Oncotarget

Research Papers:

Rapid detection of copy number variations and point mutations in BRCA1/2 genes using a single workflow by ion semiconductor sequencing pipeline

Aldo Germani, Fabio Libi, Stefano Maggi, Gianluca Stanzani, Augusto Lombardi, Patrizia Pellegrini, Mauro Mattei, Laura De Marchis, Claudio Amanti, Antonio Pizzuti, Maria Rosaria Torrisi and Maria Piane _

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Oncotarget. 2018; 9:33648-33655. https://doi.org/10.18632/oncotarget.26000

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Abstract

Aldo Germani1,2, Fabio Libi2, Stefano Maggi2,3, Gianluca Stanzani2, Augusto Lombardi2,3, Patrizia Pellegrini1,2, Mauro Mattei2, Laura De Marchis4, Claudio Amanti2,3, Antonio Pizzuti5,6, Maria Rosaria Torrisi1,2 and Maria Piane1,2

1Department of Clinical and Molecular Medicine, “Sapienza” University of Rome, Rome, Italy

2Sant’Andrea University Hospital, Rome, Italy

3Department of Medical and Surgical Sciences and Translational Medicine, Rome, Italy

4Department of Radiation, Anatomopathological, Oncological Science, “Sapienza” University of Rome, Rome, Italy

5Department of Experimental Medicine, “Sapienza” University of Rome, Rome, Italy

6Clinical Genomics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy

Correspondence to:

Maria Piane, email: maria.piane@uniroma1.it

Keywords: CNV; NGS; MLPA; MAQ; BRCA genes

Received: May 30, 2018     Accepted: August 04, 2018     Published: September 14, 2018

ABSTRACT

Molecular analysis of BRCA1 (MIM# 604370) and BRCA2 (MIM #600185) genes is essential for familial breast and ovarian cancer prevention and treatment. An efficient, rapid, cost-effective accurate strategy for the detection of pathogenic variants is crucial. Mutations detection of BRCA1/2 genes includes screening for single nucleotide variants (SNVs), small insertions or deletions (indels), and Copy Number Variations (CNVs). Sanger sequencing is unable to identify CNVs and therefore Multiplex Ligation Probe amplification (MLPA) or Multiplex Amplicon Quantification (MAQ) is used to complete the BRCA1/2 genes analysis. The rapid evolution of Next Generation Sequencing (NGS) technologies allows the search for point mutations and CNVs with a single platform and workflow. In this study we test the possibilities of NGS technology to simultaneously detect point mutations and CNVs in BRCA1/2 genes, using the OncomineTM BRCA Research Assay on Personal Genome Machine (PGM) Platform with Ion Reporter Software for sequencing data analysis (Thermo Fisher Scientific). Comparison between the NGS-CNVs, MLPA and MAQ results shows how the NGS approach is the most complete and fast method for the simultaneous detection of all BRCA mutations, avoiding the usual time consuming multistep approach in the routine diagnostic testing of hereditary breast and ovarian cancers.


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