Breast Cancer Research and Treatment

, Volume 122, Issue 1, pp 287–297 | Cite as

High-throughput resequencing in the diagnosis of BRCA1/2 mutations using oligonucleotide resequencing microarrays

  • Christopher Schroeder
  • Fanny Stutzmann
  • Bernhard H. F. Weber
  • Olaf Riess
  • Michael Bonin
Brief Report
First Online:
Received:
Accepted:

Abstract

Breast cancer is the most frequent form of carcinoma in European females (incidence 65 per 100,000). In about 10% of all cases, pedigree analysis predicts a hereditary breast-ovarian cancer syndrome (HBOC) to be causative for the disease. Frequently, mutations in two genes, BRCA1 (Chr. 17q21) and BRCA2 (Chr. 13q12), are associated with HBOC. In females, mutations in these genes result in a lifetime risk of 80–85% for breast cancer and 54% (BRCA1) or 23% (BRCA2) for ovarian cancer. Current genetic diagnostic tools for BRCA1 and BRCA2 remain laborious and expensive. Here, we present the first oligonucleotide resequencing microarray covering the complete coding sequence of both genes. In total, 36 previously characterized DNAs were resequenced; all 11 patients with single-nucleotide mutations and, due to a special mutational design, eight patients with heterozygous deletions were detected correctly. In total, 47 different single-nucleotide variants (SNVs) were found. A newly developed software, SeqC, reduced the number of ambiguous calls with the help of a statistical module comparing the acquired data to an online-database. SeqC improved the average call rate to 99% (GSeq: 97%) and reduced time and efforts for manual analysis. SeqC confirmed the results obtained by GSeq and found an additional 33 sequences changes representing 14 SNVs. In total, 945 kb were screened and the overall turnaround time for each patient took approximately 3 days, including analysis.

Keywords

Oligonucleotide resequencing microarray BRCA1 BRCA2 Breast cancer Ovarian cancer HBOC HBC HOC SeqC 
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Notes

Acknowledgments

We thank JSI medical systems and especially Joachim Strub and Dr. Volker Horejschi for assistance during data analysis. The analysis of BRCA patients was supported by a multi-center grant from the Deutsche Krebshilfe, Bonn, Germany.

Supplementary material

10549_2009_639_MOESM1_ESM.pdf (373 kb)
Supplementary material 1 (PDF 372 kb)

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Copyright information

© Springer Science+Business Media, LLC. 2009

Authors and Affiliations

  • Christopher Schroeder
    • 1
  • Fanny Stutzmann
    • 1
  • Bernhard H. F. Weber
    • 2
  • Olaf Riess
    • 1
  • Michael Bonin
    • 1
  1. 1.Department of Medical GeneticsUniversity of TübingenTubingenGermany
  2. 2.Institute of Human GeneticsUniversity of RegensburgRegensburgGermany

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