Simultaneous detection of genetic and copy number alterations in BRCA1/2 genes

Abstract

Germline mutations in BRCA1 and BRCA2 genes (BRCA1/2) predispose to hereditary breast and ovarian cancer syndrome (HBOC), and their dysregulation increases the risk of cancers. The detection of pathogenic BRCA1/2 variants is essential for the diagnosis and prevention of HBOC, and for offering treatment decisions for patients. Therefore, there is a growing demand for the development of accurate, rapid assay systems that simultaneously detect pathogenic variants and copy number alterations. Here, we tested Thermo Fisher Scientific’s newly developed Oncomine® BRCA1/2 Panel. We showed that all mutations in standard reference DNA were detected with high accuracy, and that values of allelic fractions were detected with high concordance (R2 = 0.9986). The Oncomine® BRCA1/2 Panel detected 21 pathogenic germline variants in 147 patients with breast and/or ovarian cancer, of which 20 were detected by the previously-launched Ion AmpliSeq™ BRCA1/2 Panel, except for one frameshift mutation. The Oncomine® BRCA1/2 Panel precisely captured one additional frameshift mutation, which is difficult to detect because of the homopolymer site. Large genomic deletion was identified in one sample, which was previously detected by multiplex ligation-dependent probe amplification. Oncomine® BRCA1/2 Panel could accurately detect pathogenic variant and copy number alteration, and be an alternative assay to investigate BRCA1/2 germline and somatic mutations.

Screening of BRCA1/2 genes mutations and copy number variations in patients with high risk for hereditary breast and ovarian cancer syndrome (HBOC)

“…It is considered as an alternative assay to investigate both types of BRCA1/2 genetic alterations in one workflow. This panel efficiency has been investigated by Hirotsu et al (2017) [ 34 ], and according to his study results, the Oncomine BRCA1/2 research assay panel is a highly accurate tool for analyzing variants with wide-ranging allelic fractions and for detecting copy number alterations.…”

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

“…Another study showed a better performance of the Oncomine™ BRCA Research assay compared with the Ion Ampliseq™ BRCA Panel in terms of ability to identify deletions at homopolymer sites, on target mapped reads, reduction of low-quality mapped reads and false-negative results. In the same study, using the Oncomine Panel a large deletion was identified, subsequently confirmed by MLPA [ 31 ]. The NGS-CNV analysis requires a complete validation of the "baseline", which is crucial to obtain accurate and reliable results for clinical applications.…”

Two synchronous malignancies: nodular melanoma and renal cell carcinoma in a patient with an underlying germlineBRCA2mutation

“…Breast cancer susceptibility genes 1 and 2 ( BRCA1 and BRCA2 ) are tumour suppressor genes that maintain genomic integrity 1 2. Mutations in BRCA1 and BRCA2 lead to defective double-stranded DNA repair, dysregulation of the cell cycle and chromosomal aberrations 3–6.…”