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Hahn E, Mighton C, Fisher Y, Wong A, Di Gioacchino V, Watkins N, Mayers J, Bombard Y, Charames GS, Lerner-Ellis J. Variant classification changes over time in the clinical molecular diagnostic laboratory setting. J Med Genet 2024; 61:788-793. [PMID: 38806232 DOI: 10.1136/jmg-2023-109772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/12/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Variant classification in the setting of germline genetic testing is necessary for patients and their families to receive proper care. Variants are classified as pathogenic (P), likely pathogenic (LP), uncertain significance (VUS), likely benign (LB) and benign (B) using the standards and guidelines recommended by the American College of Medical Genetics and the Association for Molecular Pathology, with modifications for specific genes. As the literature continues to rapidly expand, and evidence continues to accumulate, prior classifications can be updated accordingly. In this study, we aim to characterise variant reclassifications in Ontario. METHODS DNA samples from patients seen at hereditary cancer clinics in Ontario from January 2012 to April 2022 were submitted for testing. Patients met provincial eligibility criteria for testing for hereditary cancer syndromes or polycystic kidney disease. Reclassification events were determined to be within their broader category of significance (B to LB or vice versa, or P to LP or vice versa) or outside of their broader category as significance (ie, significant reclassifications from B/LB or VUS or P/LP, from P/LP to VUS or B/LB, or from VUS to any other category). RESULTS Of the 8075 unique variants included in this study, 23.7% (1912) of variants were reassessed, and 7.2% (578) of variants were reclassified. Of these, 351 (60.7%) variants were reclassified outside of their broader category of significance. Overall, the final classification was significantly different for 336 (58.1%) variants. Importantly, most reclassified variants were downgraded to a more benign classification (n=245; 72.9%). Of note, most reclassified VUS was downgraded to B/LB (n=233; 84.7%). CONCLUSIONS The likelihood for reclassification of variants on reassessment is high. Most reclassified variants were downgraded to a more benign classification. Our findings highlight the importance of periodic variant reassessment to ensure timely and appropriate care for patients and their families.
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Affiliation(s)
- Elan Hahn
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Genomics Health Services Research Program, St Michael's Hospital Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Yael Fisher
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andrew Wong
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Vanessa Di Gioacchino
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Watkins
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Justin Mayers
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, St Michael's Hospital Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - George S Charames
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
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Zhang Y, Wu H, Gan C, Rao H, Wang Q, Guo X. BRCA1 and BRCA2 germline mutations in Chinese Hakka breast cancer patients. BMC Med Genomics 2024; 17:3. [PMID: 38167124 PMCID: PMC10763220 DOI: 10.1186/s12920-023-01772-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVE To investigate the prevalence of BRCA1/2 gene variants and evaluate the clinical and pathological characteristics associated with these variants in Chinese Hakka breast cancer patients. METHODS A total of 409 breast cancer patients were analyzed based on next-generation sequencing results, with 337 categorized as non-carriers and 72 as carriers of BRCA1/2 variants. Data on the patients' BRCA1/2 gene mutation status, clinical and pathological characteristics, as well as menstrual and reproductive information, were collected, analyzed, compared, and tabulated. Logistic regression analysis was performed to explore the relationship between clinical characteristics and pathogenic variants. RESULTS Among the patients, 72 were identified as carriers of pathogenic or likely pathogenic variants in BRCA1/2, while 337 had likely benign or benign mutations. The BRCA1 c.2635G > T (p. Glu879*) variant was detected at a high frequency, accounting for 12.5% (4/32) of the BRCA1 mutations, while the c.5164_5165del (p.Ser1722Tyrfs*4) variant was common among the BRCA2 mutations, accounting for 17.5% (7/40). It was observed that a higher proportion of BRCA1 carriers had the triple-negative breast cancer subtype, whereas more BRCA2 carriers exhibited estrogen receptor (ER) + and progesterone receptor (PR) + subtypes. Multivariate logistic regression analysis revealed that a family history of cancer (OR = 2.36, 95% CI = 1.00-5.54), bilateral cancer (OR = 4.78, 95% CI 1.61-14.20), human epidermal growth factor receptor 2 (HER2)- (OR = 8.23, 95% CI 3.25-20.84), and Ki67 ≥ 15% (OR = 3.88, 95% CI 1.41-10.65) were associated with BRCA1/2 mutations, with the age at diagnosis, age at menarche, and premenopausal status serving as covariates. CONCLUSIONS The most common pathogenic variant of the BRCA1 and BRCA2 in breast cancer patients was c.2635G > T and c.5164_5165del, respectively. Additionally, a family history of cancer, bilateral cancer, HER2-, and Ki67 ≥ 15% were identified as independent predictors of BRCA1/2 pathogenic variants.
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Affiliation(s)
- Yinmei Zhang
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
- Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou, China
| | - Heming Wu
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
| | - Caiyan Gan
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
- Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou, China
| | - Hui Rao
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China
| | - Qiuming Wang
- Department of Medical Oncology, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, People's Republic of China
| | - Xueming Guo
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China.
- Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou, China.
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Imyanitov EN, Kuligina ES, Sokolenko AP, Suspitsin EN, Yanus GA, Iyevleva AG, Ivantsov AO, Aleksakhina SN. Hereditary cancer syndromes. World J Clin Oncol 2023; 14:40-68. [PMID: 36908677 PMCID: PMC9993141 DOI: 10.5306/wjco.v14.i2.40] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/09/2022] [Accepted: 02/15/2023] [Indexed: 02/21/2023] Open
Abstract
Hereditary cancer syndromes (HCSs) are arguably the most frequent category of Mendelian genetic diseases, as at least 2% of presumably healthy subjects carry highly-penetrant tumor-predisposing pathogenic variants (PVs). Hereditary breast-ovarian cancer and Lynch syndrome make the highest contribution to cancer morbidity; in addition, there are several dozen less frequent types of familial tumors. The development of the majority albeit not all hereditary malignancies involves two-hit mechanism, i.e. the somatic inactivation of the remaining copy of the affected gene. Earlier studies on cancer families suggested nearly fatal penetrance for the majority of HCS genes; however, population-based investigations and especially large-scale next-generation sequencing data sets demonstrate that the presence of some highly-penetrant PVs is often compatible with healthy status. Hereditary cancer research initially focused mainly on cancer detection and prevention. Recent studies identified multiple HCS-specific drug vulnerabilities, which translated into the development of highly efficient therapeutic options.
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Affiliation(s)
- Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Ekaterina S Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Evgeny N Suspitsin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Grigoriy A Yanus
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Aglaya G Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Alexandr O Ivantsov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Svetlana N Aleksakhina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
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Bell KA, Kim R, Aronson M, Gillies B, Ali Awan A, Chun K, Hart J, Healey R, Kim L, Klaric G, Panabaker K, Sabatini PJB, Sadikovic B, Selvarajah S, Smith AC, Stockley TL, Vaags AK, Eisen A, Pollett A, Feilotter H. Development of a comprehensive approach to adult hereditary cancer testing in Ontario. J Med Genet 2022:jmg-2022-108945. [PMID: 36564171 DOI: 10.1136/jmg-2022-108945] [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: 09/16/2022] [Accepted: 12/10/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genetic testing for hereditary cancer susceptibility has advanced over time due to the discovery of new risk genes, improved technology and decreased cost. In the province of Ontario, testing eligibility criteria were initially developed to include hereditary breast, ovarian and colorectal cancer syndromes. The rapid evolution of genetic technologies has facilitated the ability to interrogate a large number of genes concurrently. This, coupled with new knowledge about risk genes, necessitated a coordinated approach to expanding the scope of genes and indications tested and synchronisation of access and test utilisation across the province as required in a publicly funded universal healthcare system. METHODS Ontario Health-Cancer Care Ontario convened expert working groups to develop a standardised and comprehensive cancer gene list for adults and accompanying hereditary cancer testing (HCT) criteria using an evidence-based framework and broad laboratory and clinical genetics engagement. RESULTS A standardised 76-cancer-gene panel, organised into 13 larger disease site panels and 25 single/small gene panels, was developed and endorsed by the working groups. Provincial genetic testing eligibility criteria were updated to align with the new panels and to guide clinical decision-making. In the first year following the implementation of these changes, 10 564 HCT panels were performed with an overall mutation detection rate of 12.2%. CONCLUSION Using an evidence framework and broad clinical engagement to develop and endorse an updated guidance document, cancer genetic testing for adults in Ontario is now standardised and coordinated across the province.
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Affiliation(s)
| | - Raymond Kim
- Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Brittany Gillies
- Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Arif Ali Awan
- Division of Medical Oncology, Ottawa Hospital Cancer Centre, Ottawa, Ontario, Canada
| | - Kathy Chun
- The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer Hart
- Pathology and Laboratory Medicine Program, Ontario Health, Toronto, Ontario, Canada
| | - Rachel Healey
- Pathology and Laboratory Medicine Program, Ontario Health, Toronto, Ontario, Canada
| | - Linda Kim
- Department of Laboratory Medicine and Genetics, Credit Valley Hospital Site, Mississauga, Ontario, Canada
| | - Goran Klaric
- Pathology and Laboratory Medicine Program, Ontario Health, Toronto, Ontario, Canada
| | - Karen Panabaker
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Verspeeten Clinical Genome Centre, Western University, London, Ontario, Canada
| | - Shamini Selvarajah
- Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada
| | | | - Tracy L Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Andrea K Vaags
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Andrea Eisen
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Aaron Pollett
- Pathology and Laboratory Medicine Program, Ontario Health, Toronto, Ontario, Canada.,Division of Diagnostic Medical Genetics, Sinai Health System, Toronto, Ontario, Canada
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
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D'Arcy BM, Arrington J, Weisman J, McClellan SB, Vandana , Yang Z, Deivanayagam C, Blount J, Prakash A. PMS2 variant results in loss of ATPase activity without compromising mismatch repair. Mol Genet Genomic Med 2022; 10:e1908. [PMID: 35189042 PMCID: PMC9034662 DOI: 10.1002/mgg3.1908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 02/01/2023] Open
Abstract
Hereditary cancer syndromes account for approximately 5%-10% of all diagnosed cancer cases. Lynch syndrome (LS) is an autosomal dominant hereditary cancer condition that predisposes individuals to an elevated lifetime risk for developing colorectal, endometrial, and other cancers. LS results from a pathogenic mutation in one of four mismatch repair (MMR) genes (MSH2, MSH6, MLH1, and PMS2). The diagnosis of LS is often challenged by the identification of missense mutations, termed variants of uncertain significance, whose functional effect on the protein is not known. Of the eight PMS2 variants initially selected for this study, we identified a variant within the N-terminal domain where asparagine 335 is mutated to serine, p.Asn335Ser, which lacked ATPase activity, yet appears to be proficient in MMR. To expand our understanding of this functional dichotomy, we performed biophysical and structural studies, and noted that p.Asn335Ser binds to ATP but is unable to hydrolyze it to ADP. To examine the impact of p.Asn335Ser on MMR, we developed a novel in-cell fluorescent-based microsatellite instability reporter that revealed p.Asn335Ser maintained genomic stability. We conclude that in the absence of gross structural changes, PMS2 ATP hydrolysis is not necessary for proficient MMR and that the ATPase deficient p.Asn335Ser variant is likely benign.
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Affiliation(s)
- Brandon M. D'Arcy
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
| | - Jennifer Arrington
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
| | - Justin Weisman
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
| | - Steven B. McClellan
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Flow Cytometry Shared Resource LabMitchell Cancer InstituteMobileAlabamaUSA
| | - Vandana
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
| | - Zhengrong Yang
- Department of Biochemistry and Molecular GeneticsSchool of Medicine University of Alabama at BirminghamBirminghamAlabamaUSA
| | - Champion Deivanayagam
- Department of Biochemistry and Molecular GeneticsSchool of Medicine University of Alabama at BirminghamBirminghamAlabamaUSA
| | | | - Aishwarya Prakash
- Mitchell Cancer InstituteUniversity of South Alabama HealthMobileAlabamaUSA
- Department of Biochemistry and Molecular BiologyUniversity of South AlabamaMobileAlabamaUSA
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Tumor BRCA Testing in High Grade Serous Carcinoma: Mutation Rates and Optimal Tissue Requirements. Cancers (Basel) 2020; 12:cancers12113468. [PMID: 33233347 PMCID: PMC7700467 DOI: 10.3390/cancers12113468] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Approximately 25% of women diagnosed with tubo-ovarian high-grade serous carcinoma have germline deleterious mutations in BRCA1 or BRCA2, characteristic of hereditary breast and ovarian cancer syndrome, while somatic mutations have been detected in 3–7%. We set out to determine the mutation rates and optimal tissue requirements for tumor BRCA testing in 291 tissue samples. Initial testing was successful in 78% and deemed indeterminate in 13%. Repeat testing was successful in 67% of retested samples, with an overall success rate of 86%. Clinically significant BRCA variants were identified in 17% of patients. Successful sequencing was dependent on sample type, tumor cellularity and size (p ≤ 0.001) but not on neoadjuvant chemotherapy or age of blocks. In summary, our study shows a 17% tumor BRCA mutation rate, with an overall success rate of 86%. Biopsy and cytology samples and post-chemotherapy specimens can be used, and optimal tumors measure ≥5 mm in size with at least 20% cellularity. Abstract Background: Approximately 25% of women diagnosed with tubo-ovarian high-grade serous carcinoma have germline deleterious mutations in BRCA1 or BRCA2, characteristic of hereditary breast and ovarian cancer syndrome, while somatic mutations have been detected in 3–7%. We set out to determine the BRCA mutation rates and optimal tissue requirements for tumor BRCA testing in patients diagnosed with tubo-ovarian high-grade serous carcinoma. Methods: Sequencing was performed using a multiplexed polymerase chain reaction-based approach on 291 tissue samples, with a minimum sequencing depth of 500X and an allele frequency of >5%. Results: There were 253 surgical samples (87%), 35 biopsies (12%) and 3 cytology cell blocks (1%). The initial failure rate was 9% (25/291), including 9 cases (3%) with insufficient tumor, and 16 (6%) with non-amplifiable DNA. Sequencing was successful in 78% (228/291) and deemed indeterminate due to failed exons or variants below the limit of detection in 13% (38/291). Repeat testing was successful in 67% (28/42) of retested samples, with an overall success rate of 86% (251/291). Clinically significant (pathogenic, likely pathogenic) variants were identified in 17% (48/276) of complete and indeterminate cases. Successful sequencing was dependent on sample type, tumor cellularity and size (p ≤ 0.001) but not on neoadjuvant chemotherapy or age of blocks (p > 0.05). Conclusions: Our study shows a 17% tumor BRCA mutation rate, with an overall success rate of 86%. Biopsy and cytology samples and post-chemotherapy specimens can be used for tumor BRCA testing, and optimal tumors measure ≥5 mm in size with at least 20% cellularity.
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