Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples
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Márton Zsolt Enyedi1, Gábor Jaksa2, Lajos Pintér2, Farkas Sükösd3, Zoltán Gyuris2, Adrienn Hajdu2,3, Erika Határvölgyi2, Katalin Priskin2, Lajos Haracska1
1Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
2Delta Bio 2000 Ltd., Szeged 6726, Hungary
3Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
Lajos Haracska, email: [email protected]
Keywords: NGS, BRCA1-BRCA2, germline, multiplex PCR, FFPE
Received: May 31, 2016 Accepted: July 19, 2016 Published: August 12, 2016
The development of breast and ovarian cancer is strongly connected to the inactivation of the BRCA1 and BRCA2 genes by different germline and somatic alterations, and their diagnosis has great significance in targeted tumor therapy, since recently approved PARP inhibitors show high efficiency in the treatment of BRCA-deficient tumors. This raises the need for new diagnostic methods that are capable of performing an integrative mutation analysis of the BRCA genes not only from germline DNA but also from formalin-fixed and paraffin-embedded (FFPE) tumor samples. Here we describe the development of such a methodology based on next-generation sequencing and a new bioinformatics software for data analysis. The diagnostic method was initially developed on an Illumina MiSeq NGS platform using germline-mutated stem cell lines and then adapted for the Ion Torrent PGM NGS platform as well. We also investigated the usability of NGS coverage data for the detection of copy number variations and exon deletions as a replacement of the conventional MLPA technique. Finally, we tested the developed workflow on FFPE samples from breast and ovarian cancer patients. Our method meets the sensitivity and specificity requirements for the genetic diagnosis of breast and ovarian cancers both from germline and FFPE samples.
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