Breast Cancer Research and Treatment

, Volume 165, Issue 3, pp 765–770 | Cite as

Detection of BRCA1 gross rearrangements by droplet digital PCR

  • Elena V. Preobrazhenskaya
  • Ilya V. Bizin
  • Ekatherina Sh. Kuligina
  • Alla Yu. Shleykina
  • Evgeny N. Suspitsin
  • Olga A. Zaytseva
  • Elena I. Anisimova
  • Sergey A. Laptiev
  • Tatiana V. Gorodnova
  • Alexey M. Belyaev
  • Evgeny N. Imyanitov
  • Anna P. SokolenkoEmail author
Brief Report



Large genomic rearrangements (LGRs) constitute a significant share of pathogenic BRCA1 mutations. Multiplex ligation-dependent probe amplification (MLPA) is a leading method for LGR detection; however, it is entirely based on the use of commercial kits, includes relatively time-consuming hybridization step, and is not convenient for large-scale screening of recurrent LGRs.

Materials and methods

We developed and validated the droplet digital PCR (ddPCR) assay, which covers the entire coding region of BRCA1 gene and is capable to precisely quantitate the copy number for each exon.


141 breast cancer (BC) patients, who demonstrated evident clinical features of hereditary BC but turned out to be negative for founder BRCA1/2 mutations, were subjected to the LGR analysis. Four patients with LGR were identified, with three cases of exon 8 deletion and one women carrying the deletion of exons 5–7. Excellent concordance with MLPA test was observed. Exon 8 copy number was tested in additional 720 BC and 184 ovarian cancer (OC) high-risk patients, and another four cases with the deletion were revealed; MLPA re-analysis demonstrated that exon 8 loss was a part of a larger genetic alteration in two cases, while the remaining two patients had isolated defect of exon 8. Long-range PCR and next generation sequencing of DNA samples carrying exon 8 deletion revealed two types of recurrent LGRs.


Droplet digital PCR is a reliable tool for the detection of large genomic rearrangements.


Large genomic rearrangements Droplet digital PCR BRCA1 mutation 



Breast cancer


Droplet digital polymerase chain reaction


Large genomic rearrangements


Multiplex ligation-dependent probe amplification


Next generation sequencing


Ovarian cancer



This work has been supported by the Russian Science Foundation (Grant 14-25-00111).

Compliance with ethical standards

Conflict of interest

The authors declares that they have no conflict of interest.

Supplementary material

10549_2017_4357_MOESM1_ESM.pdf (284 kb)
Supplementary material 1 (PDF 284 kb)
10549_2017_4357_MOESM2_ESM.pdf (892 kb)
Supplementary material 2 (PDF 891 kb)


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Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  • Elena V. Preobrazhenskaya
    • 1
  • Ilya V. Bizin
    • 2
  • Ekatherina Sh. Kuligina
    • 1
  • Alla Yu. Shleykina
    • 1
  • Evgeny N. Suspitsin
    • 1
    • 3
  • Olga A. Zaytseva
    • 1
  • Elena I. Anisimova
    • 4
  • Sergey A. Laptiev
    • 5
  • Tatiana V. Gorodnova
    • 1
  • Alexey M. Belyaev
    • 1
  • Evgeny N. Imyanitov
    • 1
    • 3
    • 5
    • 6
  • Anna P. Sokolenko
    • 1
    • 3
    • 7
    Email author
  1. 1.N.N. Petrov Institute of OncologySt.-PetersburgRussia
  2. 2.Peter the Great St.-Petersburg Polytechnic UniversitySt.-PetersburgRussia
  3. 3.St.-Petersburg State Pediatric Medical UniversitySt.-PetersburgRussia
  4. 4.Leningrad Regional Oncology CenterSt.-PetersburgRussia
  5. 5.Pavlov First St.-Petersburg State Medical UniversitySt.-PetersburgRussia
  6. 6.I.I. Mechnikov North-Western Medical UniversitySt.-PetersburgRussia
  7. 7.Laboratory of Molecular OncologyN.N. Petrov Institute of OncologySt.-PetersburgRussia

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