1
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Azzollini J, Agnelli L, Conca E, Torelli T, Busico A, Capone I, Angelini M, Tamborini E, Perrone F, Vingiani A, Lorenzini D, Peissel B, Pruneri G, Manoukian S. Prevalence of BRCA homopolymeric indels in an ION Torrent-based tumour-to-germline testing workflow in high-grade ovarian carcinoma. Sci Rep 2023; 13:7781. [PMID: 37179432 PMCID: PMC10182972 DOI: 10.1038/s41598-023-33857-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Tumour DNA sequencing is essential for precision medicine since it guides therapeutic decisions but also fosters the identification of patients who may benefit from germline testing. Notwithstanding, the tumour-to-germline testing workflow presents a few caveats. The low sensitivity for indels at loci with sequences of identical bases (homopolymers) of ion semiconductor-based sequencing techniques represents a well-known limitation, but the prevalence of indels overlooked by these techniques in high-risk populations has not been investigated. In our study, we addressed this issue at the homopolymeric regions of BRCA1/2 in a retrospectively selected cohort of 157 patients affected with high-grade ovarian cancer and negative at tumour testing by ION Torrent sequencing. Variant allele frequency (VAF) of indels at each of the 29 investigated homopolymers was systematically revised with the IGV software. Thresholds to discriminate putative germline variants were defined by scaling the VAF to a normal distribution and calculating the outliers that exceeded the mean + 3 median-adjusted deviations of a control population. Sanger sequencing of the outliers confirmed the occurrence of only one of the five putative indels in both tumour and blood from a patient with a family history of breast cancer. Our results indicated that the prevalence of homopolymeric indels overlooked by ion semiconductor techniques is seemingly low. A careful evaluation of clinical and family history data would further help minimise this technique-bound limitation, highlighting cases in which a deeper look at these regions would be recommended.
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Affiliation(s)
- Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Luca Agnelli
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
- Medical Oncology 1 Department, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Elena Conca
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Tommaso Torelli
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
- Medical Oncology 1 Department, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Adele Busico
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Iolanda Capone
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Marta Angelini
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Elena Tamborini
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Federica Perrone
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Andrea Vingiani
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
- Oncology and Hemato-Oncology Department, University of Milan, Milan, Italy
| | - Daniele Lorenzini
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
| | - Giancarlo Pruneri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy
- Oncology and Hemato-Oncology Department, University of Milan, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133, Milan, Italy.
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2
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Azzollini J, Vingiani A, Agnelli L, Tamborini E, Perrone F, Conca E, Capone I, Busico A, Peissel B, Rosina E, Ducceschi M, Mantiero M, Lopez S, Raspagliesi F, Niger M, Duca M, Damian S, Proto C, de Braud F, Pruneri G, Manoukian S. Management of BRCA Tumour Testing in an Integrated Molecular Tumour Board Multidisciplinary Model. Front Oncol 2022; 12:857515. [PMID: 35463374 PMCID: PMC9026437 DOI: 10.3389/fonc.2022.857515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Tumour testing of the BRCA1/2 genes is routinely performed in patients with different cancer histological subtypes. To accurately identify patients with tumour-detected germline pathogenic variants (PVs) is a relevant issue currently under investigation. This study aims at evaluating the performance of the tumour-to-germline diagnostic flowchart model defined at our Institutional Molecular Tumour Board (MTB). Results from tumour BRCA sequencing of 641 consecutive unselected cancer patients were discussed during weekly MTB meetings with the early involvement of clinical geneticists for appropriate referral to genetic counselling. The overall tumour detection rate of BRCA1/2 PVs was 8.7% (56/641), ranging from 24.4% (31/127) in high-grade ovarian cancer to 3.9% (12/304) in tumours not associated with germline BRCA1/2 PVs. Thirty-seven patients with PVs (66%) were evaluated by a clinical geneticist, and in 24 of them (64.9%), germline testing confirmed the presence of the PV in blood. Nine of these patients (37.5%) were not eligible for germline testing according to the criteria in use at our institution. Cascade testing was subsequently performed on 18 relatives. The tumour-to-germline diagnostic pipeline, developed in the framework of our institutional MTB, compared with guideline-based germline testing following genetic counselling, proved to be effective in identifying a higher number of germline BRCA PVs carriers.
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Affiliation(s)
- Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Vingiani
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Oncology and Hemato-oncology Department, University of Milan, Milan, Italy
| | - Luca Agnelli
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Tamborini
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Perrone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Conca
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Iolanda Capone
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Adele Busico
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Erica Rosina
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monika Ducceschi
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mara Mantiero
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Salvatore Lopez
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesco Raspagliesi
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Niger
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Duca
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvia Damian
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Claudia Proto
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo de Braud
- Oncology and Hemato-oncology Department, University of Milan, Milan, Italy.,Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Oncology and Hemato-oncology Department, University of Milan, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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3
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Dong K, Zhang W, Cheng S, Shu W, Zhao R, Wang H. The Progress of the Specific and Rapid Genetic Detection Methods for Ovarian Cancer Diagnosis and Treatment. Technol Cancer Res Treat 2022; 21:15330338221114497. [PMID: 36062718 PMCID: PMC9446467 DOI: 10.1177/15330338221114497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cancer is a public health problem that threatens human health. Due to the lack of
specific and rapid diagnosis and treatment methods, the 5-year survival rate of
patients has not been effectively improved in the past 10 years. Abnormal gene
expression is closely related to the occurrence and development of cancer.
Cancer diagnosis and treatment methods based on genetic testing have received
extensive attention in recent years. It is essential to explore specific and
rapid cancer genetic testing methods. Taking ovarian cancer as an example, we
reviewed the progress of specific and rapid nucleic acid detection methods
related to cancer risk assessment, low-abundance mutation detection, and
methylation detection, to provide new strategies and ideas for related
research.
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Affiliation(s)
- Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
| | - Shuangshuang Cheng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
| | - Wan Shu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
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4
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El Saghir NS, Ghanem H, El Karak F, Farhat F, Ghosn M, Makdessi J, Chouaib K, Debs J, Tabchy AB. Management of breast cancer patients with BRCA gene mutations in Lebanon of the Middle East: perspectives and challenges. Hosp Pract (1995) 2021; 49:325-329. [PMID: 34547975 DOI: 10.1080/21548331.2021.1974678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND This commentary explores and discusses the challenges oncologists face in diagnosing and managing breast cancer patients with BRCA gene mutations in Lebanon and the Middle East. METHODS Key opinion leaders shared their recommendations to achieve better patient outcomes and satisfaction based on evidence-based medicine and their clinical experience in BRCA management. RESULTS Challenges associated with BRCA management can be divided into four main levels: physicians, patients, test, and treatment factors. More genetic counselors are to be identified given their important role in the management of individuals with BRCA gene mutations. CONCLUSION Genetic counseling, continuing education, infrastructure, testing, expertise, and financial support are needed to fulfill the unmet needs in the management of BRCA mutation carriers.
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Affiliation(s)
- Nagi S El Saghir
- Division of Hematology Oncology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hady Ghanem
- Division of Hematology Oncology, Lebanese American University Medical Center - Rizk Hospital, Beirut, Lebanon
| | - Fadi El Karak
- Department of Oncology-Hematology, School of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Fadi Farhat
- Division of Hematology Oncology, Hammoud Hospital University Medical Center, Saida, Lebanon
| | - Marwan Ghosn
- Hematology Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Joseph Makdessi
- Hematology and Oncology Department, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Khouloud Chouaib
- Oncology Department, Medical Affairs, Pfizer Africa - Middle East Region, Lebanon
| | - Jamil Debs
- Oncology Department, Medical Affairs, Pfizer Africa - Middle East Region, Lebanon
| | - Adel B Tabchy
- Department of Hematology/Oncology, Saint-Joseph University - School of Medicine, Beirut, Lebanon
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5
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Lemeshko VA, Teptsova TS, Ratushnyak SS, Musina NZ. Assessing the Relevance of Molecular Genetic Testing for Mutations in BRCA Genes of Patients with Ovarian and Breast Cancer. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795420100075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Rapid detection of copy number variations and point mutations in BRCA1/2 genes using a single workflow by ion semiconductor sequencing pipeline. Oncotarget 2018; 9:33648-33655. [PMID: 30263092 PMCID: PMC6154752 DOI: 10.18632/oncotarget.26000] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/04/2018] [Indexed: 01/29/2023] Open
Abstract
Molecular analysis of BRCA1 (MIM# 604370) and BRCA2 (MIM #600185) genes is essential for familial breast and ovarian cancer prevention and treatment. An efficient, rapid, cost-effective accurate strategy for the detection of pathogenic variants is crucial. Mutations detection of BRCA1/2 genes includes screening for single nucleotide variants (SNVs), small insertions or deletions (indels), and Copy Number Variations (CNVs). Sanger sequencing is unable to identify CNVs and therefore Multiplex Ligation Probe amplification (MLPA) or Multiplex Amplicon Quantification (MAQ) is used to complete the BRCA1/2 genes analysis. The rapid evolution of Next Generation Sequencing (NGS) technologies allows the search for point mutations and CNVs with a single platform and workflow. In this study we test the possibilities of NGS technology to simultaneously detect point mutations and CNVs in BRCA1/2 genes, using the OncomineTM BRCA Research Assay on Personal Genome Machine (PGM) Platform with Ion Reporter Software for sequencing data analysis (Thermo Fisher Scientific). Comparison between the NGS-CNVs, MLPA and MAQ results shows how the NGS approach is the most complete and fast method for the simultaneous detection of all BRCA mutations, avoiding the usual time consuming multistep approach in the routine diagnostic testing of hereditary breast and ovarian cancers.
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7
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Vendrell JA, Vilquin P, Larrieux M, Van Goethem C, Solassol J. Benchmarking of Amplicon-Based Next-Generation Sequencing Panels Combined with Bioinformatics Solutions for Germline BRCA1 and BRCA2 Alteration Detection. J Mol Diagn 2018; 20:754-764. [PMID: 30055349 DOI: 10.1016/j.jmoldx.2018.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/27/2018] [Accepted: 06/05/2018] [Indexed: 11/16/2022] Open
Abstract
The recent deployment of next-generation sequencing approaches in routine laboratory analysis has considerably modified the landscape of BRCA1 and BRCA2 germline alteration detection in patients with a high risk of developing breast and/or ovarian cancer. Several commercial multiplex amplicon-based panels and bioinformatics solutions are currently available. In this study, we evaluated the combinations of several BRCA testing assays and bioinformatics solutions for the identification of single-nucleotide variants, insertion/deletion variants, and copy number variations (CNVs). Four assays (BRCA Tumor, BRCA HC, Ion AmpliSeq BRCA, and Access Array BRCA) and two commercial bioinformatics solutions (SeqNext software version 4.3.1 and Sophia DDM version 5.0.13) were tested on a set of 28 previously genotyped samples. All solutions exhibited accurate detection of single-nucleotide variants and insertion/deletion variants, except for Ion AmpliSeq BRCA, which exhibited a decrease in coverage. Of interest, for CNV analysis, the best accuracy was observed with the Sophia DDM platform regardless of the BRCA kit used. Finally, the performance of the most relevant combination (BRCA Tumor and Sophia DDM) was blindly validated on an independent set of 152 samples. Altogether, our results emphasize the need to accurately compare and control both molecular next-generation sequencing approaches and bioinformatics pipelines to limit the number of discrepant alterations and to provide a powerful tool for reliable detection of genetic alterations in BRCA1 and BRCA2, notably CNVs.
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Affiliation(s)
- Julie A Vendrell
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Paul Vilquin
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Marion Larrieux
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Charles Van Goethem
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Jérôme Solassol
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France; The Institute of Cancer Research of Montpellier, INSERM U1194, University of Montpellier, Montpellier, France.
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8
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Neveling K, Mensenkamp AR, Derks R, Kwint M, Ouchene H, Steehouwer M, van Lier B, Bosgoed E, Rikken A, Tychon M, Zafeiropoulou D, Castelein S, Hehir-Kwa J, Tjwan Thung D, Hofste T, Lelieveld SH, Bertens SMM, Adan IBJF, Eijkelenboom A, Tops BB, Yntema H, Stokowy T, Knappskog PM, Høberg-Vetti H, Steen VM, Boyle E, Martin B, Ligtenberg MJL, Shendure J, Nelen MR, Hoischen A. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clin Chem 2016; 63:503-512. [PMID: 27974384 DOI: 10.1373/clinchem.2016.263897] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested gene tests, those for the breast cancer genes BRCA1 and BRCA2, and developed an automated work flow based on smMIPs. METHODS The BRCA1 and BRCA2 smMIPs were validated using 166 human genomic DNA samples with known variant status. A generic automated work flow was built to perform smMIP-based enrichment and sequencing for BRCA1, BRCA2, and the checkpoint kinase 2 (CHEK2) c.1100del variant. RESULTS Pathogenic and benign variants were analyzed in a subset of 152 previously BRCA-genotyped samples, yielding an analytical sensitivity and specificity of 100%. Following automation, blind analysis of 65 in-house samples and 267 Norwegian samples correctly identified all true-positive variants (>3000), with no false positives. Consequent to process optimization, turnaround times were reduced by 60% to currently 10-15 days. Copy number variants were detected with an analytical sensitivity of 100% and an analytical specificity of 88%. CONCLUSIONS smMIP-based genetic testing enables automated and reliable analysis of the coding sequences of BRCA1 and BRCA2. The use of single-molecule tags, double-tiled targeted enrichment, and capturing and sequencing in duplo, in combination with automated library preparation and data analysis, results in a robust process and reduces routine turnaround times. Furthermore, smMIP-based copy number variation analysis could make independent copy number variation tools like multiplex ligation-dependent probes amplification dispensable.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Hicham Ouchene
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Bart van Lier
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Ermanno Bosgoed
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Alwin Rikken
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Marloes Tychon
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Jayne Hehir-Kwa
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Djie Tjwan Thung
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Stijn M M Bertens
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Ivo B J F Adan
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Bastiaan B Tops
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Tomasz Stokowy
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Per M Knappskog
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Hildegunn Høberg-Vetti
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Vidar M Steen
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Evan Boyle
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.,Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Marcel R Nelen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands;
| | - Alexander Hoischen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.,Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, the Netherlands
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9
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Kwong A, Shin VY, Au CH, Law FBF, Ho DN, Ip BK, Wong ATC, Lau SS, To RMY, Choy G, Ford JM, Ma ESK, Chan TL. Detection of Germline Mutation in Hereditary Breast and/or Ovarian Cancers by Next-Generation Sequencing on a Four-Gene Panel. J Mol Diagn 2016; 18:580-94. [PMID: 27157322 DOI: 10.1016/j.jmoldx.2016.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 03/01/2016] [Accepted: 03/21/2016] [Indexed: 10/21/2022] Open
Abstract
Mutation in BRCA1/BRCA2 genes accounts for 20% of familial breast cancers, 5% to 10% of which may be due to other less penetrant genes which are still incompletely studied. Herein, a four-gene panel was used to examine the prevalence of BRCA1, BRCA2, TP53, and PTEN in hereditary breast and ovarian cancers in Southern Chinese population. In this cohort, 948 high-risk breast and/or ovarian patients were recruited for genetic screening by next-generation sequencing (NGS). The performance of our NGS pipeline was evaluated with 80 Sanger-validated known mutations and eight negative cases. With appropriate bioinformatics analysis pipeline, the detection sensitivity of NGS is comparable with Sanger sequencing. The prevalence of BRCA1/BRCA2 germline mutations was 9.4% in our Chinese cohort, of which 48.8% of the mutations arose from hotspot mutations. With the use of a tailor-made algorithm, HomopolymerQZ, more mutations were detected compared with single mutation detection algorithm. The frequencies of PTEN and TP53 were 0.21% and 0.53%, respectively, in the Southern Chinese patients with breast and/or ovarian cancers. High-throughput NGS approach allows the incorporation of control cohort that provides an ethnicity-specific data for polymorphic variants. Our data suggest that hotspot mutations screening such as SNaPshot could be an effective preliminary screening alternative adopted in a standard clinical laboratory without NGS setup.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong, Hong Kong, People's Republic of China; Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, People's Republic of China.
| | - Vivian Y Shin
- Department of Surgery, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Chun H Au
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Fian B F Law
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, People's Republic of China; Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Dona N Ho
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Bui K Ip
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Anthony T C Wong
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Silvia S Lau
- Department of Medical Physics and Research, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Rene M Y To
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Gigi Choy
- Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - James M Ford
- Department of Medicine (Oncology), Stanford University School of Medicine, Stanford, California
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, People's Republic of China; Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
| | - Tsun L Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, People's Republic of China; Department of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, People's Republic of China
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Abstract
Despite the increasing clinical importance of germline BRCA mutation
status in managing women with ovarian cancer, few patients are currently being
tested. The traditional means of selecting patients for BRCA mutation
testing using restrictive criteria will miss many women with a mutation. To
expand access to testing and streamline the testing process, several centres in
the UK have been developing new models for BRCA testing. Trials with
these integrated models involving closer collaborations between genetics and
oncology services are now under way. In addition to testing for BRCA
mutations, there is also increasing interest in testing for other genes
associated with a predisposition to ovarian cancer. Advances in next-generation
sequencing technology have resulted in the development of comprehensive genetic
testing panels for use in the research and diagnostic settings. Interest is also
increasing in expanding testing for somatic mutations in ovarian cancer,
particularly for genes such as BRCA1 and BRCA2, whereby
mutations may allow more patients to benefit from targeted agents, including
poly(ADP-ribose) polymerase inhibitors. In this review, the issues of who should
be offered testing, how testing could be delivered, when testing should occur
and the technology and costs associated with genetic testing are addressed.
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Affiliation(s)
- Angela George
- The Royal Marsden NHS Foundation Trust, Fulham Road, London SW3 6JJ, UK
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Coppieters F, Verniers K, De Leeneer K, Vandesompele J, Lefever S. Targeted resequencing and variant validation using pxlence PCR assays. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 6:22-6. [PMID: 27077044 PMCID: PMC4822215 DOI: 10.1016/j.bdq.2015.09.001] [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: 06/21/2015] [Revised: 08/14/2015] [Accepted: 09/06/2015] [Indexed: 11/10/2022]
Abstract
The advent of next-generation sequencing technologies had a profound impact on molecular diagnostics. PCR is a popular method for target enrichment of disease gene panels. Using our proprietary primer-design pipeline, primerXL, we have created almost one million assays covering over 98% of the human exome. Here we describe the assay specification and both in silico and wet-lab validation of a selected set of 2294 assays using both next-generation sequencing and Sanger sequencing. Using a universal PCR protocol without optimization, these assays result in high coverage uniformity and limited non-specific coverage. In addition, data indicates a positive correlation between the predictive in silico specificity score and the amount of assay non-specific coverage.
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Affiliation(s)
- Frauke Coppieters
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- pxlence, Dendermonde, Belgium
| | | | - Kim De Leeneer
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- pxlence, Dendermonde, Belgium
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- pxlence, Dendermonde, Belgium
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12
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Hereditary ovarian cancer: not only BRCA 1 and 2 genes. BIOMED RESEARCH INTERNATIONAL 2015; 2015:341723. [PMID: 26075229 PMCID: PMC4449870 DOI: 10.1155/2015/341723] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 01/10/2023]
Abstract
More than one-fifth of ovarian tumors have hereditary susceptibility and, in about 65-85% of these cases, the genetic abnormality is a germline mutation in BRCA genes. Nevertheless, several other suppressor genes and oncogenes have been associated with hereditary ovarian cancers, including the mismatch repair (MMR) genes in Lynch syndrome, the tumor suppressor gene, TP53, in the Li-Fraumeni syndrome, and several other genes involved in the double-strand breaks repair system, such as CHEK2, RAD51, BRIP1, and PALB2. The study of genetic discriminators and deregulated pathways involved in hereditary ovarian syndromes is relevant for the future development of molecular diagnostic strategies and targeted therapeutic approaches. The recent development and implementation of next-generation sequencing technologies have provided the opportunity to simultaneously analyze multiple cancer susceptibility genes, reduce the delay and costs, and optimize the molecular diagnosis of hereditary tumors. Particularly, the identification of mutations in ovarian cancer susceptibility genes in healthy women may result in a more personalized cancer risk management with tailored clinical and radiological surveillance, chemopreventive approaches, and/or prophylactic surgeries. On the other hand, for ovarian cancer patients, the identification of mutations may provide potential targets for biologic agents and guide treatment decision-making.
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13
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Kluska A, Balabas A, Paziewska A, Kulecka M, Nowakowska D, Mikula M, Ostrowski J. New recurrent BRCA1/2 mutations in Polish patients with familial breast/ovarian cancer detected by next generation sequencing. BMC Med Genomics 2015; 8:19. [PMID: 25948282 PMCID: PMC4429836 DOI: 10.1186/s12920-015-0092-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/23/2015] [Indexed: 12/19/2022] Open
Abstract
Background Targeted PCR-based genetic testing for BRCA1 and BRCA2 can be performed at a lower cost than full gene testing; however, it may overlook mutations responsible for familial breast and/or ovarian cancers. In the present study, we report the utility of next generation sequencing (NGS) to identify new pathogenic variants of BRCA1/2. Methods BRCA1 and BRCA2 exons were amplified using the Ion AmpliSeq BRCA1/2 Panel and sequenced on the Ion Torrent PGM sequencer in 512 women with familial and/or only early onset breast and/or ovarian cancers who were negative for selected BRCA1/2 mutations. Results 146 single nucleotide variants (SNVs) and 32 indels were identified. Of them, 14 SNVs and 17 indels were considered as pathogenic or likely pathogenic. One and 18 pathogenic mutations had been detected previously in the Polish and other populations, respectively, and 12 deleterious mutations were previously unknown. Eight mutations were recurrent; Q563X (BRCA1), N3124I (BRCA2) and c.4516delG (BRCA1) were found in eight, six and four patients, respectively, and two other mutations (c.9118-2A > G and c.7249delCA in BRCA2) were detected in three patients each. Altogether, BRCA1/2 pathogenic mutations were identified in 52 out of 512 (10%) patients. Conclusions NGS substantially improved the detection rates of a wide spectrum of mutations in Polish patients with familial breast and/or ovarian cancer. Although targeted screening for specific BRCA1 mutations can be offered to all Polish breast or ovarian cancer patients, NGS-based testing is justified in patients with breast or ovarian cancer likely related to BRCA1/2 who test negative for the selected BRCA1/2 pathogenic mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0092-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Dorota Nowakowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland. .,Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
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