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Author Notes:

Corresponding author: M. Katharine Rudd, katie.rudd@emory.edu

Conceived and designed the experiments: PB MKR.

Performed the experiments: PB KEH.

Analyzed the data: PB KEH KNC MKR.

Contributed to the writing of the manuscript: MKR.

We thank Cheryl Strauss for editorial assistance and members of the Rudd laboratory for helpful discussions.

The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the March of Dimes.

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

The authors confirm that all data underlying the findings are fully available without restriction.

All relevant data are within the paper and its Supporting Information files.


Research Funding:

This work was supported by a grant from the National Institutes of Health (grant number MH092902 to MKR) and a grant from the March of Dimes (grant number #12-FY11-203 to MKR).


  • Bacterial evolution
  • Antibiotic resistance
  • Recombination
  • Mobile genetic elements
  • Coalescent analysis
  • Phylogeography

Tandem Repeats and G-Rich Sequences Are Enriched at Human CNV Breakpoints

Journal Title:



Volume 9, Number 7


, Pages e101607-e101607

Type of Work:

Article | Final Publisher PDF


Chromosome breakage in germline and somatic genomes gives rise to copy number variation (CNV) responsible for genomic disorders and tumorigenesis. DNA sequence is known to play an important role in breakage at chromosome fragile sites; however, the sequences susceptible to double-strand breaks (DSBs) underlying CNV formation are largely unknown. Here we analyze 140 germline CNV breakpoints from 116 individuals to identify DNA sequences enriched at breakpoint loci compared to 2800 simulated control regions. We find that, overall, CNV breakpoints are enriched in tandem repeats and sequences predicted to form G-quadruplexes. G-rich repeats are overrepresented at terminal deletion breakpoints, which may be important for the addition of a new telomere. Interstitial deletions and duplication breakpoints are enriched in Alu repeats that in some cases mediate non-allelic homologous recombination (NAHR) between the two sides of the rearrangement. CNV breakpoints are enriched in certain classes of repeats that may play a role in DNA secondary structure, DSB susceptibility and/or DNA replication errors.

Copyright information:

© 2014 Bose et al.

This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).
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