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Lebedeva A, Veselovsky E, Kavun A, Belova E, Grigoreva T, Orlov P, Subbotovskaya A, Shipunov M, Mashkov O, Bilalov F, Shatalov P, Kaprin A, Shegai P, Diuzhev Z, Migiaev O, Vytnova N, Mileyko V, Ivanov M. Untapped Potential of Poly(ADP-Ribose) Polymerase Inhibitors: Lessons Learned From the Real-World Clinical Homologous Recombination Repair Mutation Testing. World J Oncol 2024; 15:562-578. [PMID: 38993246 PMCID: PMC11236374 DOI: 10.14740/wjon1820] [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: 01/17/2024] [Accepted: 04/29/2024] [Indexed: 07/13/2024] Open
Abstract
Background Testing for homologous recombination deficiency (HRD) mutations is pivotal to assess individual risk, to proact preventive measures in healthy carriers and to tailor treatments for cancer patients. Increasing prominence of poly(ADP-ribose) polymerase (PARP) inhibitors with remarkable impact on molecular-selected patient survival across diverse nosologies, ingrains testing for BRCA genes and beyond in clinical practice. Nevertheless, testing strategies remain a question of debate. While several pathogenic BRCA1/2 gene variants have been described as founder pathogenic mutations frequently found in patients from Russia, other homologous recombination repair (HRR) genes have not been sufficiently explored. In this study, we present real-world data of routine HRR gene testing in Russia. Methods We evaluated clinical and sequencing data from cancer patients who had germline/somatic next-generation sequencing (NGS) HRR gene testing in Russia (BRCA1/2/ATM/CHEK2, or 15 HRR genes). The primary objectives of this study were to evaluate the frequency of BRCA1/2 and non-BRCA gene mutations in real-world unselected patients from Russia, and to determine whether testing beyond BRCA1/2 is feasible. Results Data of 2,032 patients were collected from February 2021 to February 2023. Most had breast (n = 715, 35.2%), ovarian (n = 259, 12.7%), pancreatic (n = 85, 4.2%), or prostate cancer (n = 58, 2.9%). We observed 586 variants of uncertain significance (VUS) and 372 deleterious variants (DVs) across 487 patients, with 17.6% HRR-mutation positivity. HRR testing identified 120 (11.8%) BRCA1/2-positive, and 172 (16.9%) HRR-positive patients. With 51 DVs identified in 242 formalin-fixed paraffin-embedded (FFPE), testing for variant origin clarification was required in one case (0.4%). Most BRCA1/2 germline variants were DV (121 DVs, 26 VUS); in non-BRCA1/2 genes, VUS were ubiquitous (53 DVs, 132 VUS). In silico prediction identified additional 4.9% HRR and 1.2% BRCA1/2/ATM/CHEK2 mutation patients. Conclusions Our study represents one of the first reports about the incidence of DV and VUS in HRR genes, including genes beyond BRCA1/2, identified in cancer patients from Russia, assessed by NGS. In silico predictions of the observed HRR gene variants suggest that non-BRCA gene testing is likely to result in higher frequency of patients who are candidates for PARP inhibitor therapy. Continuing sequencing efforts should clarify interpretation of frequently observed non-BRCA VUS.
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Affiliation(s)
- Alexandra Lebedeva
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Egor Veselovsky
- OncoAtlas LLC, Moscow, Russia
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Ekaterina Belova
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Grigoreva
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Orlov
- The Federal Research Center for Fundamental and Translational Medicine (NIIECM FRC FTM), Novosibirsk, Russia
| | - Anna Subbotovskaya
- The Federal Research Center for Fundamental and Translational Medicine (NIIECM FRC FTM), Novosibirsk, Russia
| | - Maksim Shipunov
- The Federal Research Center for Fundamental and Translational Medicine (NIIECM FRC FTM), Novosibirsk, Russia
| | - Oleg Mashkov
- State Budgetary Institution of Healthcare Republican Medical Genetic Center, Ufa, Russia
| | - Fanil Bilalov
- State Budgetary Institution of Healthcare Republican Medical Genetic Center, Ufa, Russia
| | - Peter Shatalov
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Andrey Kaprin
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Peter Shegai
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | | | | | | | - Vladislav Mileyko
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Maxim Ivanov
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
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Nepomuceno TC, Lyra P, Zhu J, Yi F, Martin RH, Lupu D, Peterson L, Peres LC, Berry A, Iversen ES, Couch FJ, Mo Q, Monteiro AN. Assessment of BRCA1 and BRCA2 Germline Variant Data From Patients With Breast Cancer in a Real-World Data Registry. JCO Clin Cancer Inform 2024; 8:e2300251. [PMID: 38709234 PMCID: PMC11161245 DOI: 10.1200/cci.23.00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/12/2024] [Accepted: 03/13/2024] [Indexed: 05/07/2024] Open
Abstract
PURPOSE The emergence of large real-world clinical databases and tools to mine electronic medical records has allowed for an unprecedented look at large data sets with clinical and epidemiologic correlates. In clinical cancer genetics, real-world databases allow for the investigation of prevalence and effectiveness of prevention strategies and targeted treatments and for the identification of barriers to better outcomes. However, real-world data sets have inherent biases and problems (eg, selection bias, incomplete data, measurement error) that may hamper adequate analysis and affect statistical power. METHODS Here, we leverage a real-world clinical data set from a large health network for patients with breast cancer tested for variants in BRCA1 and BRCA2 (N = 12,423). We conducted data cleaning and harmonization, cross-referenced with publicly available databases, performed variant reassessment and functional assays, and used functional data to inform a variant's clinical significance applying American College of Medical Geneticists and the Association of Molecular Pathology guidelines. RESULTS In the cohort, White and Black patients were over-represented, whereas non-White Hispanic and Asian patients were under-represented. Incorrect or missing variant designations were the most significant contributor to data loss. While manual curation corrected many incorrect designations, a sizable fraction of patient carriers remained with incorrect or missing variant designations. Despite the large number of patients with clinical significance not reported, original reported clinical significance assessments were accurate. Reassessment of variants in which clinical significance was not reported led to a marked improvement in data quality. CONCLUSION We identify the most common issues with BRCA1 and BRCA2 testing data entry and suggest approaches to minimize data loss and keep interpretation of clinical significance of variants up to date.
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Affiliation(s)
- Thales C. Nepomuceno
- Department of Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Paulo Lyra
- Department of Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Jianbin Zhu
- AdventHealth Research Institute, Orlando, FL
| | - Fanchao Yi
- AdventHealth Research Institute, Orlando, FL
| | - Rachael H. Martin
- Department of Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | | | | | - Lauren C. Peres
- Department of Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Anna Berry
- AdventHealth Cancer Institute, Orlando, FL
| | | | | | - Qianxing Mo
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Alvaro N. Monteiro
- Department of Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
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Bypass of premature stop codons and generation of functional BRCA2 by exon skipping. J Hum Genet 2020; 65:805-809. [PMID: 32393813 DOI: 10.1038/s10038-020-0768-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/08/2020] [Accepted: 04/21/2020] [Indexed: 11/08/2022]
Abstract
A pathogenic mutation in BRCA2 significantly increases the risk of breast and ovarian cancers making it imperative to examine the functional consequences of variants of uncertain clinical significance. Variants that are predicted to result in a truncated protein are unambiguously classified as pathogenic. We have previously shown how a pathogenic splice site variant known to generate a premature termination codon (PTC) in exon 9 and a nonsense mutation at exon 7, can generate functional BRCA2 by skipping exons 4-7 and restoring the reading frame. Using a well-established mouse embryonic stem cell-based assay, we functionally characterize here one splice site mutation and 11 pathogenic BRCA2 variants that are either nonsense mutation or generate PTC in different exons ranging from exons 4 to 7. Our study shows that five variants can restore the open reading frame by exon skipping and generate a functional protein. This suggests further need to exercise prudence when classifying clearly pathogenic variants.
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Germline Missense Variants in BRCA1: New Trends and Challenges for Clinical Annotation. Cancers (Basel) 2019; 11:cancers11040522. [PMID: 31013702 PMCID: PMC6520942 DOI: 10.3390/cancers11040522] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/13/2019] [Accepted: 03/30/2019] [Indexed: 12/24/2022] Open
Abstract
Genetic testing allows for the identification of germline DNA variations, which are associated with a significant increase in the risk of developing breast cancer (BC) and ovarian cancer (OC). Detection of a BRCA1 or BRCA2 pathogenic variant triggers several clinical management actions, which may include increased surveillance and prophylactic surgery for healthy carriers or treatment with the PARP inhibitor therapy for carriers diagnosed with cancer. Thus, standardized validated criteria for the annotation of BRCA1 and BRCA2 variants according to their pathogenicity are necessary to support clinical decision-making and ensure improved outcomes. Upon detection, variants whose pathogenicity can be inferred by the genetic code are typically classified as pathogenic, likely pathogenic, likely benign, or benign. Variants whose impact on function cannot be directly inferred by the genetic code are labeled as variants of uncertain clinical significance (VUS) and are evaluated by multifactorial likelihood models that use personal and family history of cancer, segregation data, prediction tools, and co-occurrence with a pathogenic BRCA variant. Missense variants, coding alterations that replace a single amino acid residue with another, are a class of variants for which determination of clinical relevance is particularly challenging. Here, we discuss current issues in the missense variant classification by following a typical life cycle of a BRCA1 missense variant through detection, annotation and information dissemination. Advances in massively parallel sequencing have led to a substantial increase in VUS findings. Although the comprehensive assessment and classification of missense variants according to their pathogenicity remains the bottleneck, new developments in functional analysis, high throughput assays, data sharing, and statistical models are rapidly changing this scenario.
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