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Mutation spectrum revealed by breakpoint sequencing of human germline CNVs

Nature Genetics volume 42, pages 385391 (2010) | Download Citation

Abstract

Precisely characterizing the breakpoints of copy number variants (CNVs) is crucial for assessing their functional impact. However, fewer than 10% of known germline CNVs have been mapped to the single-nucleotide level. We characterized the sequence breakpoints from a dataset of all CNVs detected in three unrelated individuals in previous array-based CNV discovery experiments. We used targeted hybridization-based DNA capture and 454 sequencing to sequence 324 CNV breakpoints, including 315 deletions. We observed two major breakpoint signatures: 70% of the deletion breakpoints have 1−30 bp of microhomology, whereas 33% of deletion breakpoints contain 1−367 bp of inserted sequence. The co-occurrence of microhomology and inserted sequence is low (10%), suggesting that there are at least two different mutational mechanisms. Approximately 5% of the breakpoints represent more complex rearrangements, including local microinversions, suggesting a replication-based strand switching mechanism. Despite a rich literature on DNA repair processes, reconstruction of the molecular events generating each of these mutations is not yet possible.

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Acknowledgements

This research was funded by Wellcome Trust grant 077014/Z/05/Z. We thank the Wellcome Trust Sanger Institute for informatics and sequencing support, H. Lam for sharing sequenced CNV breakpoint locations and colleagues at NimbleGen for support and discussions.

Author information

Affiliations

  1. Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

    • Donald F Conrad
    • , Christine Bird
    • , Ben Blackburne
    • , Sarah Lindsay
    • , Lira Mamanova
    • , Daniel J Turner
    •  & Matthew E Hurles
  2. Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Charles Lee

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Contributions

D.F.C. and M.E.H. designed the study. L.M. and D.J.T. performed pulldown and sequencing experiments. D.F.C., B.B., C.B., S.L. and M.E.H. analyzed the data. C.B. performed validation experiments. D.F.C. and M.E.H. wrote the paper with contributions from C.B., B.B. and C.L.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Matthew E Hurles.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–5 and Supplementary Note

Excel files

  1. 1.

    Supplementary Table 1

    CNV breakpoint locations

  2. 2.

    Supplementary Table 2

    PCR validation primers

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DOI

https://doi.org/10.1038/ng.564

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