation, chromosomal inversions, chromosomal breakpoints, human cancer, somatic rearrangements, breakpoint resolution, cancer genomics
MeSH terms
Chromosome Aberrations, Humans, Chromosome Inversion, Neoplasms, Translocation, Genetic, In Situ Hybridization, Fluorescence, Chromosome Breakpoints, DNA Copy Number Variations

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