A Whole Germline BRCA2 Gene Deletion: How to Learn from CNV In Silico Analysis

Scaglione, Giovanni Luca; Concolino, Paola; Bonis, Maria De; Paolis, Elisa De; Minucci, Angelo; Ferrandina, Gabriella; Capoluongo, Ettore

doi:10.3390/ijms19040961

Cited by 13 publications

(7 citation statements)

References 25 publications

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“…Only four cases have been reported in the literature, of which one was recorded for somatic tissue [55]. This LGR was described for three BC patients, one French male patient with a family history of breast and pancreatic cancer [56], and two female BC patients from Italy [57] and the USA [31], respectively. The female patients represented high-risk patients.…”

Section: Discussionmentioning

confidence: 99%

The contribution of large genomic rearrangements in BRCA1 and BRCA2 to South African familial breast cancer

et al. 2020

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Background Pathogenic variants that occur in the familial breast cancer genes (BRCA1/2) lead to truncated ineffective proteins in the majority of cases. These variants are mostly represented by small deletions/insertions, nonsense- and splice-site variants, although some larger pathogenic rearrangements occur. Currently, their contribution to familial breast cancer (BC) and ovarian cancer (OVC) in South Africa (SA) is unknown. Methods Seven hundred and forty-four patients affected with BC or OVC were screened for larger genomic rearrangements (LGRs) by means of multiplex ligation-dependent probe amplification or Next Generation Sequencing using the Oncomine™ BRCA research assay. Results The patients represented mostly medium to high-risk families, but also included lower risk patients without a family history of the disease, diagnosed at an early age of onset (< 40 years). Eight LGRs were detected (1.1%); seven in BRCA1 with a single whole gene deletion (WGD) detected for BRCA2. These eight LGRs accounted for 8.7% of the 92 BRCA1/2 pathogenic variants identified in the 744 cases. The pathogenic LGRs ranged from WGDs to the duplication of a single exon. Conclusions Larger rearrangements in BRCA1/2 contributed to the overall mutational burden of familial BC and OVC in SA. Almost a quarter of all pathogenic variants in BRCA1 were LGRs (7/30, 23%). The spectrum observed included two WGDs, one each for BRCA1 and BRCA2.

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Section: Discussionmentioning

confidence: 99%

The contribution of large genomic rearrangements in BRCA1 and BRCA2 to South African familial breast cancer

et al. 2020

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“…However the possibility of analyzing all types of mutations through a single workflow offered by the NGS is appealing. Therefore several research groups have tested different NGS platforms for CNVs detection by implementing and validating customized workflow [ 21 , 28 – 30 ].…”

Section: Discussionmentioning

confidence: 99%

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

Germani

Libi²,

Maggi³

et al. 2018

Oncotarget

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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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“…After the GS QC assay and quantification, the libraries were sequenced using the Illumina MiSeq platform (Illumina, San Diego, CA, USA) following our molecular diagnostic routine validated setting [26,27,28]. After NGS, the sequencing fastq.gz files from MiSeq were analyzed with a CE-IVD (CE-marked In Vitro Diagnostic Medical Device) bioinformatics tool, Amplicon Suite (SmartSeq srl, Novara, Italy), to investigate the coverage parameters.…”

Section: Methodsmentioning

confidence: 99%

Automated Workflow for Somatic and Germline Next Generation Sequencing Analysis in Routine Clinical Cancer Diagnostics

Muscarella

Fabrizio

Bonis

et al. 2019

Cancers

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Thanks to personalized medicine trends and collaborations between industry, clinical research groups and regulatory agencies, next generation sequencing (NGS) is turning into a common practice faster than one could have originally expected. When considering clinical applications of NGS in oncology, a rapid workflow for DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissue samples, as well as producing high quality library preparation, can be real challenges. Here we consider these targets and how applying effective automation technology to NGS workflows may help improve yield, timing and quality-control. We firstly evaluated DNA recovery from archived FFPE blocks from three different manual extraction methods and two automated extraction workstations. The workflow was then implemented to somatic (lung/colon panel) and germline (BRCA1/2) library preparation for NGS analysis exploiting two automated workstations. All commercial kits gave good results in terms of DNA yield and quality. On the other hand, the automated workstation workflow has been proven to be a valid automatic extraction system to obtain high quality DNA suitable for NGS analysis (lung/colon Ampli-seq panel). Moreover, it can be efficiently integrated with an open liquid handling platform to provide high-quality libraries from germline DNA with more reproducibility and high coverage for targeted sequences in less time (BRCA1/2). The introduction of automation in routine workflow leads to an improvement of NGS standardization and increased scale up of sample preparations, reducing labor and timing, with optimization of reagents and management.

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A Whole Germline BRCA2 Gene Deletion: How to Learn from CNV In Silico Analysis

Cited by 13 publications

References 25 publications

The contribution of large genomic rearrangements in BRCA1 and BRCA2 to South African familial breast cancer

The contribution of large genomic rearrangements in BRCA1 and BRCA2 to South African familial breast cancer

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

Automated Workflow for Somatic and Germline Next Generation Sequencing Analysis in Routine Clinical Cancer Diagnostics

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