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Mutation spectrum revealed by breakpoint sequencing of human germline CNVs

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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Figure 1: Experimental overview.
Figure 2: Confidence intervals.
Figure 3: Properties of the pulldown experiment.
Figure 4: Summary of sequence content at deletion breaks.
Figure 5: Inverted sequence at complex CNV breakpoints.

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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

Authors and Affiliations

Authors

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.

Corresponding author

Correspondence to Matthew E Hurles.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 and Supplementary Note (PDF 203 kb)

Supplementary Table 1

CNV breakpoint locations (XLS 110 kb)

Supplementary Table 2

PCR validation primers (XLS 42 kb)

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Conrad, D., Bird, C., Blackburne, B. et al. Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat Genet 42, 385–391 (2010). https://doi.org/10.1038/ng.564

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