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Zhou H, He X, Zhao J, Mei Z, Zhang X, Yuan W, Dong H. A MALDI-TOF mass spectrometry-based method for detection of copy number variations in BRCA1 and BRCA2 genes. Front Mol Biosci 2024; 10:1301652. [PMID: 38274092 PMCID: PMC10808477 DOI: 10.3389/fmolb.2023.1301652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Background: Identifying germline mutations in BRCA1 and BRCA2 genes (BRCAs) would benefit the carriers in multiple aspects. In addition to single-nucleotide variations and small indels, copy number variations (CNVs) is also an indispensable component of identifiable mutations in BRCAs. A sensitive, rapid and throughput-flexible method to detect CNVs would be preferred to meet the rising clinical requirements for BRCAs testing. Methods: We developed a MALDI-TOF-MS-based method (MS assay) which included three steps: first, multiplex end-point PCR followed by a single base extension reaction; second, automated analyte transfer and data acquisition; third, data analysis. We applied MS assay to detect CNVs in BRCAs in 293 Chinese patients with ovarian or pancreatic cancer. All the samples were examined by targeted next-generation sequencing (TS) simultaneously. Samples were further cross-validated by multiplex ligation-dependent probe amplification (MLPA) if the results from MS assay and TS were inconsistent. Long range PCR was then applied to identify the exact breakpoints in BRCAs. Results: MS assay introduced highly multiplexed panels to detect CNVs of BRCAs semi-quantitatively. Simplified on-board data analysis was available for MS assay and no complex bioinformatics was needed. The turnaround time of MS assay was less than 8 hours with a hands-on time of only 40 min. Compared to TS, MS assay exhibited higher sensitivity (100% vs. 75%) and was more flexible in throughput, with the reagent cost per sample remaining constant no matter how many samples were examined per assay. A total of eight CNVs in BRCAs were detected from the 293 samples, and the molecular breakpoints were successfully identified in five samples through long-range PCR followed by Sanger sequencing. Conclusion: Our results suggested that MS assay might be an effective method in primary screening for CNVs in genes such as BRCAs, especially when short turnaround time and/or high sensitivity is a top priority.
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Affiliation(s)
- Hongjun Zhou
- Nanjing Shenyou Institute of Genome Research, Nanjing, China
| | - Xin He
- Agena Bioscience (Shanghai) Co., Ltd., Shanghai, China
| | - Jiadong Zhao
- Nanjing Shenyou Institute of Genome Research, Nanjing, China
| | - Zhu Mei
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiayan Zhang
- Nanjing Shenyou Institute of Genome Research, Nanjing, China
| | - Wen Yuan
- Nanjing Shenyou Institute of Genome Research, Nanjing, China
| | - Hui Dong
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Ng CCY, Lim S, Lim AH, Md Nasir ND, Zhang J, Rajasegaran V, Lee JY, Kok JST, Thike AA, Lim JX, Weng R, Yee S, Choudhury Y, Chan JY, Tan PH, Tan MH, Teh BT. A comprehensive next generation sequencing tissue assay for Asian-prevalent cancers—Analytical validation and performance evaluation with clinical samples. Front Mol Biosci 2022; 9:963243. [PMID: 36213130 PMCID: PMC9532579 DOI: 10.3389/fmolb.2022.963243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: A well-validated diagnostic assay with curated biomarkers complements clinicopathological factors to facilitate early diagnosis and ensure timely treatment delivery. This study focuses on an Asian-centric cancer diagnostic assay designed and thoroughly validated against commercially available standard references and a cohort of over 200 clinical specimens spanning 12 diverse Asian-centric cancer types. Methods: The assay uses hybrid-capture probes capable of profiling DNA aberrations from 572 cancer-related genes and 91 RNA fusion partners. The panel can detect clinically-tractable biomarkers such as microsatellite instability (MSI) and tumor mutation burden (TMB). Results: Analytical evaluation demonstrated 100% specificity and 99.9% sensitivity within a ≥5% VAF limit of detection (LoD) for SNV/Indels. RNA-based fusion features an LoD of ≥5 copies per nanogram input when evaluated against commercial references. Excellent linearity and concordance were observed when benchmarking against orthogonal methods in identifying MSI status, TMB scores and RNA fusions. Actionable genetic alterations were identified in 65% of the clinical samples. Conclusion: These results demonstrate a molecular diagnostic assay that accurately detects genomic alterations and complex biomarkers. The data also supports an excellent performance of this assay for making critical diagnoses and well-informed therapeutic decisions in Asian prevalent cancers.
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Affiliation(s)
- Cedric Chuan-Young Ng
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Sandy Lim
- Diagnostics Development Hub (DxD Hub), A National Platform Hosted by A*STAR, Singapore, Singapore
| | - Abner Herbert Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Nur Diyana Md Nasir
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Jingxian Zhang
- Diagnostics Development Hub (DxD Hub), A National Platform Hosted by A*STAR, Singapore, Singapore
| | - Vikneswari Rajasegaran
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Yi Lee
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Jessica Sook Ting Kok
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
| | - Aye Aye Thike
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | | | - Ruifen Weng
- Diagnostics Development Hub (DxD Hub), A National Platform Hosted by A*STAR, Singapore, Singapore
| | - Sidney Yee
- Diagnostics Development Hub (DxD Hub), A National Platform Hosted by A*STAR, Singapore, Singapore
| | | | - Jason Yongsheng Chan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Puay Hoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Min-Han Tan
- Lucence Diagnostics Pte Ltd, Singapore, Singapore
- *Correspondence: Bin Tean Teh, ; Min-Han Tan,
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore, Singapore
- *Correspondence: Bin Tean Teh, ; Min-Han Tan,
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Hua D, Tian Q, Wang X, Bei T, Cui L, Zhang B, Bao C, Bai Y, Zhao X, Yuan P. Next-generation sequencing based detection of BRCA1 and BRCA2 large genomic rearrangements in Chinese cancer patients. Front Oncol 2022; 12:898916. [PMID: 36147908 PMCID: PMC9487528 DOI: 10.3389/fonc.2022.898916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
BRCA1/2 mutation is a biomarker for guiding multiple solid tumor treatment. However, the prevalence of BRCA1/2 large genomic rearrangements (LGRs) in Chinese cancer patients has not been well revealed partially due to technical difficulties in LGR detection. This study utilized next-generation sequencing (NGS) to analyze the BRCA1/2 mutation profile, including LGR, in 56126 Chinese cancer patients. We also reported that two ovarian and breast cancer patients with NGS-determined BRCA1/2 LGR benefited from PARP inhibitors (PARPi). DNA sequencing identified BRCA1/2 variants (including LGR, pathogenic and likely-pathogenic variants) in 2108 individuals. Seventy patients were discovered to harbor germline LGRs in BRCA1 and 14 had germline LGRs in BRCA2. Among the LGRs detected, exon 1-2 deletion was the predominant LGR (14/70) in BRCA1, and exon 22-24 deletion was the most frequent LGR (3/14) in BRCA2. Notably, the BRCA1 exon 7 deletion was a novel LGR and was identified in six patients, suggesting a specific LGR in Chinese cancer patients. The prevalence analysis of BRCA1 and BRCA2 LGRs across multiple cancers revealed that BRCA1 LGR more frequently occurred in ovarian cancer (1.31%, 33/2526), and BRCA2 LGR was more commonly seen in cholangiocarcinoma (0.47%, 2/425). Two ovarian and breast cancer patients with BRCA1/2 LGR benefited from PARPi therapy. This is the first study to reveal the BRCA1/2 LGR profile of a Chinese pan-cancer cohort by using an NGS-based assay. Two breast and ovarian cancer patients harboring NGS-determined BRCA1/2 LGR benefited from PARPi, indicating that NGS-based detection of BRCA1/2 LGR has the potential to guide PARPi treatment.
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Affiliation(s)
- Dingchao Hua
- Department of Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Qiuhong Tian
- Department of Medical Oncology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xue Wang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Bei
- Department of Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Lina Cui
- Department of Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Bei Zhang
- Department of Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Celimuge Bao
- Department of Medical Affairs, 3D Medicines Inc., Shanghai, China
| | - Yuezong Bai
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaochen Zhao
- Department of Medical Affairs, 3D Medicines Inc., Shanghai, China
- *Correspondence: Xiaochen Zhao, ; Peng Yuan,
| | - Peng Yuan
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Xiaochen Zhao, ; Peng Yuan,
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Pinheiro M, Peixoto A, Santos C, Escudeiro C, Bizarro S, Pinto P, Santos R, Pinto C, Guerra J, Silva J, Teixeira MR. Pathogenicity reclassification of two BRCA1/BRCA2 exonic duplications after identification of genomic breakpoints and tandem orientation. Cancer Genet 2020; 248-249:18-24. [PMID: 32971473 DOI: 10.1016/j.cancergen.2020.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 07/30/2020] [Accepted: 09/07/2020] [Indexed: 10/23/2022]
Abstract
The genomic consequence and clinical interpretation of large duplications are difficult to infer without determining the location and orientation of the duplicated sequence. We aimed to characterize two intragenic duplications detected in two hereditary breast and ovarian cancer syndrome (HBOC) families, namely BRCA1 exon 4 to 6 and BRCA2 exon 17 to 18, previously detected by multiplex ligation probe amplification and initially classified as variants of unknown significance. Using long range PCR, with duplication-specific primers, we were able to ascertain the genomic breakpoints and observed that the two rearrangements occurred in tandem and in direct orientation. The BRCA1 c.134+440_441+870dup and BRCA2 c.7806-2083_8332-1512dup duplications here identified are predicted to cause frameshifts that create a premature stop codon and were reclassified as pathogenic. Furthermore, both families present phenotypic traits typical of HBOC syndrome. We also observed that the genomic breakpoints of these two duplications occurred within highly homologous Alu elements. Concluding, we characterized two in tandem BRCA1 and BRCA2 duplications that likely occurred by Alu-mediated homologous recombination, allowing identification of the underlying cause of the HBOC syndrome in these families.
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Affiliation(s)
- Manuela Pinheiro
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Catarina Santos
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Carla Escudeiro
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Susana Bizarro
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Pedro Pinto
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Rui Santos
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Carla Pinto
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Joana Guerra
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - João Silva
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute of Porto, Rua Dr. António Bernardino Almeida, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Largo Prof. Abel Salazar, Porto 4099-003, Portugal.
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Qin Z, Kuok CN, Dong H, Jiang L, Zhang L, Guo M, Leong HK, Wang L, Meng G, Wang SM. Can population BRCA screening be applied in non-Ashkenazi Jewish populations? Experience in Macau population. J Med Genet 2020; 58:587-591. [DOI: 10.1136/jmedgenet-2020-107181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022]
Abstract
BackgroundPathogenic mutation in BRCA genes causes high cancer risk. Identifying the mutation carriers plays key roles in preventing BRCA mutation-related cancer. Population screening has demonstrated its power for comprehensive identification of the mutation carriers. However, it is only recommended for the Ashkenazi Jewish population with high prevalence of three founder mutations, but not for non-Ashkenazi Jewish populations as the cost-effectiveness could be too low due to their lower mutation prevalence and lack of founder mutation. Population screening would not benefit the majority of the human population for BRCA mutation-related cancer prevention.MethodsWe used population BRCA screening in 6000 residents, 1% of the Macau population, an ethnic Chinese population with unique genetic, linguistic and cultural features, and its BRCA mutation has not been analysed before.ResultsWe called BRCA variants, identified 18 carriers with 14 pathogenic mutations and determined the prevalence of 0.29% in the population (95% CI 0.15% to 0.42%). We compared the testing cost between the Ashkenazi Jewish population, the Sephardi Jewish population and the Macau population, and observed only a few fold differences.ConclusionOur study shows that testing cost is not the most important factor in considering population BRCA screening, at least for the populations in the developed countries/regions, regardless of the status of mutation prevalence and founder mutation.
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Cao WM, Zheng YB, Gao Y, Ding XW, Sun Y, Huang Y, Lou CJ, Pan ZW, Peng G, Wang XJ. Comprehensive mutation detection of BRCA1/2 genes reveals large genomic rearrangements contribute to hereditary breast and ovarian cancer in Chinese women. BMC Cancer 2019; 19:551. [PMID: 31174498 PMCID: PMC6555923 DOI: 10.1186/s12885-019-5765-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 05/29/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mutated BRCA1/2 genes are associated with hereditary breast and ovarian cancer (HBOC). So far most of the identified BRCA1/2 pathogenic variants are single nucleotide variants (SNVs) or insertions/deletions (Indels). However, large genomic rearrangements (LGRs) such as copy number variants (CNVs) are also playing an important role in HBOC predisposition. Their frequency and spectrum have been well studied in western populations but remain largely unknown for Chinese population. METHODS Peripheral blood samples were collected from 218 unrelated familial breast and/or ovarian cancer (FBOC) patients living in Eastern China. PCR-based Sanger sequencing and panel-based next-generation sequencing (NGS) were performed to detect pathogenic SNVs and Indels in BRCA1/2 genes. For the patients lacking small pathogenic variants, multiplex ligation dependent probe amplification (MLPA) assay was conducted to screen for LGRs. RESULTS In total, we identified 44 samples (20.1%) carrying small pathogenic variants (26 in BRCA1 and 18 in BRCA2, respectively). Among the rest of 174 samples, five were found carrying novel deleterious LGRs in BRCA1 which are exon5-7dup (1 patient), exon13-14dup (2 patients), and exon1-22del (2 patients). No LGR was found in BRCA2. Overall, LGRs accounted for 16.1% (5/31) of BRCA1 pathogenic variants, and were detected in 2.3% (5/218) of all FBOC patients. , CONCLUSIONS LGR variants in BRCA1 gene play a significant role in Chinese HBOC patients. MLPA or other similar LGR-detecting methods should be recommended along with nucleotide sequencing as the initial screening approach for Chinese HBOC women.
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Affiliation(s)
- Wen-Ming Cao
- Department of Medical Oncology, Zhejiang Cancer Hospital, 1 Banshan East Road, Hangzhou, 310022, China
| | - Ya-Bing Zheng
- Department of Medical Oncology, Zhejiang Cancer Hospital, 1 Banshan East Road, Hangzhou, 310022, China
| | - Yun Gao
- Institute of Cancer Research, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Xiao-Wen Ding
- Department of Breast Cancer Surgery, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Yan Sun
- Department of Medical Oncology, Zhejiang Cancer Hospital, 1 Banshan East Road, Hangzhou, 310022, China
| | - Yuan Huang
- Department of Medical Oncology, Zhejiang Cancer Hospital, 1 Banshan East Road, Hangzhou, 310022, China
| | - Cai-Jin Lou
- Department of Medical Oncology, Zhejiang Cancer Hospital, 1 Banshan East Road, Hangzhou, 310022, China
| | - Zhi-Wen Pan
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Guang Peng
- Department of Clinical Cancer Prevention, the University of Texas, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiao-Jia Wang
- Department of Medical Oncology, Zhejiang Cancer Hospital, 1 Banshan East Road, Hangzhou, 310022, China.
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Identification and Characterization of a New BRCA2 Rearrangement in an Italian Family with Hereditary Breast and Ovarian Cancer Syndrome. Mol Diagn Ther 2018. [PMID: 28620890 DOI: 10.1007/s40291-017-0288-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Many studies document the involvement of BRCA1/2 gene rearrangements in genetic predisposition to breast and ovarian cancer. Large genomic rearrangements (LGRs) of BRCA1 account for 0-27% of all disease-causing mutations in various populations, while LGRs in BRCA2 are rarer. Here, we describe a novel BRCA2 LGR, involving the duplication of exons 4-26, in an Italian family with hereditary breast and ovarian cancer (HBOC) syndrome. OBJECTIVE Our purpose was to provide an effective characterization of this variant using a combination of different methods able to establish the exact breakpoints of the duplication. METHODS A multiplex amplicon quantification (MAQ) assay was used as the primary screening method in the detection of LGRs. Array comparative genomic hybridization (CGH), reverse transcriptase polymerase chain reaction (RT-PCR) and long-range PCR were used for the careful characterization of the rearrangement and breakpoint regions. The Repeat Masker program was employed to identify Alu sequences at breakpoint junctions. RESULTS Array CGH and long-range PCR strategies revealed that the BRCA2 exons 4-26 duplication (g.12016_87170dup) involved exactly 75,154 bp nucleotides between intron 3 and intron 26 of the gene. Given that no Alu repeats were found at the junction sites, we support the hypothesis that the new duplication could be the result of a microhomology-mediated event (MH) involving very short homologous sequences at an upstream breakpoint. DISCUSSION LGR investigation is mandatory in BRCA1/2 routine testing in order to provide a complete result for a targeted therapeutic decision. Nevertheless, the characterization and classification of novel BRCA1/2 variants represents a crucial step in the support of genetic counselling. Our results, including a comprehensive co-segregation analysis, indicate that the novel duplication identifed has a pathogenic role and would be considered a causing-disease variant in genetic and oncologic counselling.
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Schmidt AY, Hansen TVO, Ahlborn LB, Jønson L, Yde CW, Nielsen FC. Next-Generation Sequencing-Based Detection of Germline Copy Number Variations in BRCA1/BRCA2: Validation of a One-Step Diagnostic Workflow. J Mol Diagn 2017; 19:809-816. [PMID: 28822785 DOI: 10.1016/j.jmoldx.2017.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/23/2017] [Accepted: 07/12/2017] [Indexed: 12/19/2022] Open
Abstract
Genetic testing of BRCA1/2 includes screening for single nucleotide variants and small insertions/deletions and for larger copy number variations (CNVs), primarily by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). With the advent of next-generation sequencing (NGS), it has become feasible to provide CNV information and sequence data using a single platform. We report the use of NGS gene panel sequencing on the Illumina MiSeq platform and JSI SeqPilot SeqNext software to call germline CNVs in BRCA1 and BRCA2. For validation 18 different BRCA1/BRCA2 CNVs previously identified by MLPA in 48 Danish breast and/or ovarian cancer families were analyzed. Moreover, 120 patient samples previously determined as negative for BRCA1/BRCA2 CNVs by MLPA were included in the analysis. Comparison of the NGS data with the data from MLPA revealed that the sensitivity was 100%, whereas the specificity was 95%. Taken together, this study validates a one-step bioinformatics work-flow to call germline BRCA1/2 CNVs using data obtained by NGS of a breast cancer gene panel. The work-flow represents a robust and easy-to-use method for full BRCA1/2 screening, which can be easily implemented in routine diagnostic testing and adapted to genes other than BRCA1/2.
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Affiliation(s)
- Ane Y Schmidt
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lise B Ahlborn
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lars Jønson
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christina W Yde
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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9
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Buleje J, Guevara-Fujita M, Acosta O, Huaman FDP, Danos P, Murillo A, Pinto JA, Araujo JM, Aguilar A, Ponce J, Vigil C, Castaneda C, Calderon G, Gomez HL, Fujita R. Mutational analysis of BRCA1 and BRCA2 genes in Peruvian families with hereditary breast and ovarian cancer. Mol Genet Genomic Med 2017; 5:481-494. [PMID: 28944232 PMCID: PMC5606899 DOI: 10.1002/mgg3.301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 12/21/2022] Open
Abstract
Background Breast cancer is one of the most prevalent malignancies in the world. In Peru, breast cancer is the second cause of death among women. Five to ten percent of patients present a high genetic predisposition due to BRCA1 and BRCA2 germline mutations. Methods We performed a comprehensive analysis of BRCA1 and BRCA2 genes by Sanger sequencing and multiplex ligation‐dependent probe amplification (MLPA) to detect large rearrangements in patients from 18 families, which met the criteria for hereditary breast cancer. Results In this series, we found four pathogenic mutations, three previously reported (BRCA1: c.302‐1G>C and c.815_824dup10; BRCA2: c.5946delT) and a duplication of adenines in exon 15 in BRCA1 gene (c.4647_4648dupAA, ClinVar SCV000256598.1). We also found two exonic and four intronic variants of unknown significance and 28 polymorphic variants. Conclusion This is the first report to determine the spectrum of mutations in the BRCA1/BRCA2 genes in Peruvian families selected by clinical and genetic criteria. The alteration rate in BRCA1/BRCA2 with proven pathogenic mutation was 22.2% (4 out 18) and this finding could be influenced by the reduced sample size or clinical criteria. In addition, we found three known BRCA1/BRCA2 mutations and a BRCA1 c.4647_4648dupAA as a novel pathogenic mutation.
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Affiliation(s)
- Jose Buleje
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Maria Guevara-Fujita
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Oscar Acosta
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Francia D P Huaman
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Pierina Danos
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Alexis Murillo
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
| | - Joseph A Pinto
- Unidad de Investigación Básica y TraslacionalOncosalud-AUNALimaPerú
| | | | - Alfredo Aguilar
- Unidad de Investigación Básica y TraslacionalOncosalud-AUNALimaPerú
| | | | | | | | | | | | - Ricardo Fujita
- Centro de Genética y Biología MolecularFacultad de Medicina HumanaUniversidad de San Martín de PorresLimaPerú
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10
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McVeigh TP, Cody N, Carroll C, Duff M, Farrell M, Bradley L, Gallagher D, McDevitt T, Green AJ. Recurrent large genomic rearrangements in BRCA1 and BRCA2 in an Irish case series. Cancer Genet 2017; 214-215:1-8. [PMID: 28595730 DOI: 10.1016/j.cancergen.2017.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/24/2017] [Accepted: 02/25/2017] [Indexed: 12/12/2022]
Abstract
Mutations in BRCA1 and BRCA2 confer a highly increased risk of cancers, mainly of the breast and ovary. Most variants are point mutations or small insertions/deletions detectable by Sanger sequencing. Large genomic rearrangements, including deletions/duplications of multiple exons, are not routinely detectable by Sanger sequencing, but can be reliably identified by Multiplex Ligation-dependent Probe Amplification (MLPA), and account for 5-17% mutations in different populations. Comprehensive mutation testing using these two methods has been facilitated via our centre since 2005. The aim of this study was to investigate the incidence of and phenotype associated with large genomic rearrangements in BRCA1 and BRCA2 in an Irish cohort. An observational cohort study was undertaken. Patients with large genomic rearrangements in BRCA1/BRCA2 were identified from a prospectively maintained database of MLPA test results. Phenotypic and genotypic data were retrieved by chart review. Large genomic rearrangements in BRCA1 were identified in 49 families; and in BRCA2 in 7 families, representing ~11% of mutations in BRCA1/BRCA2 in Ireland. The most common large genomic rearrangement in BRCA1 was deletion of exons 1-23 (11 families, 7 from Co. Galway). Other common mutations included deletions of exon 3 (8 families) and exons 1-2 (6 families). Deletion of exons 19-20 in BRCA2 represented the familial mutation in five families, all from East Ireland (Wexford/Wicklow/Dublin). It is evident that a significant proportion of highly penetrant pathogenic variants in BRCA1 and BRCA2 will be missed if testing is limited to PCR-based Sanger sequencing alone. Screening for large genomic rearrangements in BRCA1 and BRCA2 in the routine diagnostic workflow is critical to avoid false negative results.
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Affiliation(s)
- Terri P McVeigh
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland.
| | - Nuala Cody
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Cliona Carroll
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Marie Duff
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Michael Farrell
- Cancer Genetics Service, Mater Misericordiae University Hospital, Ireland
| | - Lisa Bradley
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - David Gallagher
- Cancer Genetics Service, Mater Misericordiae University Hospital, Ireland; Cancer Genetics Service, St James' University Hospital, UK
| | - Trudi McDevitt
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Andrew J Green
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
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Shi T, Wang P, Xie C, Yin S, Shi D, Wei C, Tang W, Jiang R, Cheng X, Wei Q, Wang Q, Zang R. BRCA1andBRCA2mutations in ovarian cancer patients from China: ethnic-related mutations inBRCA1associated with an increased risk of ovarian cancer. Int J Cancer 2017; 140:2051-2059. [PMID: 28176296 DOI: 10.1002/ijc.30633] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/19/2017] [Accepted: 01/24/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Tingyan Shi
- Ovarian Cancer Program; Division of Gynecologic Oncology, Department of Gynecology & Obstetrics, Zhongshan hospital, Fudan University; Shanghai 200032 China
| | - Pan Wang
- Ovarian Cancer Program; Division of Gynecologic Oncology, Department of Gynecology & Obstetrics, Zhongshan hospital, Fudan University; Shanghai 200032 China
| | - Caixia Xie
- Shanghai Topgen Bio-Pharm Co, Ltd; Shanghai China
| | - Sheng Yin
- Ovarian Cancer Program; Division of Gynecologic Oncology, Department of Gynecology & Obstetrics, Zhongshan hospital, Fudan University; Shanghai 200032 China
| | - Di Shi
- Ovarian Cancer Program; Division of Gynecologic Oncology, Department of Gynecology & Obstetrics, Zhongshan hospital, Fudan University; Shanghai 200032 China
| | | | - Wenbin Tang
- Ovarian Cancer Program; Division of Gynecologic Oncology, Department of Gynecology & Obstetrics, Zhongshan hospital, Fudan University; Shanghai 200032 China
| | - Rong Jiang
- Ovarian Cancer Program; Division of Gynecologic Oncology, Department of Gynecology & Obstetrics, Zhongshan hospital, Fudan University; Shanghai 200032 China
| | - Xi Cheng
- Gynecologic Oncology, Fudan University Shanghai Cancer Center; Shanghai China
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center; Shanghai China
- Duke Cancer Institute, Duke University Medical Center; Durham NC
| | - Qing Wang
- Plateforme de génomique des cancers; Centre Léon Bérard, Laboratoire de la génétique constitutionnelle HCL-CLB; Lyon France
| | - Rongyu Zang
- Ovarian Cancer Program; Division of Gynecologic Oncology, Department of Gynecology & Obstetrics, Zhongshan hospital, Fudan University; Shanghai 200032 China
- Gynecologic Oncology, Fudan University Shanghai Cancer Center; Shanghai China
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12
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Characteristics of BRCA1/2 mutations carriers including large genomic rearrangements in high risk breast cancer patients. Breast Cancer Res Treat 2017; 163:139-150. [PMID: 28205045 PMCID: PMC5387004 DOI: 10.1007/s10549-017-4142-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/06/2017] [Indexed: 01/04/2023]
Abstract
PURPOSE We investigated the prevalence of BRCA1/2 small mutations and large genomic rearrangements in high risk breast cancer patients who attended a genetic counseling clinic. METHODS In total 478 patients were assessed for BRCA1/2 mutations by direct sequencing, of whom, 306 were identified as non-carriers of BRCA1/2 mutation and assessed for large rearrangement mutations by multiplex ligation-dependent probe amplification. Family history and clinicopathological characteristics of patients were evaluated. RESULTS Sixty-three mutation carriers (13.2%) were identified with BRCA1 mutations (6.3%) and BRCA2 mutations (6.9%), respectively. Mutation frequency was affected by familial and personal factors. Breast cancer patients with family history of breast and ovarian cancer showed the highest prevalence of BRCA1/2 mutations (67%), and triple-negative breast cancer (TNBC) patients showed high BRCA1 mutation prevalence (25%). The three probands of BRCA1 deletion (1%) represented both familial risk and personal or clinicopathological risk factors as two with TNBC and one with bilateral ovarian cancer. DISCUSSION This is the largest study assessing large genomic rearrangement prevalence in Korea and BRCA1 deletion frequency was low as 1% in patients without BRCA1/2 small mutations. For clinical utility of large genomic rearrangement testing needs further study.
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Riahi A, Chabouni-Bouhamed H, Kharrat M. Prevalence of BRCA1 and BRCA2 large genomic rearrangements in Tunisian high risk breast/ovarian cancer families: Implications for genetic testing. Cancer Genet 2016; 210:22-27. [PMID: 28212807 DOI: 10.1016/j.cancergen.2016.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 08/23/2016] [Accepted: 11/14/2016] [Indexed: 12/11/2022]
Abstract
Germline mutations in the BRCA tumor suppressor genes account for a substantial proportion of hereditary breast/ovarian cancer. However, this contribution is lower than expected. This underestimation can partly be explained by the BRCA alterations missed by using Sanger sequencing methods. Thus, large genomic rearrangements (LGRs) in BRCA1 and BRCA2 are responsible for 4-28% of all inherited BRCA mutations. In this study, Multiplex ligation-dependent probe amplification (MLPA) assay was used for detection of large rearrangements of BRCA1 and BRCA2 genes in 36 unrelated high-risk breast/ovarian cancer patients negative for BRCA1/2 point mutations. MLPA assay for all exons of both genes and for 1100delC variant of CHEK2 gene were performed. Positive MLPA results were confirmed by real-time quantitative PCR (qPCR). Two different rearrangements in the BRCA1 gene were identified consisting of exon 5 deletion and exon 20 duplication. MLPA analysis did not reveal any large genomic rearrangements in BRCA2 gene. Overall BRCA1/2 LGRs prevalence among high-risk Tunisian patients was 5.5%. Quantitative real-time PCR confirmed MPLA findings. Our results suggest the usefulness of screening for LGRs in BRCA genes in the Tunisian population. To avoid false-negative results, we suggest that MLPA should be used in genetic testing programs. These results are important for guidance counseling and clinical management of Tunisian high-risk patients.
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Affiliation(s)
- Aouatef Riahi
- Faculté de Médecine de Tunis, Laboratoire Génétique Humaine, University Tunis El manar, Tunis, Tunisia.
| | - Habiba Chabouni-Bouhamed
- Faculté de Médecine de Tunis, Laboratoire Génétique Humaine, University Tunis El manar, Tunis, Tunisia
| | - Maher Kharrat
- Faculté de Médecine de Tunis, Laboratoire Génétique Humaine, University Tunis El manar, Tunis, Tunisia
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14
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Contribution of BRCA1 large genomic rearrangements to early-onset and familial breast/ovarian cancer in Pakistan. Breast Cancer Res Treat 2016; 161:191-201. [PMID: 27826754 DOI: 10.1007/s10549-016-4044-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/01/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Germline mutations in BRCA1 and BRCA2 (BRCA1/2) account for the majority of hereditary breast and/or ovarian cancers. Pakistan has one of the highest rates of breast cancer incidence in Asia, where BRCA1/2 small-range mutations account for 17% of early-onset and familial breast/ovarian cancer patients. We report the first study from Pakistan evaluating the prevalence of BRCA1/2 large genomic rearrangements (LGRs) in breast and/or ovarian cancer patients who do not harbor small-range BRCA1/2 mutations. MATERIALS AND METHODS Both BRCA1/2 genes were comprehensively screened for LGRs using multiplex ligation-dependent probe amplification in 120 BRCA1/2 small-range mutations negative early-onset or familial breast/ovarian cancer patients from Pakistan (Group 1). The breakpoints were characterized by long-range PCR- and DNA-sequencing analyses. An additional cohort of 445 BRCA1/2 negative high-risk patients (Group 2) was analyzed for the presence of LGRs identified in Group 1. RESULTS Three different BRCA1 LGRs were identified in Group 1 (4/120; 3.3%), two of these were novel. Exon 1-2 deletion was observed in two unrelated patients: an early-onset breast cancer patient and another bilateral breast cancer patient from a hereditary breast cancer (HBC) family. Novel exon 20-21 deletion was detected in a 29-year-old breast cancer patient from a HBC family. Another novel exon 21-24 deletion was identified in a breast-ovarian cancer patient from a hereditary breast and ovarian cancer family. The breakpoints of all deletions were characterized. Screening of the 445 patients in Group 2 for the three LGRs revealed ten additional patients harboring exon 1-2 deletion or exon 21-24 deletion (10/445; 2.2%). No BRCA2 LGRs were identified. CONCLUSIONS LGRs in BRCA1 are found with a considerable frequency in Pakistani breast/ovarian cancer cases. Our findings suggest that BRCA1 exons 1-2 deletion and exons 21-24 deletion should be included in the recurrent BRCA1/2 mutations panel for genetic testing of high-risk Pakistani breast/ovarian cancer patients.
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15
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Sedghi M, Esfandiari E, Fazel-Najafabadi E, Salehi M, Salavaty A, Fattahpour S, Dehghani L, Nouri N, Mokarian F. Genomic rearrangement screening of the BRCA1 from seventy Iranian high-risk breast cancer families. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2016; 21:95. [PMID: 28163741 PMCID: PMC5244654 DOI: 10.4103/1735-1995.193167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/01/2016] [Accepted: 07/01/2016] [Indexed: 01/23/2023]
Abstract
Background: The second leading cause of cancer deaths in women is breast cancer. Germline mutations in susceptibility breast cancer gene BRCA1 increase the lifetime risk of breast cancer. Eighty-one large genomic rearrangements (LGRs) have been reported up to date in BRCA1 gene, and evaluation of these rearrangements helps with precise risk assessment in high-risk individuals. In this study, we have investigated LGRs in BRCA1 among Iranian high-risk breast cancer families. Materials and Methods: Seventy patients with breast cancer who were identified negative for point mutations or small deletions/insertions of BRCA1 gene were selected. Deletions and duplications of BRCA1 gene were evaluated using multiplex ligation-dependent probe amplification (MLPA). Results: Two deletions, deletion of exons 1A/1B-2 and exon 24, were detected in two patients with breast cancer. The former alteration was found in a woman with a strong family history of breast cancer while the latter one was detected in a woman with early onset of breast cancer. Conclusion: Although our data confirm that LGRs in BRCA1 comprise a relatively small proportion of mutations in hereditary breast cancer in the Iranian population, MLPA analysis might be considered for screening of LGRs in high-risk individuals. It is worth to note that our results are consistent with previous studies in various Asian and European countries.
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Affiliation(s)
- Maryam Sedghi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Esfandiari
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Esmat Fazel-Najafabadi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Division of Genetics and Molecular Biology, Medical School, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abbas Salavaty
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shirin Fattahpour
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Leila Dehghani
- Department of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Isfahan Neurosciences Research Center, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Nayerossadat Nouri
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fariborz Mokarian
- Department of Oncology, Isfahan University of Medical Sciences, Isfahan, Iran
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Abstract
Increased demand for BRCA testing is placing pressures on diagnostic laboratories to raise their mutation screening capacity and handle the challenges associated with classifying BRCA sequence variants for clinical significance, for example interpretation of pathogenic mutations or variants of unknown significance, accurate determination of large genomic rearrangements and detection of somatic mutations in DNA extracted from formalin-fixed, paraffin-embedded tumour samples. Many diagnostic laboratories are adopting next-generation sequencing (NGS) technology to increase their screening capacity and reduce processing time and unit costs. However, migration to NGS introduces complexities arising from choice of components of the BRCA testing workflow, such as NGS platform, enrichment method and bioinformatics analysis process. An efficient, cost-effective accurate mutation detection strategy and a standardised, systematic approach to the reporting of BRCA test results is imperative for diagnostic laboratories. This review covers the challenges of BRCA testing from the perspective of a diagnostics laboratory.
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Affiliation(s)
- Andrew J Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
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17
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Cao WM, Gao Y, Yang HJ, Xie SN, Ding XW, Pan ZW, Ye WW, Wang XJ. Novel germline mutations and unclassified variants of BRCA1 and BRCA2 genes in Chinese women with familial breast/ovarian cancer. BMC Cancer 2016; 16:64. [PMID: 26852015 PMCID: PMC4744435 DOI: 10.1186/s12885-016-2107-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 02/01/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Germline mutations in the BRCA1 and BRCA2 genes greatly increase a woman's risk of developing breast and/or ovarian cancer. The prevalence and distribution of such mutations differ across races/ethnicities. Several studies have investigated Chinese women with high-risk breast cancer, but the full spectrum of the mutations in these two genes remains unclear. METHODS In this study, 133 unrelated Chinese women with familial breast/ovarian cancer living in Zhejiang, eastern China, were enrolled between the years 2008 and 2014. The complete coding regions and exon-intron boundaries of BRCA1 and BRCA2 were screened by PCR-sequencing assay. Haplotype analysis was performed to confirm BRCA1 and BRCA2 founder mutations. In silico predictions were performed to identify the non-synonymous amino acid changes that were likely to disrupt the functions of BRCA1 and BRCA2. RESULTS A total of 23 deleterious mutations were detected in the two genes in 31 familial breast/ovarian cancer patients with a total mutation frequency of 23.3% (31/133). The highest frequency of 50.0% (8/16) was found in breast cancer patients with a history of ovarian cancer. The frequencies of BRCA1 and BRCA2 mutations were 13.5 % (18/133) and 9.8% (13/133), respectively. We identified five novel deleterious mutations (c.3295delC, c.3780_3781delAG, c.4063_4066delAATC, c.5161 > T and c.5173insA) in BRCA1 and seven (c.1-40delGA, c.4487delC, c.469_473delAAGTC, c.5495delC, c.6141T > A, c.6359C > G and c.7588C > T) in BRCA2, which accounted for 52.2% (12/23) of the total mutations. Six recurrent mutations were found, including four (c.3780_3781delAG, c.5154G > A, c.5468-1del8 and c.5470_5477del8) in BRCA1 and two (c.3109C > T and c.5682C > G) in BRCA2. Two recurrent BRCA1 mutations (c.5154G > A and c.5468-1del8) were identified as putative founder mutations. We also found 11 unclassified variants, and nine of these are novel. The possibility was that each of the non-synonymous amino acid changes would disrupt the function of BRCA1 and BRCA2 varied according to the different algorithms used. CONCLUSIONS BRCA1 and BRCA2 mutations accounted for a considerable proportion of hereditary breast/ovarian cancer patients from eastern China and the spectrum of the mutations of these two genes exhibited some unique features. The two BRCA1 putative founder mutations may provide a cost-effective option to screen Chinese population, while founder effects of the two mutations should be investigated in a lager sample size of patients.
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Affiliation(s)
- Wen-Ming Cao
- />Department of Medical Oncology, Zhejiang Cancer Hospital, 38 Guangji Road, Hangzhou, 310022 China
| | - Yun Gao
- />Institute of Cancer Research, Zhejiang Cancer Hospital, Hangzhou, 310022 China
| | - Hong-Jian Yang
- />Department of Breast Cancer Surgery, Zhejiang Cancer Hospital, Hangzhou, 310022 China
| | - Shang-Nao Xie
- />Department of Breast Cancer Surgery, Zhejiang Cancer Hospital, Hangzhou, 310022 China
| | - Xiao-Wen Ding
- />Department of Breast Cancer Surgery, Zhejiang Cancer Hospital, Hangzhou, 310022 China
| | - Zhi-Wen Pan
- />Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou, 310022 China
| | - Wei-Wu Ye
- />Department of Medical Oncology, Zhejiang Cancer Hospital, 38 Guangji Road, Hangzhou, 310022 China
| | - Xiao-Jia Wang
- />Department of Medical Oncology, Zhejiang Cancer Hospital, 38 Guangji Road, Hangzhou, 310022 China
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18
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Kwong A, Shin VY, Ho JCW, Kang E, Nakamura S, Teo SH, Lee ASG, Sng JH, Ginsburg OM, Kurian AW, Weitzel JN, Siu MT, Law FBF, Chan TL, Narod SA, Ford JM, Ma ESK, Kim SW. Comprehensive spectrum of BRCA1 and BRCA2 deleterious mutations in breast cancer in Asian countries. J Med Genet 2015; 53:15-23. [PMID: 26187060 DOI: 10.1136/jmedgenet-2015-103132] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/02/2015] [Indexed: 12/20/2022]
Abstract
Approximately 5%-10% of breast cancers are due to genetic predisposition caused by germline mutations; the most commonly tested genes are BRCA1 and BRCA2 mutations. Some mutations are unique to one family and others are recurrent; the spectrum of BRCA1/BRCA2 mutations varies depending on the geographical origins, populations or ethnic groups. In this review, we compiled data from 11 participating Asian countries (Bangladesh, Mainland China, Hong Kong SAR, Indonesia, Japan, Korea, Malaysia, Philippines, Singapore, Thailand and Vietnam), and from ethnic Asians residing in Canada and the USA. We have additionally conducted a literature review to include other Asian countries mainly in Central and Western Asia. We present the current pathogenic mutation spectrum of BRCA1/BRCA2 genes in patients with breast cancer in various Asian populations. Understanding BRCA1/BRCA2 mutations in Asians will help provide better risk assessment and clinical management of breast cancer.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, Hong Kong Departments of Medicine (Oncology) and Genetics, Stanford University School of Medicine, Stanford, California, USA Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong, Hong Kong
| | - Vivian Y Shin
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - John C W Ho
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, Hong Kong
| | - Eunyoung Kang
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Seigo Nakamura
- Department of Surgery, Division of Breast Surgical Oncology, Showa University School of Medicine, Tokyo, Japan
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Selangor, Malaysia Faculty of Medicine, University Malaya Cancer Research Institute, University Malaya, Subang Jaya, Malaysia
| | - Ann S G Lee
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore Office of Clinical & Academic Faculty Affairs, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Jen-Hwei Sng
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ophira M Ginsburg
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Allison W Kurian
- Departments of Medicine (Oncology) and Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jeffrey N Weitzel
- Division of Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, California, USA
| | - Man-Ting Siu
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Fian B F Law
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, Hong Kong Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, Hong Kong
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, Hong Kong Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, Hong Kong
| | - Steven A Narod
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - James M Ford
- Departments of Medicine (Oncology) and Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, Hong Kong Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, Hong Kong
| | - Sung-Won Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
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19
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Cho JY, Cho DY, Ahn SH, Choi SY, Shin I, Park HG, Lee JW, Kim HJ, Yu JH, Ko BS, Ku BK, Son BH. Large genomic rearrangement of BRCA1 and BRCA2 genes in familial breast cancer patients in Korea. Fam Cancer 2015; 13:205-11. [PMID: 24566764 DOI: 10.1007/s10689-014-9704-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We screened large genomic rearrangements of the BRCA1 and BRCA2 genes in Korean, familial breast cancer patients. Multiplex ligation-dependent probe amplification assay was used to identify BRCA1 and BRCA2 genomic rearrangements in 226 Korean familial breast cancer patients with risk factors for BRCA1 and BRCA2 mutations, who previously tested negative for point mutations in the two genes. We identified only one large deletion (c.4186-1593_4676-1465del) in BRCA1. No large rearrangements were found in BRCA2. Our result indicates that large genomic rearrangement in the BRCA1 and BRCA2 genes does not seem like a major determinant of breast cancer susceptibility in the Korean population. A large-scale study needs to validate our result in Korea.
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Affiliation(s)
- Ja Young Cho
- Division of Breast and Endocrine Surgery, Department of Surgery College of Medicine, University of Ulsan, Asan Medical Center, 388-1 Pungnap-dong, Songpa-gu, Seoul, 138-736, Korea
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20
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Seong MW, Cho SI, Kim KH, Chung IY, Kang E, Lee JW, Park SK, Lee MH, Choi DH, Yom CK, Noh WC, Chang MC, Park SS, Kim SW. A multi-institutional study of the prevalence of BRCA1 and BRCA2 large genomic rearrangements in familial breast cancer patients. BMC Cancer 2014; 14:645. [PMID: 25176351 PMCID: PMC4164743 DOI: 10.1186/1471-2407-14-645] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 08/26/2014] [Indexed: 11/13/2022] Open
Abstract
Background Large genomic rearrangements (LGRs) in the BRCA1/2 genes are frequently observed in breast cancer patients who are negative for BRCA1/2 small mutations. Here, we examined 221 familial breast cancer patients from 37 hospitals to estimate the contribution of LGRs, in a nationwide context, to the development of breast cancer. Methods Direct sequencing or mutation scanning followed by direct sequencing was performed to screen small mutations. BRCA1/2 small mutation-negative patients were screened for the presence of LGRs using a multiple ligation-dependent probe amplification (MLPA) assay. Results Using a combined strategy to detect the presence of small mutations and LGRs, we identified BRCA1/2 small mutations in 78 (35.3%) out of 221 familial breast cancer patients and BRCA1 LGRs in 3 (2.1%) out of 143 BRCA1/2 small mutation-negative patients: the deletion of exons 11–13, the deletion of exons 13–15, and whole gene deletion of exons 1-24. The novel deletion of exons 11–13 is thought to result from a non-homologous recombination event mediated by a microhomology sequence comprised of 3 or 4 base pairs: c.3416_4357 + 1863delins187 (NG_005905.2: g.33369_44944delins187). Conclusions In this study, we showed that LGRs were found in 3.7% (3/81) of the patients who had mutations in BRCA1 or BRCA2, and 7.5% (3/40) of patients with mutations in BRCA1. This suggests that the contribution of LGRs to familial breast cancer in this population might be comparable to that in other ethnic populations. Given these findings, an MLPA to screen for mutations in the BRCA1 gene is recommended as an initial screening test in highly selective settings.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sung-Won Kim
- Department of Surgery, Seoul National University Bundang Hospital, Sungnam, Korea.
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21
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Hasmad HN, Sivanandan K, Lee V, Yip CH, Mohd Taib NA, Teo SH. Identification of a recurrent BRCA1 exon 21-22 genomic rearrangement in Malay breast cancer patients. Clin Genet 2014; 87:392-4. [PMID: 25066186 DOI: 10.1111/cge.12451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/24/2014] [Accepted: 06/26/2014] [Indexed: 11/28/2022]
Affiliation(s)
- H N Hasmad
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Malaysia
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22
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De Silva S, Tennekoon KH, Karunanayake EH, Amarasinghe I, Angunawela P. Analysis of BRCA1and BRCA2 large genomic rearrangements in Sri Lankan familial breast cancer patients and at risk individuals. BMC Res Notes 2014; 7:344. [PMID: 24906410 PMCID: PMC4057568 DOI: 10.1186/1756-0500-7-344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 05/29/2014] [Indexed: 11/10/2022] Open
Abstract
Background Majority of mutations found to date in the BRCA1/BRCA2 genes in breast and/or ovarian cancer families are point mutations or small insertions and deletions scattered over the coding sequence and splice junctions. Such mutations and sequence variants of BRCA1 and BRCA2 genes were previously identified in a group of Sri Lankan breast cancer patients. Large genomic rearrangements have been characterized in BRCA1 and BRCA2 genes in several populations but these have not been characterized in Sri Lankan breast cancer patients. Findings A cohort of familial breast cancer patients (N = 57), at risk individuals (N = 25) and healthy controls (N = 23) were analyzed using multiplex ligation-dependent probe amplification method to detect BRCA1 and BRCA2 large genomic rearrangements. One familial breast cancer patient showed an ambiguous deletion in exon 6 of BRCA1 gene. Full sequencing of the ambiguous region was used to confirm MLPA results. Ambiguous deletion detected by MLPA was found to be a false positive result confirming that BRCA1 large genomic rearrangements were absent in the subjects studied. No BRCA2 rearrangement was also identified in the cohort. Conclusion Thus this study demonstrates that BRCA1 and BRCA2 large genomic rearrangements are unlikely to make a significant contribution to aetiology of breast cancer in Sri Lanka.
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Affiliation(s)
| | - Kamani Hemamala Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka.
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Kim H, Choi DH. Distribution of BRCA1 and BRCA2 Mutations in Asian Patients with Breast Cancer. J Breast Cancer 2013; 16:357-65. [PMID: 24454456 PMCID: PMC3893336 DOI: 10.4048/jbc.2013.16.4.357] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 09/19/2013] [Indexed: 11/30/2022] Open
Abstract
Breast cancer is the most prevalent cancer in Asian females, and the incidence of breast cancer has been increasing in Asia. Because Asian patients develop breast cancer at a younger age than their Caucasian counterparts, the contributions of BRCA1 and BRCA2 (BRCA1/2) mutations in Asians are expected to be different than in Caucasians. The prevalence of BRCA1/2 mutations in the Asian population varies among countries and studies. Most Asian studies have reported more frequent mutations in BRCA2 than in BRCA1, with the exception of studies from India and Pakistan. In addition, the contribution of large genomic rearrangements of BRCA1/2 genes is relatively small in Asian populations in comparison to other ethnic populations. Various statistical models for the prediction of BRCA1/2 mutations have underestimated the risk of having these genetic mutations in Asians, especially in predicting BRCA2 gene mutation. Until recently, BRCA1/2 mutation analyses in Asia were mostly conducted by independent single institutions with different patient selection criteria and using various genotyping methods. However, a couple of Asian groups have initiated nationwide studies collecting BRCA1/2 mutational data. These national collaborative studies will help a comprehensive understanding of the prevalence of BRCA1/2 mutations in the Asian population.
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Affiliation(s)
- Haeyoung Kim
- Department of Radiation Oncology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
| | - Doo Ho Choi
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Abstract
Breast cancer is the most common malignancy among women and has a strong genetic background. So far, 13 breast cancer susceptibility genes of high or moderate penetrance have been identified. This review summarizes findings on these genes in Han Chinese. BRCA1 and BRCA2 are the 2 most important susceptibility genes. They have a relatively low mutation rate, and the most frequent sites of mutation are in exon 11. Frameshift mutations are the main type of mutation. Founder mutations may also exist, and BRCA-associated breast cancer has specific clinicopathologic characteristics. TP53 and PALB2 are relatively rare susceptibility genes. The relationship between the other 9 genes and breast cancer has not been fully elucidated. At present, the mutation spectrum for these susceptibility genes is not well understood in the Chinese population, and there are few reports on prognosis and clinical intervention in high-risk populations. Therefore, the true value of genetic counseling for breast cancer has yet to be realized. This article reviews studies of hereditary breast cancer in the Han Chinese population, highlights potential inadequacies, and provides a foundation for genetic counseling for breast cancer in China.
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Affiliation(s)
- Wenming Cao
- Institute of Cell Biology, Zhejiang University, Hangzhou, China
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Karami F, Mehdipour P. A comprehensive focus on global spectrum of BRCA1 and BRCA2 mutations in breast cancer. BIOMED RESEARCH INTERNATIONAL 2013; 2013:928562. [PMID: 24312913 PMCID: PMC3838820 DOI: 10.1155/2013/928562] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/31/2013] [Accepted: 08/15/2013] [Indexed: 02/05/2023]
Abstract
Breast cancer (BC) is the most common cancer of women all over the world. BRCA1 and BRCA2 gene mutations comprise the most important genetic susceptibility of BC. Except for few common mutations, the spectrum of BRCA1 and BRCA2 mutations is heterogeneous in diverse populations. 185AGdel and 5382insC are the most important BRCA1 and BRCA2 alterations which have been encountered in most of the populations. After those Ashkenazi founder mutations, 300T>G also demonstrated sparse frequency in African American and European populations. This review affords quick access to the most frequent alterations among various populations which could be helpful in BRCA screening programs.
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Affiliation(s)
- Fatemeh Karami
- Department of Medical Genetics, Tehran University of Medical Sciences, School of Medicine, Tehran, Iran
| | - Parvin Mehdipour
- Department of Medical Genetics, Tehran University of Medical Sciences, School of Medicine, Tehran, Iran
- *Parvin Mehdipour:
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Cao W, Wang X, Gao Y, Yang H, Li JC. BRCA1 germ-line mutations and tumor characteristics in eastern Chinese women with familial breast cancer. Anat Rec (Hoboken) 2012; 296:273-8. [PMID: 23175448 DOI: 10.1002/ar.22628] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 10/30/2012] [Indexed: 01/16/2023]
Abstract
Although several studies detected the BRCA1 germ-line mutations in Chinese women with familial breast cancer, most of them did not employ conventional full gene sequencing, especially in eastern China. In addition, the clinicopathological features of BRCA1-associated breast cancer in Chinese women were not well investigated. In this study, we screened the complete coding regions and exon-intron boundaries of BRCA1 by polymerase chain reaction (PCR)-sequencing assay. Immunohistochemistry analyses were performed on tumor samples to detect the expression of estrogen receptor (ER), progesterone receptor (PR), P53, and human epidermal growth factor receptor-2 (HER-2). Breast cancer patients having one or more affected relatives referred from the Zhejiang Cancer Hospital, eastern China during 2008-2011 were selected for the study. A total of 62 familial breast cancer patients received the BRCA1 germ-line mutation screening. Five deleterious mutations were detected in this cohort. The mutation rate was 11.3% (7/62). We found two novel mutations (3414delC and 5,280 C > T) and two recurrent mutations (5,273 G > A and 5589del8). BRCA1 mutation tumors tended to be negative for ER, PR, and HER-2, and exhibited high histological grade compared with tumors without BRCA1 mutations. Our study suggests that recurrent mutations may exist in eastern Chinese women with familial breast cancer and PCR-sequencing assay is a useful tool to screen these mutations. It also suggests that BRCA1-associated breast cancers in Chinese women exhibit an aggressive phenotype.
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Affiliation(s)
- Wenming Cao
- Institute of Cell Biology, Zhejiang University, Hangzhou 310058, China
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27
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Chen M, Xu R, Turner JW, Warhol M, August P, Lee P. Race and the Molecular Origins of Breast Cancer in Chinese Women. Ann Surg Oncol 2012; 19:4085-93. [DOI: 10.1245/s10434-012-2452-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Indexed: 12/17/2022]
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28
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Rare germline large rearrangements in the BRCA1/2 genes and eight candidate genes in 472 patients with breast cancer predisposition. Breast Cancer Res Treat 2012; 133:1179-90. [DOI: 10.1007/s10549-012-2009-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/26/2012] [Indexed: 01/12/2023]
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Cheeseman K, Rouleau E, Vannier A, Thomas A, Briaux A, Lefol C, Walrafen P, Bensimon A, Lidereau R, Conseiller E, Ceppi M. A diagnostic genetic test for the physical mapping of germline rearrangements in the susceptibility breast cancer genes BRCA1 and BRCA2. Hum Mutat 2012; 33:998-1009. [PMID: 22473970 DOI: 10.1002/humu.22060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 02/03/2012] [Indexed: 12/12/2022]
Abstract
The BRCA1 and BRCA2 genes are involved in breast and ovarian cancer susceptibility. About 2 to 4% of breast cancer patients with positive family history, negative for point mutations, can be expected to carry large rearrangements in one of these two genes. We developed a novel diagnostic genetic test for the physical mapping of large rearrangements, based on molecular combing (MC), a FISH-based technique for direct visualization of single DNA molecules at high resolution. We designed specific Genomic Morse Codes (GMCs), covering the exons, the noncoding regions, and large genomic portions flanking both genes. We validated our approach by testing 10 index cases with positive family history of breast cancer and 50 negative controls. Large rearrangements, corresponding to deletions and duplications with sizes ranging from 3 to 40 kb, were detected and characterized on both genes, including four novel mutations. The nature of all the identified mutations was confirmed by high-resolution array comparative genomic hybridization (aCGH) and breakpoints characterized by sequencing. The developed GMCs allowed to localize several tandem repeat duplications on both genes. We propose the developed genetic test as a valuable tool to screen large rearrangements in BRCA1 and BRCA2 to be combined in clinical settings with an assay capable of detecting small mutations.
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Affiliation(s)
- Kevin Cheeseman
- Genomic Vision, 80–84 rue des Meuniers,Bagneux, Paris, France
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Ruiz de Garibay G, Gutiérrez-Enríquez S, Garre P, Bonache S, Romero A, Palomo L, Sánchez de Abajo A, Benítez J, Balmaña J, Pérez-Segura P, Díaz-Rubio E, Díez O, Caldés T, de la Hoya M. Characterization of four novel BRCA2 large genomic rearrangements in Spanish breast/ovarian cancer families: review of the literature, and reevaluation of the genetic mechanisms involved in their origin. Breast Cancer Res Treat 2012; 133:273-83. [PMID: 22434521 DOI: 10.1007/s10549-011-1909-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 11/30/2011] [Indexed: 11/30/2022]
Abstract
Large genomic rearrangements (LGRs) at the BRCA2 locus explain a non-negligible proportion of hereditary breast and ovarian cancer (HBOC) syndromes. The multiplex ligation and probe amplification (MLPA) assay has permitted in recent years to identify several families carrying LGRs at this locus, but very few such alterations have been fully characterized at the molecular level. Yet, molecular characterization is essential to identify recurrent alterations, to analyze the genetic mechanisms underlying such alterations, or to investigate potential genotype/phenotype relationships. We have used MLPA to identify BRCA2 LGRs in 7 out of 813 Spanish HBOC families previously tested negative for BRCA1 and BRCA2 small genomic alterations (substitutions and indels) and BRCA1 LGRs. We used a combination of long-range PCR, restriction mapping, and cDNA analysis to characterize the alterations at the molecular level. We found that Del Exon1-Exon2, Del Exon12-Exon16 and Del Exon22-Exon24 explain one family each, while Del Exon2 appears to be a Spanish founder mutation explaining four independent families. Finally, we have combined our data with a comprehensive review of the literature to reevaluate the genetic mechanisms underlying LGRs at the BRCA2 locus. Our study substantially increases the spectrum of BRCA2 LGRs fully characterized at the molecular level. Further on, we provide data to suggest that non-allelic homologous recombination has been overestimated as a mechanism underlying these alterations, while the opposite might be true for microhomology-mediated events.
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Affiliation(s)
- Gorka Ruiz de Garibay
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos, Hospital Clínico San Carlos, C/Martín Lagos s/n, 28040 Madrid, Spain
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Kwong A, Wong CHN, Shea C, Suen DTK, Choi CLY. Choice of management of southern Chinese BRCA mutation carriers. World J Surg 2011; 34:1416-26. [PMID: 20182723 DOI: 10.1007/s00268-010-0477-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Mutations in the BRCA genes confer greater risk of developing breast, ovarian, and prostate cancer. Families carrying the mutation can have intensive surveillance and take preventative measures. This is the first report on the uptake of such interventions in Chinese mutation carriers residing in Asia. METHODS Breast and ovarian cancer index patients and family members referred for genetic counselling and testing who are found to carry the BRCA mutations were included in this multicenter study. RESULTS A total of 31 patients with breast and/or ovarian cancer were found to carry BRCA1 or BRCA2 mutations. Forty-one tested family members also carried the mutations. Of the females, 85.7% of the index patients opted for breast surveillance and 23.8% for prophylactic mastectomy. Of the family members, 82.4% chose breast surveillance and 17.7% had prophylactic mastectomy. The majority of index patients and family members preferred ovarian surveillance (84 and 82.4%). Amongst the index patients, 32% decided for prophylactic salpingo-oophorectomy; 17.6% of the family members who did not have history of ovarian cancer decided to have prophylactic salpingo-oophorectomy. All male index patients agreed to breast and prostate surveillance, including breast clinical examination and PSA monitoring. For those male family members found to be BRCA mutation carriers, 56.3% agreed to have breast surveillance and 66.7% agreed to have prostate surveillance. No index patient or family member agreed to any form of chemoprevention. CONCLUSIONS Chinese BRCA mutation carriers have a higher uptake of cancer surveillance than prophylactic surgery and have a lack of interest in the use of chemoprevention drugs.
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Affiliation(s)
- Ava Kwong
- Division of Breast Surgery, The University of Hong Kong Li Ka Shing Faculty of Medicine, Hong Kong, Hong Kong, China.
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32
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Manguoğlu E, Güran Ş, Yamaç D, Şimşek M, Akdeniz S, Çolak T, Gülkesen H, Lüleci G. Genomic Large Rearrangement Screening ofBRCA1andBRCA2Genes in High-Risk Turkish Breast/Ovarian Cancer Patients by Using Multiplex Ligation-Dependent Probe Amplification Assay. Cancer Invest 2010; 29:73-7. [DOI: 10.3109/07357907.2010.512599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Spectrum of BRCA1/2 point mutations and genomic rearrangements in high-risk breast/ovarian cancer Chilean families. Breast Cancer Res Treat 2010; 126:705-16. [PMID: 20859677 DOI: 10.1007/s10549-010-1170-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 09/06/2010] [Indexed: 11/27/2022]
Abstract
The distribution of BRCA1/2 germline mutations in breast/ovarian cancer (BC/OC) families varies among different populations. In the Chilean population, there are only two reports of mutation analysis of BRCA1/2, and these included a low number of BC and/or OC patients. Moreover, the prevalence of BRCA1/2 genomic rearrangements in Chilean and in other South American populations is unknown. In this article, we present the mutation-detection data corresponding to a set of 326 high-risk families analyzed by conformation-sensitive gel electrophoresis and heteroduplex analysis. To determine the contribution of BRCA1/2 LGRs in Chilean BC patients, we analyzed 56 high-risk subjects with no pathogenic BRCA1/2 point mutations. Germline BRCA1/2 point mutations were found in 23 (7.1%) of the 326 Chilean families. Families which had at least three BC and/or OC cases showed the highest frequency of mutations (15.9%). We identified 14 point pathogenic mutations. Three recurrent mutations in BRCA1 (c.187_188delAG, c.2605_2606delTT, and c.3450_3453delCAAG) and three in BRCA2 (c.4969_4970insTG, c.5374_5377delTATG, and c.6503_6504delTT) contributed to 63.6 and 66.7% of all the deleterious mutations of each gene, which may reflect the presence of region-specific founder effects. Taken together BRCA1/2 recurrent point mutations account for 65.2% (15/23) of the BRCA1/2 (+) families. No large deletions or duplications involving BRCA1/2 were identified in a subgroup of 56 index cases negative for BRCA1/2 point mutations. Our study, which is the largest conducted to date in a South American population, provides a comprehensive analysis on the type and distribution of BRCA1/2 mutations and allelic variants.
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34
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Comprehensive BRCA1 and BRCA2 mutation analyses and review of French Canadian families with at least three cases of breast cancer. Fam Cancer 2010; 9:507-17. [DOI: 10.1007/s10689-010-9372-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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35
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Kang P, Mariapun S, Phuah SY, Lim LS, Liu J, Yoon SY, Thong MK, Mohd Taib NA, Yip CH, Teo SH. Large BRCA1 and BRCA2 genomic rearrangements in Malaysian high risk breast-ovarian cancer families. Breast Cancer Res Treat 2010; 124:579-84. [PMID: 20617377 DOI: 10.1007/s10549-010-1018-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 06/23/2010] [Indexed: 12/11/2022]
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36
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Searching for large genomic rearrangements of the BRCA1 gene in a Nigerian population. Breast Cancer Res Treat 2010; 124:573-7. [PMID: 20596889 DOI: 10.1007/s10549-010-1006-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 06/18/2010] [Indexed: 02/02/2023]
Abstract
BRCA1/2 germline mutations predispose to breast and ovarian cancer. Large genomic rearrangements (LGRs) have widened the mutational spectrum of the BRCA1 gene, but the frequencies vary in different populations. In this study, we want to determine the spectrum of LGRs in BRCA1 gene in Nigerian breast cancer patients. The multiplex ligation-dependent probe amplification (MLPA) assay was used to screen BRCA1 rearrangements in 352 patients who previously tested negative for BRCA1 and BRCA2 point mutations and small insertions/deletions. Positive MLPA result was confirmed and located by long-range PCR. The breakpoints of the candidate rearrangement were characterized by sequencing. A novel deletion of BRCA1 exon 21 (c.5277 + 480_5332 + 672del) was detected in 1 out of 352 Nigerian breast cancer patients (0.3% occurrence frequency). Further analysis of breakpoints revealed that the deletion involves two Alu-elements: one AluSg in intron 20 and the AluY in intron 21. These data suggest that while BRCA1 genomic rearrangement exists, they do not contribute significantly to BRCA1-associated risk in the Nigerian population.
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Identification of novel large genomic rearrangements at the BRCA1 locus in Malaysian women with breast cancer. Cancer Epidemiol 2010; 34:442-7. [PMID: 20451485 DOI: 10.1016/j.canep.2010.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 03/29/2010] [Accepted: 04/12/2010] [Indexed: 11/23/2022]
Abstract
BACKGROUND The incidence of breast cancer has been on the rise in Malaysia. It is suggested that a subset of breast cancer cases were associated with germline mutation in breast cancer susceptibility (BRCA) genes. Most of the BRCA mutations reported in Malaysia were point mutations, small deletions and insertions. Here we report the first study of BRCA large genomic rearrangements (LGRs) in Malaysia. We aimed to detect the presence of LGRs in the BRCA genes of Malaysian patients with breast cancer. METHODS Multiplex ligation-dependent probe amplification (MLPA) for BRCA LGRs was carried out on 100 patients (60 were high-risk breast cancer patients previously tested negative/positive for BRCA1 and BRCA2 mutations, and 40 were sporadic breast cancer patients), recruited from three major referral centres, Universiti Kebangsaan Malaysia Medical Centre (UKMMC), Hospital Kuala Lumpur (HKL) and Hospital Putrajaya (HPJ). RESULTS Two novel BRCA1 rearrangements were detected in patients with sporadic breast cancer; both results were confirmed by quantitative PCR. No LGRs were found in patients with high-risk breast cancer. The two large genomic rearrangements detected were genomic amplifications of exon 3 and exon 10. No BRCA2 genomic rearrangement was found in both high-risk and sporadic breast cancer patients. CONCLUSION These results will be helpful to understand the mutation spectrum of BRCA1 and BRCA2 genes in Malaysian patients with breast cancer. Further studies involving larger samples are required to establish a genetic screening strategy for both high-risk and sporadic breast cancer patients.
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Large genomic rearrangements of the BRCA1 and BRCA2 genes: review of the literature and report of a novel BRCA1 mutation. Breast Cancer Res Treat 2010; 125:325-49. [PMID: 20232141 DOI: 10.1007/s10549-010-0817-z] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 02/22/2010] [Indexed: 10/19/2022]
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del Valle J, Feliubadaló L, Nadal M, Teulé A, Miró R, Cuesta R, Tornero E, Menéndez M, Darder E, Brunet J, Capellà G, Blanco I, Lázaro C. Identification and comprehensive characterization of large genomic rearrangements in the BRCA1 and BRCA2 genes. Breast Cancer Res Treat 2009; 122:733-43. [DOI: 10.1007/s10549-009-0613-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 10/20/2009] [Indexed: 11/25/2022]
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Ewald IP, Ribeiro PLI, Palmero EI, Cossio SL, Giugliani R, Ashton-Prolla P. Genomic rearrangements in BRCA1 and BRCA2: A literature review. Genet Mol Biol 2009; 32:437-46. [PMID: 21637503 PMCID: PMC3036053 DOI: 10.1590/s1415-47572009005000049] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 12/08/2008] [Indexed: 12/17/2022] Open
Abstract
Women with mutations in the breast cancer genes BRCA1 or BRCA2 have an increased lifetime risk of developing breast, ovarian and other BRCA-associated cancers. However, the number of detected germline mutations in families with hereditary breast and ovarian cancer (HBOC) syndrome is lower than expected based upon genetic linkage data. Undetected deleterious mutations in the BRCA genes in some high-risk families are due to the presence of intragenic rearrangements such as deletions, duplications or insertions that span whole exons. This article reviews the molecular aspects of BRCA1 and BRCA2 rearrangements and their frequency among different populations. An overview of the techniques used to screen for large rearrangements in BRCA1 and BRCA2 is also presented. The detection of rearrangements in BRCA genes, especially BRCA1, offers a promising outlook for mutation screening in clinical practice, particularly in HBOC families that test negative for a germline mutation assessed by traditional methods.
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Affiliation(s)
- Ingrid Petroni Ewald
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS Brazil
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Seong MW, Cho SI, Noh DY, Han W, Kim SW, Park CM, Park HW, Kim SY, Kim JY, Park SS. Low contribution of BRCA1/2 genomic rearrangement to high-risk breast cancer in the Korean population. Fam Cancer 2009; 8:505-8. [PMID: 19669600 DOI: 10.1007/s10689-009-9279-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 07/30/2009] [Indexed: 11/25/2022]
Affiliation(s)
- Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital and Clinical Research Institute, Chongno-gu, Seoul 110-744, Korea
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Analysis of BRCA1/BRCA2 genes' contribution to breast cancer susceptibility in high risk Jewish Ashkenazi women. Fam Cancer 2008; 8:127-33. [PMID: 18798010 DOI: 10.1007/s10689-008-9216-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 09/03/2008] [Indexed: 10/21/2022]
Abstract
BACKGROUND Three mutations in BRCA1 (185delAG 5382InsC) and BRCA2 (6174delT) can be detected in a substantial proportion of Jewish Ashkenazi breast/ovarian cancer families. Family-specific pathogenic mutations in both genes can be detected in up to 5% of high risk Ashkenazim. The contribution of major gene rearrangements and seemingly pathogenic missense mutations to inherited breast cancer predisposition has never been systematically evaluated in Ashkenazim. MATERIAL AND METHODS High risk, Jewish Ashkenazi women, non-carriers of the predominant Jewish BRCA1/BRCA2 mutations, were genotyped for major gene rearrangements in BRCA1/BRCA2 using Multiplex ligation-dependent probe amplification (MLPA), and for the occurrence rate of 6 seemingly pathogenic missense mutations in BRCA1 (R866C, R331S, R841W, Y179C, C61G, M1008I) using a modified restriction enzyme assay. RESULTS Overall, 105 Jewish Ashkenazi high risk women, participated in the study: 104 with breast cancer [age at diagnosis (mean +/- SD) 51.05 +/- 11.13 years], one was affected with ovarian cancer (61 years). Two were found to carry the M1008I mutation in BRCA1 and none harbored any of the other missense mutations. MLPA reveled four changes (amplifications of exons 5, 17, 19 and 21) in BRCA1 in five patients, and six patients exhibited 4 MLPA-detectable abnormalities in BRCA2 (amplifications in exons 1b, 2, and deletions in exons 11a and 25). None of these abnormalities could be confirmed using quantitative PCR (qPCR) analysis. CONCLUSIONS Major gene rearrangements involving BRCA1 BRCA2 contribute little to the burden of inherited predisposition of breast cancer in Ashkenazi Jews.
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Engert S, Wappenschmidt B, Betz B, Kast K, Kutsche M, Hellebrand H, Goecke TO, Kiechle M, Niederacher D, Schmutzler RK, Meindl A. MLPA screening in the BRCA1 gene from 1,506 German hereditary breast cancer cases: novel deletions, frequent involvement of exon 17, and occurrence in single early-onset cases. Hum Mutat 2008; 29:948-58. [PMID: 18431737 DOI: 10.1002/humu.20723] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We present a comprehensive analysis of 1,506 German families for large genomic rearrangements (LGRs) in the BRCA1 gene and of 450 families in the BRCA2 gene by the multiplex ligation-dependent probe amplification (MLPA) technique. A total of 32 pathogenic rearrangements in the BRCA1 gene were found, accounting for 1.6% of all mutations, but for 9.6% of all BRCA1 mutations identified in a total of 1,996 families, including 490 with small pathogenic BRCA1/2 mutations. Considering only high risk groups for hereditary breast/ovarian cancer, the prevalence of rearrangements is 2.1%. Interestingly, deletions involving exon 17 of the BRCA1 gene seem to be most frequent in Germany. Apart from recurrent aberrations like del ex17, dupl ex13, and del ex22, accounting for more than 50% of all BRCA1 LGRs, we could fully characterize 11 novel deletions. Moreover, one novel deletion involving exons 1-7 and one deletion affecting the entire BRCA1 gene were identified. All rearrangements were detected in families with: 1) at least two breast cancer cases prior to the age of 51 years; 2) breast and ovarian cancer cases; 3) ovarian cancer only families with at least two ovarian cancer cases; or 4) a single breast cancer case prior to the age of 36 years, while no mutations were detected in breast cancer only families with no or only one breast cancer case prior to the age of 51 years. Analysis for gross rearrangements in 412 high-risk individuals, revealed no event in the BRCA2 gene and only two known CHEK2 mutations. However, in an additional 38 high-risk families with cooccurrence of female breast/ovarian and male breast cancer, one rearrangement in the BRCA2 gene was found. In summary, we advise restricting BRCA1 MLPA screening to those subgroups that revealed LGRs and recommend BRCA2 MLPA screening only for families presenting with cooccurrence of female and male breast cancer.
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Affiliation(s)
- Stefanie Engert
- Department of Obstetrics and Gynecology, Division of Tumor Genetics, Technical University, Munich, Germany
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Hansen TVO, Jønson L, Albrechtsen A, Andersen MK, Ejlertsen B, Nielsen FC. Large BRCA1 and BRCA2 genomic rearrangements in Danish high risk breast-ovarian cancer families. Breast Cancer Res Treat 2008; 115:315-23. [PMID: 18546071 DOI: 10.1007/s10549-008-0088-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Accepted: 05/30/2008] [Indexed: 10/22/2022]
Abstract
BRCA1 and BRCA2 germ-line mutations predispose to breast and ovarian cancer. Large genomic rearrangements of BRCA1 account for 0-36% of all disease causing mutations in various populations, while large genomic rearrangements in BRCA2 are more rare. We examined 642 East Danish breast and/or ovarian cancer patients in whom a deleterious mutation in BRCA1 and BRCA2 was not detected by sequencing using the multiplex ligation-dependent probe amplification (MLPA) assay. We identified 15 patients with 7 different genomic rearrangements, including a BRCA1 exon 5-7 deletion with a novel breakpoint, a BRCA1 exon 13 duplication, a BRCA1 exon 17-19 deletion, a BRCA1 exon 3-16 deletion, and a BRCA2 exon 20 deletion with a novel breakpoint as well as two novel BRCA1 exon 17-18 and BRCA1 exon 19 deletions. The large rearrangements in BRCA1 and BRCA2 accounted for 9.2% (15/163) of all BRCA1 and BRCA2 mutations in East Denmark. Nine patients had the exon 3-16 deletion in BRCA1. By SNP analysis we find that the patients share a 5 Mb fragment of chromosome 17, including BRCA1, indicating that the exon 3-16 deletion represents a Danish founder mutation.
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Affiliation(s)
- Thomas v O Hansen
- Department of Clinical Biochemistry 4111, Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark.
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Chou LS, Lyon E, Mao R. Molecular diagnosis utility of multiplex ligation-dependent probe amplification. ACTA ACUST UNITED AC 2008; 2:373-85. [DOI: 10.1517/17530059.2.4.373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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