Detection of BRCA1/2 large genomic rearrangements in breast and ovarian cancer patients: an overview of the current methods

Incidence of breast cancer ranges from 27 per 100,000 in Middle Africa and Eastern Asia to 92 per 100,000 in Northern America. It is the fifth most common cause of death from cancer in women, with an estimated 522,000 deaths per year (6.4% of the total). Autosomal dominant inheritance of these cancers is characterized by transmission of cancer predisposition from generation to generation, with around 5-10% of all breast cancers being associated with inherited mutations in BRCA1, BRCA2 and other genes. Breast and ovarian cancers are strongly associated with BRCA1 and BRCA2 mutations. In this study, we genotyped BRCA1 gene for large genomic rearrangements in breast and ovarian cancer patients from Bosnia and Herzegovina, with aim to assess frequency of large BRCA1 mutations (exon deletions/duplications) in this group. We collected 59 breast cancer samples, as well as other data concerning patients’ histopathological parameters of tumor, like age at diagnosis, cancer type, TNM class, cancer grade, as well as estrogen, progesterone and Her2/neu expression. Following DNA extraction from breast cancer samples (tissue after biopsy), BRCA1 mutations were identified by Multiplex Ligase - Dependent Probe Amplification (MLPA) analysis. Biostatistical analyses were conducted using MedCalc v.9.2.0.0 software. In all statistical tests p<0.05 was considered significant. Mean age at diagnosis was 54±1.75 (range 17 – 80). BRCA1 genomic rearrangements were found in 22% of breast and ovarian cancer patients. Statistically significant associations and correlations were found between BRCA1 genomic rearrangements and cancer type, estrogen, progesterone and Her2/neu expression, but not cancer grade, size, invasiveness or patients’ age

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Comprehensive mutation detection of BRCA1/2 genes reveals large genomic rearrangements contribute to hereditary breast and ovarian cancer in Chinese women

BMC Cancer ◽

10.1186/s12885-019-5765-3 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Wen-Ming Cao ◽

Ya-Bing Zheng ◽

Yun Gao ◽

Xiao-Wen Ding ◽

Yan Sun ◽

...

Keyword(s):

Ovarian Cancer ◽

Mutation Detection ◽

Chinese Women ◽

Genomic Rearrangements ◽

Breast And Ovarian Cancer ◽

Large Genomic Rearrangements

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Large genomic rearrangements in BRCA1 and BRCA2 genes in breast and ovarian cancer families in Poland

Hereditary Cancer in Clinical Practice ◽

10.1186/1897-4287-10-s3-a2 ◽

2012 ◽

Vol 10 (Suppl 3) ◽

pp. A2

Author(s):

Helena Bielecka ◽

Bohdan Górski

Keyword(s):

Ovarian Cancer ◽

Genomic Rearrangements ◽

Breast And Ovarian Cancer ◽

Brca1 And Brca2 ◽

Large Genomic Rearrangements ◽

Brca1 And Brca2 Genes

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Large genomic rearrangements in BRCA1 and BRCA2 genes in breast and ovarian cancer families in Poland

Hereditary Cancer in Clinical Practice ◽

10.1186/1897-4287-10-s1-a1 ◽

2012 ◽

Vol 10 (Suppl 1) ◽

pp. A1

Author(s):

Helena Bielecka ◽

Bohdan Górski

Keyword(s):

Ovarian Cancer ◽

Genomic Rearrangements ◽

Breast And Ovarian Cancer ◽

Brca1 And Brca2 ◽

Large Genomic Rearrangements ◽

Brca1 And Brca2 Genes

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Identification of novel BRCA1 large genomic rearrangements by a computational algorithm of amplicon-based Next-Generation Sequencing data

PeerJ ◽

10.7717/peerj.7972 ◽

2019 ◽

Vol 7 ◽

pp. e7972

Author(s):

Arianna Nicolussi ◽

Francesca Belardinilli ◽

Valentina Silvestri ◽

Yasaman Mahdavian ◽

Virginia Valentini ◽

...

Keyword(s):

Ovarian Cancer ◽

Next Generation Sequencing ◽

Cancer Patients ◽

Genomic Rearrangements ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Large Genomic Rearrangements ◽

Hereditary Breast Ovarian Cancer ◽

Ngs Data ◽

Generation Sequencing

Background Genetic testing for BRCA1/2 germline mutations in hereditary breast/ovarian cancer patients requires screening for single nucleotide variants, small insertions/deletions and large genomic rearrangements (LGRs). These studies have long been run by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). The recent introduction of next-generation sequencing (NGS) platforms dramatically improved the speed and the efficiency of DNA testing for nucleotide variants, while the possibility to correctly detect LGRs by this mean is still debated. The purpose of this study was to establish whether and to which extent the development of an analytical algorithm could help us translating NGS sequencing via an Ion Torrent PGM platform into a tool suitable to identify LGRs in hereditary breast-ovarian cancer patients. Methods We first used NGS data of a group of three patients (training set), previously screened in our laboratory by conventional methods, to develop an algorithm for the calculation of the dosage quotient (DQ) to be compared with the Ion Reporter (IR) analysis. Then, we tested the optimized pipeline with a consecutive cohort of 85 uncharacterized probands (validation set) also subjected to MLPA analysis. Characterization of the breakpoints of three novel BRCA1 LGRs was obtained via long-range PCR and direct sequencing of the DNA products. Results In our cohort, the newly defined DQ-based algorithm detected 3/3 BRCA1 LGRs, demonstrating 100% sensitivity and 100% negative predictive value (NPV) (95% CI [87.6–99.9]) compared to 2/3 cases detected by IR (66.7% sensitivity and 98.2% NPV (95% CI [85.6–99.9])). Interestingly, DQ and IR shared 12 positive results, but exons deletion calls matched only in five cases, two of which confirmed by MLPA. The breakpoints of the 3 novel BRCA1 deletions, involving exons 16–17, 21–22 and 20, have been characterized. Conclusions Our study defined a DQ-based algorithm to identify BRCA1 LGRs using NGS data. Whether confirmed on larger data sets, this tool could guide the selection of samples to be subjected to MLPA analysis, leading to significant savings in time and money.

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Complex Characterization of Germline Large Genomic Rearrangements of the BRCA1 and BRCA2 Genes in High-Risk Breast Cancer Patients—Novel Variants from a Large National Center

International Journal of Molecular Sciences ◽

10.3390/ijms21134650 ◽

2020 ◽

Vol 21 (13) ◽

pp. 4650

Author(s):

Anikó Bozsik ◽

Tímea Pócza ◽

János Papp ◽

Tibor Vaszkó ◽

Henriett Butz ◽

...

Keyword(s):

Ovarian Cancer ◽

Cancer Patients ◽

Brca1 Mutation ◽

Transcript Level ◽

Genomic Rearrangements ◽

Breast Cancer Patients ◽

Brca1 And Brca2 ◽

Large Genomic Rearrangements ◽

Amplification Method

Large genomic rearrangements (LGRs) affecting one or more exons of BRCA1 and BRCA2 constitute a significant part of the mutation spectrum of these genes. Since 2004, the National Institute of Oncology, Hungary, has been involved in screening for LGRs of breast or ovarian cancer families enrolled for genetic testing. LGRs were detected by multiplex ligation probe amplification method, or next-generation sequencing. Where it was possible, transcript-level characterization of LGRs was performed. Phenotype data were collected and analyzed too. Altogether 28 different types of LGRs in 51 probands were detected. Sixteen LGRs were novel. Forty-nine cases were deletions or duplications in BRCA1 and two affected BRCA2. Rearrangements accounted for 10% of the BRCA1 mutations. Three exon copy gains, two complex rearrangements, and 23 exon losses were characterized by exact breakpoint determinations. The inferred mechanisms for LGR formation were mainly end-joining repairs utilizing short direct homologies. Comparing phenotype features of the LGR-carriers to that of the non-LGR BRCA1 mutation carriers, revealed no significant differences. Our study is the largest comprehensive report of LGRs of BRCA1/2 in familial breast and ovarian cancer patients in the Middle and Eastern European region. Our data add novel insights to genetic interpretation associated to the LGRs.

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