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Innella G, Ferrari S, Miccoli S, Luppi E, Fortuno C, Parsons MT, Spurdle AB, Turchetti D. Clinical implications of VUS reclassification in a single-centre series from application of ACMG/AMP classification rules specified for BRCA1/2. J Med Genet 2024; 61:483-489. [PMID: 38160042 DOI: 10.1136/jmg-2023-109694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND BRCA1/2 testing is crucial to guide clinical decisions in patients with hereditary breast/ovarian cancer, but detection of variants of uncertain significance (VUSs) prevents proper management of carriers. The ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) BRCA1/2 Variant Curation Expert Panel (VCEP) has recently developed BRCA1/2 variant classification guidelines consistent with ClinGen processes, specified against the ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular-Pathology) classification framework. METHODS The ClinGen-approved BRCA1/2-specified ACMG/AMP classification guidelines were applied to BRCA1/2 VUSs identified from 2011 to 2022 in a series of patients, retrieving information from the VCEP documentation, public databases, literature and ENIGMA unpublished data. Then, we critically re-evaluated carrier families based on new results and checked consistency of updated classification with main sources for clinical interpretation of BRCA1/2 variants. RESULTS Among 166 VUSs detected in 231 index cases, 135 (81.3%) found in 197 index cases were classified by applying BRCA1/2-specified ACMG/AMP criteria: 128 (94.8%) as Benign/Likely Benign and 7 (5.2%) as Pathogenic/Likely Pathogenic. The average time from the first report as 'VUS' to classification using this approach was 49.4 months. Considering that 15 of these variants found in 64 families had already been internally reclassified prior to this work, this study provided 121 new reclassifications among the 151 (80.1%) remaining VUSs, relevant to 133/167 (79.6%) families. CONCLUSIONS These results demonstrated the effectiveness of new BRCA1/2 ACMG/AMP classification guidelines for VUS classification within a clinical cohort, and their important clinical impact. Furthermore, they suggested a cadence of no more than 3 years for regular review of VUSs, which however requires time, expertise and resources.
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Affiliation(s)
- Giovanni Innella
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Simona Ferrari
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Sara Miccoli
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Elena Luppi
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Cristina Fortuno
- Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Michael T Parsons
- Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Daniela Turchetti
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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Fortuno C, Michailidou K, Parsons M, Dolinsky JS, Pesaran T, Yussuf A, Mester JL, Hruska KS, Hiraki S, O’Connor R, Chan RC, Kim S, Tavtigian SV, Goldgar D, James PA, Spurdle AB. Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelines. Hum Mol Genet 2024; 33:724-732. [PMID: 38271184 PMCID: PMC11000651 DOI: 10.1093/hmg/ddae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
Since first publication of the American College of Medical Genetics and Genomics/Association for Medical Pathology (ACMG/AMP) variant classification guidelines, additional recommendations for application of certain criteria have been released (https://clinicalgenome.org/docs/), to improve their application in the diagnostic setting. However, none have addressed use of the PS4 and PP4 criteria, capturing patient presentation as evidence towards pathogenicity. Application of PS4 can be done through traditional case-control studies, or "proband counting" within or across clinical testing cohorts. Review of the existing PS4 and PP4 specifications for Hereditary Cancer Gene Variant Curation Expert Panels revealed substantial differences in the approach to defining specifications. Using BRCA1, BRCA2 and TP53 as exemplar genes, we calibrated different methods proposed for applying the "PS4 proband counting" criterion. For each approach, we considered limitations, non-independence with other ACMG/AMP criteria, broader applicability, and variability in results for different datasets. Our findings highlight inherent overlap of proband-counting methods with ACMG/AMP frequency codes, and the importance of calibration to derive dataset-specific code weights that can account for potential between-dataset differences in ascertainment and other factors. Our work emphasizes the advantages and generalizability of logistic regression analysis over simple proband-counting approaches to empirically determine the relative predictive capacity and weight of various personal clinical features in the context of multigene panel testing, for improved variant interpretation. We also provide a general protocol, including instructions for data formatting and a web-server for analysis of personal history parameters, to facilitate dataset-specific calibration analyses required to use such data for germline variant classification.
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Affiliation(s)
- Cristina Fortuno
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Michael Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | | | - Tina Pesaran
- Ambry Genetics, Aliso Viejo, CA 92656, United States
| | - Amal Yussuf
- Ambry Genetics, Aliso Viejo, CA 92656, United States
| | | | | | | | | | - Raymond C Chan
- Color Genomics, Inc., Burlingame, CA 94010, United States
| | - Serra Kim
- Color Genomics, Inc., Burlingame, CA 94010, United States
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, United States
| | - David Goldgar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, United States
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
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Jasiak A, Koczkowska M, Stukan M, Wydra D, Biernat W, Izycka-Swieszewska E, Buczkowski K, Eccles MR, Walker L, Wasag B, Ratajska M. Analysis of BRCA1 and BRCA2 alternative splicing in predisposition to ovarian cancer. Exp Mol Pathol 2023; 130:104856. [PMID: 36791903 DOI: 10.1016/j.yexmp.2023.104856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND The mRNA splicing is regulated on multiple levels, resulting in the proper distribution of genes' transcripts in each cell and maintaining cell homeostasis. At the same time, the expression of alternative transcripts can change in response to underlying genetic variants, often missed during routine diagnostics. AIM The main aim of this study was to define the frequency of aberrant splicing in BRCA1 and BRCA2 genes in blood RNA extracted from ovarian cancer patients who were previously found negative for the presence of pathogenic alterations in the 25 most commonly analysed ovarian cancer genes, including BRCA1 and BRCA2. MATERIAL AND METHODS Frequency and spectrum of splicing alterations in BRCA1 and BRCA2 genes were analysed in blood RNA from 101 ovarian cancer patients and healthy controls (80 healthy women) using PCR followed by gel electrophoresis and Sanger sequencing. The expression of splicing events was examined using RT-qPCR. RESULTS We did not identify any novel, potentially pathogenic splicing alterations. Nevertheless, we detected six naturally occurring transcripts, named BRCA1ΔE9-10, BRCA1ΔE11, BRCA1ΔE11q, and BRCA2ΔE3, BRCA2ΔE12 and BRCA2ΔE17-18 of which three (BRCA1ΔE11q, BRCA1ΔE11 and BRCA2ΔE3) were significantly higher expressed in the ovarian cancer cohort than in healthy controls (p ≤ 0.0001). CONCLUSIONS This observation indicates that the upregulation of selected naturally occurring transcripts can be stimulated by non-genetic mechanisms and be a potential systemic response to disease progression and/or treatment. However, this hypothesis requires further examination.
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Affiliation(s)
- Anna Jasiak
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland.
| | - Magdalena Koczkowska
- 3P Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland; Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Maciej Stukan
- Department of Gynecologic Oncology, Gdynia Oncology Center, Pomeranian Hospitals, Gdynia, Poland; Department Oncological Propedeutics, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Wydra
- Department of Gynaecology, Gynaecological Oncology and Gynaecological Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Biernat
- Department of Pathology, Medical University of Gdansk, Gdansk, Poland
| | | | - Kamil Buczkowski
- Department of Pathology & Neuropathology, Medical University of Gdansk, Gdansk, Poland
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Logan Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Bartosz Wasag
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland; Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Magdalena Ratajska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand.
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