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Li C, Luo Y, Xie Y, Zhang Z, Liu Y, Zou L, Xiao F. Structural and functional prediction, evaluation, and validation in the post-sequencing era. Comput Struct Biotechnol J 2024; 23:446-451. [PMID: 38223342 PMCID: PMC10787220 DOI: 10.1016/j.csbj.2023.12.031] [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: 10/20/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/16/2024] Open
Abstract
The surge of genome sequencing data has underlined substantial genetic variants of uncertain significance (VUS). The decryption of VUS discovered by sequencing poses a major challenge in the post-sequencing era. Although experimental assays have progressed in classifying VUS, only a tiny fraction of the human genes have been explored experimentally. Thus, it is urgently needed to generate state-of-the-art functional predictors of VUS in silico. Artificial intelligence (AI) is an invaluable tool to assist in the identification of VUS with high efficiency and accuracy. An increasing number of studies indicate that AI has brought an exciting acceleration in the interpretation of VUS, and our group has already used AI to develop protein structure-based prediction models. In this review, we provide an overview of the previous research on AI-based prediction of missense variants, and elucidate the challenges and opportunities for protein structure-based variant prediction in the post-sequencing era.
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Affiliation(s)
- Chang Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yixuan Luo
- Beijing Normal University, Beijing, China
| | - Yibo Xie
- Information Center, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Zaifeng Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lihui Zou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Xiao
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Normal University, Beijing, China
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Takamatsu S, Hillman RT, Yoshihara K, Baba T, Shimada M, Yoshida H, Kajiyama H, Oda K, Mandai M, Okamoto A, Enomoto T, Matsumura N. Molecular classification of ovarian high-grade serous/endometrioid carcinomas through multi-omics analysis: JGOG3025-TR2 study. Br J Cancer 2024; 131:1340-1349. [PMID: 39215190 DOI: 10.1038/s41416-024-02837-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Considerable interobserver variability exists in diagnosis of ovarian high-grade endometrioid carcinoma (HGEC) and high-grade serous carcinoma (HGSC) due to histopathological similarities. While homologous recombination deficiency (HRD) correlates with drug sensitivity in HGSC, the molecular features of HGEC are unclear. METHODS Fresh-frozen samples from 15 ovarian HGECs and 274 ovarian HGSCs in the JGOG-TR2 cohort were submitted to targeted DNA sequencing, RNA sequencing, DNA methylation array, and SNP array. We additionally analyzed 555 ovarian HGSCs from TCGA-OV and 287 endometrial high-grade carcinomas from TCGA-UCEC. RESULTS Unsupervised clustering using copy number signatures identified four distinct tumor groups (C1, C2, C3 and C4). C1 (n = 41) showed CCNE1 amplification and poor survival. C2 (n = 160) and C3 (n = 59) showed high BRCA1/2 alteration frequency with low and moderate ploidy, respectively. C4 (n = 22) was characterized by favorable outcome, higher HGEC proportion, no BRCA1/2 alteration or CCNE1 amplification, and low levels of HRD score, ploidy, intra-tumoral heterogeneity, cell proliferation rate, and WT1 gene expression. Notably, C4 exhibited a normal endometrium-like DNA methylation profile, thus, defined as "HGEC-type" tumors, which were also identified in TCGA-OV and TCGA-UCEC. CONCLUSIONS Ovarian "HGEC-type" tumors present a non-HRD status, favorable prognosis, and endometrial differentiation, possibly constituting a subset of clinically diagnosed HGSCs.
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Affiliation(s)
- Shiro Takamatsu
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - R Tyler Hillman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- CPRIT Scholar in Cancer Research, Houston, TX, USA
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tsukasa Baba
- Department of Obstetrics and Gynecology, Iwate Medical University, Morioka, Japan
| | - Muneaki Shimada
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroshi Yoshida
- Department of Obstetrics and Gynecology, Tokai University Graduate School of Medicine, Isehara, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Katsutoshi Oda
- Division of Integrative Genomics, The University of Tokyo, Tokyo, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Noriomi Matsumura
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan.
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Toda S, Hiroshima Y, Iwasaki H, Masudo K. Genomic Landscape and Clinical Features of Advanced Thyroid Carcinoma: A National Database Study in Japan. J Clin Endocrinol Metab 2024; 109:2784-2792. [PMID: 38630010 DOI: 10.1210/clinem/dgae271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Indexed: 10/17/2024]
Abstract
CONTEXT The relationship between the genomic profile and prognosis of advanced thyroid carcinoma requiring drug therapy has not been reported. OBJECTIVE To evaluate the treatment period and overall survival time for each genetic alteration in advanced thyroid carcinoma that requires drug therapy. METHODS We conducted a retrospective observational study using a national database in Japan, which included 552 cases of thyroid carcinoma out of 53 543 patients in the database. RESULTS The database included anaplastic thyroid carcinoma (23.6%), poorly differentiated thyroid carcinoma (10.0%), and differentiated thyroid carcinoma (66.4%). The most common genetic abnormalities were TERT promoter (66.3%), BRAF (56.7%), and TP53 (32.2%). The typical driver genes were BRAF V600E (55.0%), RAS (18.5%), RET fusion (4.7%), NTRK fusion (1.6%), and ALK fusion (0.4%). The most common regimen was lenvatinib, and the time to treatment failure was not different despite the presence of BRAF or RAS mutations. In differentiated thyroid carcinoma and poorly differentiated thyroid carcinoma, TP53 alterations independently predicted worse overall survival (hazard ratio = 2.205, 95% confidence interval: 1.135-4.283). In anaplastic thyroid carcinoma, no genetic alterations were associated with overall survival. CONCLUSION Genetic abnormalities with treatment options were found in 62.7% of advanced thyroid carcinomas. TP53 abnormality was an independent poor prognostic factor for overall survival in differentiated thyroid carcinoma. The time to treatment failure for lenvatinib was not different based on genetic profile.
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Affiliation(s)
- Soji Toda
- Department of Endocrine Surgery, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
- Department of Breast and Thyroid Surgery, Yokohama City University Medical Center, Kanagawa 232-0024, Japan
| | - Yukihiko Hiroshima
- Department of Cancer Genome Medicine, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
- Research Institute Division of Advanced Cancer Therapeutics, Kanagawa Cancer Center Research Institute, Kanagawa 241-8515, Japan
| | - Hiroyuki Iwasaki
- Department of Endocrine Surgery, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
| | - Katsuhiko Masudo
- Department of Endocrine Surgery, Kanagawa Cancer Center, Kanagawa 241-8515, Japan
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Stark Z, Glazer D, Hofmann O, Rendon A, Marshall CR, Ginsburg GS, Lunt C, Allen N, Effingham M, Hastings Ward J, Hill SL, Ali R, Goodhand P, Page A, Rehm HL, North KN, Scott RH. A call to action to scale up research and clinical genomic data sharing. Nat Rev Genet 2024:10.1038/s41576-024-00776-0. [PMID: 39375561 DOI: 10.1038/s41576-024-00776-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2024] [Indexed: 10/09/2024]
Abstract
Genomic data from millions of individuals have been generated worldwide to drive discovery and clinical impact in precision medicine. Lowering the barriers to using these data collectively is needed to equitably realize the benefits of the diversity and scale of population data. We examine the current landscape of global genomic data sharing, including the evolution of data sharing models from data aggregation through to data visiting, and for certain use cases, cross-cohort analysis using federated approaches across multiple environments. We highlight emerging examples of best practice relating to participant, patient and community engagement; evolution of technical standards, tools and infrastructure; and impact of research and health-care policy. We outline 12 actions we can all take together to scale up efforts to enable safe global data sharing and move beyond projects demonstrating feasibility to routinely cross-analysing research and clinical data sets, optimizing benefit.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- University of Melbourne, Melbourne, Victoria, Australia.
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA.
| | - Oliver Hofmann
- Australian Genomics, Melbourne, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Melbourne, Victoria, Australia
| | | | - Christian R Marshall
- Division of Genome Diagnostics, Pediatric Laboratory Medicine Department, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Geoffrey S Ginsburg
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Chris Lunt
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Naomi Allen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- UK Biobank, Stockport, UK
| | | | | | - Sue L Hill
- National Health Service England, London, UK
| | - Raghib Ali
- Our Future Health, Manchester, UK
- Oxford University Hospitals NHS Trust, Oxford, UK
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Angela Page
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Heidi L Rehm
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn N North
- Australian Genomics, Melbourne, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Richard H Scott
- Genomics England, London, UK
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
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Buonaiuto R, Neola G, Caltavituro A, Longobardi A, Mangiacotti FP, Cefaliello A, Lamia MR, Pepe F, Ventriglia J, Malapelle U, Troncone G, Giuliano M, Arpino G, Pignata S, De Angelis C. Efficacy of PARP inhibitors in advanced high-grade serous ovarian cancer according to BRCA domain mutations and mutation type. Front Oncol 2024; 14:1412807. [PMID: 39314634 PMCID: PMC11416912 DOI: 10.3389/fonc.2024.1412807] [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: 04/05/2024] [Accepted: 08/22/2024] [Indexed: 09/25/2024] Open
Abstract
Objective Preclinical studies have emphasized the potential connection between BRCA specific domains defects and the activity of Poly ADP-ribose polymerase inhibitors (PARPi). Nevertheless, real-world evidence regarding the impact of BRCA domain defects and mutations on PARPi efficacy are limited. The aim of his study was to evaluate the efficacy of PARPi in terms of progression free survival (PFS) according to BRCA domains defects and mutation types. Methods A retrospective analysis was performed among 79 BRCA mutated patients, diagnosed with advanced High-grade serous ovarian carcinoma (HGSOC) who received first- and second-line platinum- based chemotherapy followed by PARPi maintenance treatment. PFS was evaluated according to BRCA1 [Really Interesting Gene (RING), DNA Binding (DBD), Serine Cluster (SCD), BRCA1 C-terminal (BRCT)] and BRCA2 [RAD-51 Domain (RAD-51 BD), DBD] specific domain defects and mutation types [missense (MS), nonsense (NS), frameshift (FS), splicing (S), or large rearrangements (LR)]. Results After a median follow-up of 51 months, no significant difference in PFS was observed between the BRCA functional domains or mutation types in the BRCA1 and BRCA2 subgroups. Patients with BRCA2 DBD and RAD51-BD defects had the longest (39.8 months) and shortest (24.1 months) median PFS, respectively (p = 0.11). Additionally, patients with BRCA1 DBD defects had the greatest benefit (median PFS = 33.8 months) while those with BRCA1 RING domain mutations experienced the worst outcome (median PFS = 30.9 months (p = 0.43). Conclusion The efficacy of maintenance treatment with PARPi is independent by BRCA domain defects or mutation types. Patients DBD domain defects experienced numerically longer median PFS compared to those with other BRCA1/2 alterations.
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Affiliation(s)
- Roberto Buonaiuto
- Scuola Superiore Meridionale (SSM), Clinical and Translational Oncology, Naples, Italy
- Department of Medical Oncology, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Giuseppe Neola
- Department of Medical Oncology, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Aldo Caltavituro
- Scuola Superiore Meridionale (SSM), Clinical and Translational Oncology, Naples, Italy
- Department of Medical Oncology, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Alessandra Longobardi
- Department of Medical Oncology, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Federica Pia Mangiacotti
- Department of Medical Oncology, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Amedeo Cefaliello
- Department of Medical Oncology, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Maria Rosaria Lamia
- Department of Medical Oncology, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Public Health Department, University of Naples Federico II, Naples, Italy
| | - Jole Ventriglia
- Urology and Gynecology Department, Istituto Nazionale Tumori IRCCS, Fondazione G. Pascale, Naples, Italy
| | - Umberto Malapelle
- Public Health Department, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Public Health Department, University of Naples Federico II, Naples, Italy
| | - Mario Giuliano
- Department of Medical Oncology, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Grazia Arpino
- Department of Medical Oncology, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Sandro Pignata
- Urology and Gynecology Department, Istituto Nazionale Tumori IRCCS, Fondazione G. Pascale, Naples, Italy
| | - Carmine De Angelis
- Department of Medical Oncology, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
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Parsons MT, de la Hoya M, Richardson ME, Tudini E, Anderson M, Berkofsky-Fessler W, Caputo SM, Chan RC, Cline MS, Feng BJ, Fortuno C, Gomez-Garcia E, Hadler J, Hiraki S, Holdren M, Houdayer C, Hruska K, James P, Karam R, Leong HS, Martins A, Mensenkamp AR, Monteiro AN, Nathan V, O'Connor R, Pedersen IS, Pesaran T, Radice P, Schmidt G, Southey M, Tavtigian S, Thompson BA, Toland AE, Turnbull C, Vogel MJ, Weyandt J, Wiggins GAR, Zec L, Couch FJ, Walker LC, Vreeswijk MPG, Goldgar DE, Spurdle AB. Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel. Am J Hum Genet 2024; 111:2044-2058. [PMID: 39142283 PMCID: PMC11393667 DOI: 10.1016/j.ajhg.2024.07.013] [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: 01/19/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 08/16/2024] Open
Abstract
The ENIGMA research consortium develops and applies methods to determine clinical significance of variants in hereditary breast and ovarian cancer genes. An ENIGMA BRCA1/2 classification sub-group, formed in 2015 as a ClinGen external expert panel, evolved into a ClinGen internal Variant Curation Expert Panel (VCEP) to align with Food and Drug Administration recognized processes for ClinVar contributions. The VCEP reviewed American College of Medical Genetics and Genomics/Association of Molecular Pathology (ACMG/AMP) classification criteria for relevance to interpreting BRCA1 and BRCA2 variants. Statistical methods were used to calibrate evidence strength for different data types. Pilot specifications were tested on 40 variants and documentation revised for clarity and ease of use. The original criterion descriptions for 13 evidence codes were considered non-applicable or overlapping with other criteria. Scenario of use was extended or re-purposed for eight codes. Extensive analysis and/or data review informed specification descriptions and weights for all codes. Specifications were applied to pilot variants with pre-existing ClinVar classification as follows: 13 uncertain significance or conflicting, 14 pathogenic and/or likely pathogenic, and 13 benign and/or likely benign. Review resolved classification for 11/13 uncertain significance or conflicting variants and retained or improved confidence in classification for the remaining variants. Alignment of pre-existing ENIGMA research classification processes with ACMG/AMP classification guidelines highlighted several gaps in the research processes and the baseline ACMG/AMP criteria. Calibration of evidence strength was key to justify utility and strength of different data types for gene-specific application. The gene-specific criteria demonstrated value for improving ACMG/AMP-aligned classification of BRCA1 and BRCA2 variants.
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Affiliation(s)
- Michael T Parsons
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, 28040 Madrid Spain
| | | | - Emma Tudini
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | | | - Sandrine M Caputo
- Department of Genetics, Institut Curie, and Paris Sciences Lettres Research University, 75005 Paris, France
| | | | - Melissa S Cline
- UC Santa Cruz Genomics Institute, Genomics, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Bing-Jian Feng
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Cristina Fortuno
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Encarna Gomez-Garcia
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Johanna Hadler
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Megan Holdren
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Claude Houdayer
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics, FHU G4 Génomique, F-76000 Rouen, France
| | | | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rachid Karam
- Ambry Genetics Corporation, Aliso Viejo, CA 92656, USA
| | - Huei San Leong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | | | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, H Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Vaishnavi Nathan
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Inge Sokilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Tina Pesaran
- Ambry Genetics Corporation, Aliso Viejo, CA 92656, USA
| | - Paolo Radice
- Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Gunnar Schmidt
- Institute of Human Genetics, Hannover Medical School, 30625 Hannover, Germany
| | - Melissa Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sean Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84132, USA
| | - Bryony A Thompson
- Department of Pathology, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Clare Turnbull
- Translational Genetics Team, Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Maartje J Vogel
- Department of Human Genetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jamie Weyandt
- Ambry Genetics Corporation, Aliso Viejo, CA 92656, USA
| | - George A R Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
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Duarte CAB, dos Santos CA, de Oliveira CDD, Spautz CC, Sumita LM, Nakatani SM. Hereditary breast cancer next-generation sequencing panel evaluation in the south region of Brazil: A novel BRCA2 candidate pathogenic variant is reported. Mol Genet Genomic Med 2024; 12:e2504. [PMID: 39126233 PMCID: PMC11316010 DOI: 10.1002/mgg3.2504] [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: 03/14/2024] [Revised: 07/08/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND In this article, we delineate a loosely selected cohort comprising patients with a history of early-onset breast cancer and/or a familial occurrence of cancer. The aim of this study was to gain insights into the presence of breast cancer-related gene variants in a population from a micro-region in southern Brazil, specifically the Metropolitan Region of Curitiba. This area exhibits a highly genetically mixed population, mirroring the general characteristics of the Brazilian people. METHODS Comprehensive next-generation sequencing (NGS) multigene panel testing was conducted on 12 patients from the region, utilizing three different library preparation methods. RESULTS Two pathogenic variants and one candidate pathogenic variant were identified: BRCA2 c.8878C>T, p.Gln2960Ter; CHEK2 c.1100del, p.Thr367Metfs15, and BRCA2 c.3482dup, p.Asp1161Glufs3. CONCLUSION BRCA2 c.3482dup, a novel candidate pathogenic variant, previously unpublished, is reported. The prevalence of pathogenic variants in this small cohort is similar to that described in the literature. All different library preparation methods were equally proficient in enabling the detection of these variants.
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Affiliation(s)
| | | | | | | | - Laura Masami Sumita
- Molecular Biology Clinical LaboratoryClinimol Diagnóstico MolecularSão PauloSão PauloBrazil
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8
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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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He J, Kou SH, Li J, Ding X, Wang SM. Pathogenic variants in human DNA damage repair genes mostly arose after the latest human out-of-Africa migration. Front Genet 2024; 15:1408952. [PMID: 38948361 PMCID: PMC11211533 DOI: 10.3389/fgene.2024.1408952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Introduction The DNA damage repair (DDR) system in human genome is pivotal in maintaining genomic integrity. Pathogenic variation (PV) in DDR genes impairs their function, leading to genome instability and increased susceptibility to diseases, especially cancer. Understanding the evolution origin and arising time of DDR PV is crucial for comprehending disease susceptibility in modern humans. Methods We used big data approach to identify the PVs in DDR genes in modern humans. We mined multiple genomic databases derived from 251,214 modern humans of African and non-Africans. We compared the DDR PVs between African and non-African. We also mined the DDR PVs in the genomic data derived from 5,031 ancient humans. We used the DDR PVs from ancient humans as the intermediate to further the DDR PVs between African and non-African. Results and discussion We identified 1,060 single-base DDR PVs across 77 DDR genes in modern humans of African and non-African. Direct comparison of the DDR PVs between African and non-African showed that 82.1% of the non-African PVs were not present in African. We further identified 397 single-base DDR PVs in 56 DDR genes in the 5,031 ancient humans dated between 45,045 and 100 years before present (BP) lived in Eurasian continent therefore the descendants of the latest out-of-Africa human migrants occurred 50,000-60,000 years ago. By referring to the ancient DDR PVs, we observed that 276 of the 397 (70.3%) ancient DDR PVs were exclusive in non-African, 106 (26.7%) were shared between non-African and African, and only 15 (3.8%) were exclusive in African. We further validated the distribution pattern by testing the PVs in BRCA and TP53, two of the important genes in genome stability maintenance, in African, non-African, and Ancient humans. Our study revealed that DDR PVs in modern humans mostly emerged after the latest out-of-Africa migration. The data provides a foundation to understand the evolutionary basis of disease susceptibility, in particular cancer, in modern humans.
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Affiliation(s)
| | | | | | | | - San Ming Wang
- Department of Public Health and Medical Administration, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, University of Macau, Taipa, China
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10
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Öfverholm I, Wallander K, Haglund C, Chellappa V, Wejde J, Gellerbring A, Wirta V, Renevey A, Caceres E, Tsagkozis P, Mayrhofer M, Papakonstantinou A, Linder-Stragliotto C, Bränström R, Larsson O, Lindberg J, Lin Y, Haglund de Flon F. Comprehensive Genomic Profiling Alters Clinical Diagnoses in a Significant Fraction of Tumors Suspicious of Sarcoma. Clin Cancer Res 2024; 30:2647-2658. [PMID: 38573684 DOI: 10.1158/1078-0432.ccr-24-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE Tumor classification is a key component in personalized cancer care. For soft-tissue and bone tumors, this classification is currently based primarily on morphology assessment and IHC staining. However, these standard-of-care methods can pose challenges for pathologists. We therefore assessed how whole-genome and whole-transcriptome sequencing (WGTS) impacted tumor classification and clinical management when interpreted together with histomorphology. EXPERIMENTAL DESIGN We prospectively evaluated WGTS in routine diagnostics of 200 soft-tissue and bone tumors suspicious for malignancy, including DNA and RNA isolation from the tumor, and DNA isolation from a peripheral blood sample or any non-tumor tissue. RESULTS On the basis of specific genomic alterations or absence of presumed findings, WGTS resulted in reclassification of 7% (13/197) of the histopathologic diagnoses. Four cases were downgraded from low-grade sarcomas to benign lesions, and two cases were reclassified as metastatic malignant melanomas. Fusion genes associated with specific tumor entities were found in 30 samples. For malignant soft-tissue and bone tumors, we identified treatment relevant variants in 15% of cases. Germline pathogenic variants associated with a hereditary cancer syndrome were found in 22 participants (11%). CONCLUSIONS WGTS provides an important dimension of data that aids in the classification of soft-tissue and bone tumors, correcting a significant fraction of clinical diagnoses, and identifies molecular targets relevant for precision medicine. However, genetic findings need to be evaluated in their morphopathologic context, just as germline findings need to be evaluated in the context of patient phenotype and family history.
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Affiliation(s)
- Ingegerd Öfverholm
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Wallander
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Haglund
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Venkatesh Chellappa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Wejde
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Gellerbring
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Annick Renevey
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Eva Caceres
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Panagiotis Tsagkozis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Markus Mayrhofer
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andri Papakonstantinou
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Breast Cancer, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
| | | | - Robert Bränström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Breast Cancer, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
| | - Olle Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yingbo Lin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Felix Haglund de Flon
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
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Xiao Q, Mao X, Ploner A, Grassmann F, Rodriguez J, Eriksson M, Hall P, Czene K. Cancer risks among first-degree relatives of women with a genetic predisposition to breast cancer. J Natl Cancer Inst 2024; 116:911-919. [PMID: 38366028 PMCID: PMC11160497 DOI: 10.1093/jnci/djae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Associations between germline alterations in women and cancer risks among their relatives are largely unknown. METHODS We identified women from 2 Swedish cohorts Karolinska Mammography Project for Risk Prediction of Breast Cancer (KARMA) and prevalent KARMA (pKARMA), including 28 362 women with genotyping data and 13 226 with sequencing data. Using Swedish Multi-Generation Register, we linked these women to 133 389 first-degree relatives. Associations between protein-truncating variants in 8 risk genes and breast cancer polygenic risk score in index women and cancer risks among their relatives were modeled via Cox regression. RESULTS Female relatives of index women who were protein-truncating variant carriers in any of the 8 risk genes had an increased breast cancer risk compared with those of noncarriers (hazard ratio [HR] = 1.85, 95% confidence interval [CI] = 1.52 to 2.27), with the strongest association found for protein-truncating variants in BRCA1 and 2. These relatives had a statistically higher risk of early onset than late-onset breast cancer (P = .001). Elevated breast cancer risk was also observed in female relatives of index women with higher polygenic risk score (HR per SD = 1.28, 95% CI = 1.23 to 1.32). The estimated lifetime risk was 22.3% for female relatives of protein-truncating variant carriers and 14.4% for those related to women in the top polygenic risk score quartile. Moreover, relatives of index women with protein-truncating variant presence (HR = 1.30, 95% CI = 1.06 to 1.59) or higher polygenic risk score (HR per SD = 1.04, 95% CI = 1.01 to 1.07) were also at higher risk of nonbreast hereditary breast and ovary cancer syndrome-related cancers. CONCLUSIONS Protein-truncating variants of risk genes and higher polygenic risk score in index women are associated with an increased risk of breast and other hereditary breast and ovary syndrome-related cancers among relatives.
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Affiliation(s)
- Qingyang Xiao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Xinhe Mao
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Felix Grassmann
- Institute for Clinical Research and Systems Medicine, Health and Medical University, Potsdam, Germany
| | - Juan Rodriguez
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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Arends CM, Kopp K, Hablesreiter R, Estrada N, Christen F, Moll UM, Zeillinger R, Schmitt WD, Sehouli J, Kulbe H, Fleischmann M, Ray-Coquard I, Zeimet A, Raspagliesi F, Zamagni C, Vergote I, Lorusso D, Concin N, Bullinger L, Braicu EI, Damm F. Dynamics of clonal hematopoiesis under DNA-damaging treatment in patients with ovarian cancer. Leukemia 2024; 38:1378-1389. [PMID: 38637689 PMCID: PMC11147769 DOI: 10.1038/s41375-024-02253-3] [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: 02/10/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024]
Abstract
Clonal hematopoiesis (CH) driven by mutations in the DNA damage response (DDR) pathway is frequent in patients with cancer and is associated with a higher risk of therapy-related myeloid neoplasms (t-MNs). Here, we analyzed 423 serial whole blood and plasma samples from 103 patients with relapsed high-grade ovarian cancer receiving carboplatin, poly(ADP-ribose) polymerase inhibitor (PARPi) and heat shock protein 90 inhibitor (HSP90i) treatment within the phase II EUDARIO trial using error-corrected sequencing of 72 genes. DDR-driven CH was detected in 35% of patients and was associated with longer duration of prior PARPi treatment. TP53- and PPM1D-mutated clones exhibited substantially higher clonal expansion rates than DNMT3A- or TET2-mutated clones during treatment. Expansion of DDR clones correlated with HSP90i exposure across the three study arms and was partially abrogated by the presence of germline mutations related to homologous recombination deficiency. Single-cell DNA sequencing of selected samples revealed clonal exclusivity of DDR mutations, and identified DDR-mutated clones as the origin of t-MN in two investigated cases. Together, these results provide unique insights into the architecture and the preferential selection of DDR-mutated hematopoietic clones under intense DNA-damaging treatment. Specifically, PARPi and HSP90i therapies pose an independent risk for the expansion of DDR-CH in a dose-dependent manner.
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Affiliation(s)
- Christopher Maximilian Arends
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Klara Kopp
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Raphael Hablesreiter
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Natalia Estrada
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Friederike Christen
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ute Martha Moll
- Department of Pathology, Stony Brook University Cancer Center, Stony Brook, NY, 11794, USA
| | - Robert Zeillinger
- Department of Obstetrics and Gynaecology, Molecular Oncology Group, Comprehensive Cancer Center-Gynaecologic Cancer Unit, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Daniel Schmitt
- Department of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Jalid Sehouli
- Department of Gynaecology, European Competence Center for Ovarian Cancer, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Campus Virchow Klinikum, Berlin, Germany
- North Eastern German Society for Gynecological Cancer. Tumor Bank Ovarian Cancer Network, Berlin, Germany
| | - Hagen Kulbe
- Department of Gynaecology, European Competence Center for Ovarian Cancer, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Campus Virchow Klinikum, Berlin, Germany
- North Eastern German Society for Gynecological Cancer. Tumor Bank Ovarian Cancer Network, Berlin, Germany
| | - Maximilian Fleischmann
- Klinik für Innere Medizin II, Abteilung Hämatologie und Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Isabelle Ray-Coquard
- Centre Anticancereux Léon Bérard, University Claude Bernard Lyon, GINECO Group, Lyon, France
| | - Alain Zeimet
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Austrian AGO, Innsbruck, Austria
| | | | - Claudio Zamagni
- Division of Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Leuven Cancer Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Belgium and Luxembourg Gynaecological Oncology Group (BGOG), Leuven, Belgium
| | | | - Nicole Concin
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Austrian AGO, Innsbruck, Austria
| | - Lars Bullinger
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elena Ioana Braicu
- Department of Gynaecology, European Competence Center for Ovarian Cancer, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Campus Virchow Klinikum, Berlin, Germany
- North Eastern German Society for Gynecological Cancer. Tumor Bank Ovarian Cancer Network, Berlin, Germany
| | - Frederik Damm
- Department of Hematology, Oncology, and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Hassan AN, Mustafa MS. Breast Cancer High-Penetrance Genes BRCA1 and BRCA2 Mutations Using Next-Generation Sequencing Among Iraqi Kurdish Women. Cureus 2024; 16:e62160. [PMID: 38863777 PMCID: PMC11166091 DOI: 10.7759/cureus.62160] [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] [Accepted: 06/10/2024] [Indexed: 06/13/2024] Open
Abstract
Background BRCA1 and BRCA2 genes are the main high-penetrance genes that are responsible for most cases of inherited breast cancer. The present study aimed to detect the frequencies of inherited breast cancer caused by BRCA1 and BRCA2 genes among Kurdish breast cancer patients, including all the exome of these two genes, using next-generation sequencing (NGS). Methodology Seventy women who were diagnosed with breast cancer and registered at Nanakali Hospital in Erbil, Iraq, were included. Blood samples were collected for molecular testing (polymerase chain reaction (PCR)) targeting all exomes of BRCA1 and BRCA2 genes. All exome regions are sequenced by NGS using the Miseq system (Illumina Inc., San Diego, CA). Obtained data were visualized using Integrative Genomics Viewer (IGV 2.3 Software, Broad Institute, Cambridge, MA). Data were interpreted based on the National Center for Biotechnology Information (NCBI), Clinically Relevant Variation (ClinVar) archives, and other databases. Results Among 70 samples, more than forty-two variants have been detected, 20 on BRCA1 and 22 on BRCA2. Regarding clinical significance, six (14.28%) variants were pathogenic, four of them on the BRCA1 gene, which were: c.3607C>T, c.3544C>T, c.68_69del, and c.224_227delAAAG, and two pathogenic variants were on BRCA2 gene: c.100G>T, and c.1813delA. Also, two (4.76%) variants were conflict interpretations of pathogenicity, one (2.38%) was a variant of uncertain significant VUS, and the rest 29 (69%) variants were benign. In addition, four new variants (three in BRCA1 and one in BRCA2 gene), never previously reported, were identified. Conclusions In conclusion, analyzing the BRCA1/2 genes provide a better prediction for the risk of developing breast cancer in the future. Variant types and frequencies differ among different populations and ethnicities, the common mutations worldwide may not be prevalent in the Kurdish population. The current research findings will be useful for future screening studies of these two genes in the Kurdish population.
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Affiliation(s)
- Ahmad N Hassan
- Department of Medical Laboratory Technology, Erbil Technical Health and Medical College, Erbil Polytechnic University, Erbil, IRQ
| | - Mustafa S Mustafa
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, IRQ
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Andaluz S, Zhao B, Sinha S, Lagniton PNP, Costa DA, Ding X, Brito M, Wang SM. Using Portuguese BRCA pathogenic variation as a model to study the impact of human admixture on human health. BMC Genomics 2024; 25:416. [PMID: 38671360 PMCID: PMC11055274 DOI: 10.1186/s12864-024-10311-4] [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: 08/13/2023] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Admixture occurs between different ethnic human populations. The global colonization in recent centuries by Europeans led to the most significant admixture in human history. While admixture may enhance genetic diversity for better fitness, it may also impact on human health by transmitting genetic variants for disease susceptibility in the admixture population. The admixture by Portuguese global exploration initiated in the 15th century has reached over 20 million of Portuguese-heritage population worldwide. It provides a valuable model to study the impact of admixture on human health. BRCA1 and BRCA2 (BRCA) are two of the important tumor suppressor genes. The pathogenic variation (PV) in BRCA is well determined to cause high risk of hereditary breast and ovarian cancer. Tracing the distribution of Portuguese BRCA PV in Portuguese-heritage population will help to understand the impact of admixture on cancer susceptibility in modern humans. In this study, we analyzed the distribution of the Portuguese-originated BRCA variation in Brazilian population, which has high degree Portuguese-heritage. METHODS By comprehensive data mining, standardization and annotation, we generated a Portuguese-derived BRCA variation dataset and a Brazilian-derived BRCA variation dataset. We compared the two BRCA variation datasets to identify the BRCA variants shared between the two populations. RESULTS The Portuguese-derived BRCA variation dataset consists of 220 BRCA variants including 78 PVs from 11,482 Portuguese cancer patients, 93 (42.2%) in BRCA1 and 127 (57.7%) in BRCA2. Of the 556 Portuguese BRCA PV carriers carrying the 78 PVs, 331 (59.5%) carried the three Portuguese-BRCA founder PVs of BRCA1 c.2037delinsCC, BRCA1 c.3331_3334del and BRCA2 c.156_157insAlu. The Brazilian-derived BRCA variation dataset consists of 255 BRCA PVs from 7,711 cancer patients, 136 (53.3%) in BRCA1 and 119 (46.6%) in BRCA2. We developed an open database named dbBRCA-Portuguese ( https://genemutation.fhs.um.edu.mo/dbbrca-portuguese/ ) and an open database named dbBRCA-Brazilian ( https://genemutation.fhs.um.edu.mo/dbbrca-brazilian ) to host the BRCA variation data from Portuguese and Brazilian populations. We compared the BRCA PV datasets between Portuguese and Brazilian populations, and identified 29 Portuguese-specific BRCA PVs shared between Portuguese and Brazilian populations, 14 in BRCA1 including the Portuguese founder BRCA1 c.3331_3334del and BRCA1 c.2037delinsCC, and 15 in BRCA2 including the Portuguese founder BRCA2 c.156_157insAlu. Searching the 78 Portuguese BRCA PVs in over 5,000 ancient human genomes identified evolution origin for only 8 PVs in Europeans dated between 37,470 and 3,818 years before present, confirming the Portuguese-specificity of Portuguese BRCA PVs; comparing the 78 Portuguese BRCA PVs Portuguese, 255 Brazilian BRCA PVs, and 134 African BRCA PVs showed little overlapping, ruling out the possibility that the BRCA PVs shared between Portuguese and Brazilian may also be contributed by African. CONCLUSION Our study provides evidence that the admixture in recent human history contributed to cancer susceptibility in modern humans.
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Affiliation(s)
- Stephanie Andaluz
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Siddharth Sinha
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Philip Naderev Panuringan Lagniton
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Diogo Alpuim Costa
- Medical Oncology Department, Hospital de Cascais, Cascais; Haematology and Oncology Department, CUF Oncologia, Lisbon; NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Xiaofan Ding
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Miguel Brito
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal.
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China.
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15
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Zhao B, Li J, Sinha S, Qin Z, Kou SH, Xiao F, Lei H, Chen T, Cao W, Ding X, Wang SM. Pathogenic variants in human DNA damage repair genes mostly arose in recent human history. BMC Cancer 2024; 24:415. [PMID: 38575974 PMCID: PMC10993466 DOI: 10.1186/s12885-024-12160-6] [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: 09/21/2023] [Accepted: 03/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Genome stability is maintained by the DNA damage repair (DDR) system composed of multiple DNA repair pathways of hundreds of genes. Germline pathogenic variation (PV) in DDR genes damages function of the affected DDR genes, leading to genome instability and high risk of diseases, in particular, cancer. Knowing evolutionary origin of the PVs in human DDR genes is essential to understand the etiology of human diseases. However, answer to the issue remains largely elusive. In this study, we analyzed evolutionary origin for the PVs in human DDR genes. METHODS We identified 169 DDR genes by referring to various databases and identified PVs in the DDR genes of modern humans from ClinVar database. We performed a phylogenetic analysis to analyze the conservation of human DDR PVs in 100 vertebrates through cross-species genomic data comparison using the phyloFit program of the PHAST package and visualized the results using the GraphPad Prism software and the ggplot module. We identified DDR PVs from over 5000 ancient humans developed a database to host the DDR PVs ( https://genemutation.fhs.um.edu.mo/dbDDR-AncientHumans ). Using the PV data, we performed a molecular archeological analysis to compare the DDR PVs between modern humans and ancient humans. We analyzed evolution selection of DDR genes across 20 vertebrates using the CodeML in PAML for phylogenetic analysis. RESULTS Our phylogenic analysis ruled out cross-species conservation as the origin of human DDR PVs. Our archeological approach identified rich DDR PVs shared between modern and ancient humans, which were mostly dated within the last 5000 years. We also observed similar pattern of quantitative PV distribution between modern and ancient humans. We further detected a set of ATM, BRCA2 and CHEK2 PVs shared between human and Neanderthals. CONCLUSIONS Our study reveals that human DDR PVs mostly arose in recent human history. We propose that human high cancer risk caused by DDR PVs can be a by-product of human evolution.
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Affiliation(s)
- Bojin Zhao
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Jiaheng Li
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Siddharth Sinha
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Zixin Qin
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Si Hoi Kou
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Fengxia Xiao
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Huijun Lei
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Tianhui Chen
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, China
| | - Wenming Cao
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, China
| | - Xiaofan Ding
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China.
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16
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Mishra N, Dubey S, Kumari A, Khan MA, Kuligina ES, Preobrazhenskaya EV, Romanko AA, Yadav LR, Sarin R, Imyanitov EN, Varma AK. Structural implications of amyloidogenic rare variants Ser282Leu and Gln356Arg identified in h-BRCA1. Proteins 2024; 92:540-553. [PMID: 38037760 DOI: 10.1002/prot.26638] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Preliminary studies have shown BRCA1 (170-1600) residues to be intrinsically disordered with unknown structural details. However, thousands of clinically reported variants have been identified in this central region of BRCA1. Therefore, we aimed to characterize h-BRCA1(260-553) to assess the structural basis for pathogenicity of two rare missense variants Ser282Leu, Gln356Arg identified from the Indian and Russian populations respectively. Small-angle X-ray scattering analysis revealed WT scores Rg -32 Å, Dmax -93 Å, and Rflex-51% which are partially disordered, whereas Ser282Leu variant displayed a higher degree of disorderedness and Gln356Arg was observed to be aggregated. WT protein also possesses an inherent propensity to undergo a disorder-to-order transition in the presence of cruciform DNA and 2,2,2-Trifluoroethanol (TFE). An increased alpha-helical pattern was observed with increasing concentration of TFE for the Gln356Arg mutant whereas Ser282Leu mutant showed significant differences only at the highest TFE concentration. Furthermore, higher thermal shift was observed for WT-DNA complex compared to the Gln356Arg and Ser282Leu protein-DNA complex. Moreover, mature amyloid-like fibrils were observed with 30 μM thioflavin T (ThT) at 37°C for Ser282Leu and Gln356Arg proteins while the WT protein exists in a protofibril state as observed by TEM. Gln356Arg formed higher-order aggregates with amyloidogenesis over time as monitored by ThT fluorescence. In addition, computational analyses confirmed larger conformational fluctuations for Ser282Leu and Gln356Arg mutants than for the WT. The global structural alterations caused by these variants provide a mechanistic approach for further classification of the variants of uncertain clinical significance in BRCA1 into amyloidogenic variants which may have a significant role in disease pathogenesis.
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Affiliation(s)
- Neha Mishra
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Suchita Dubey
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Anchala Kumari
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Mudassar Ali Khan
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Ekaterina S Kuligina
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Elena V Preobrazhenskaya
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Alexandr A Romanko
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Lumbini R Yadav
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Rajiv Sarin
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Evgeny N Imyanitov
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
- Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg, Russia
| | - Ashok K Varma
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
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17
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Mishra N, Dubey S, Kumari A, Siddiqui MQ, Kuligina E, Varma AK. Variant of uncertain significance Arg866Cys enhances disorderedness of h-BRCA1 (759-1064) region. Int J Biochem Cell Biol 2024; 168:106527. [PMID: 38242199 DOI: 10.1016/j.biocel.2024.106527] [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: 04/17/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
High structural flexibility has been reported in the central region of BRCA1, which hinders the structural and functional evaluations of mutations identified in the domain. Additionally, the need to categorize variants of unknown significance (VUS) has increased due to the growth in the number of variants reported in clinical settings. Therefore, unraveling the disease-causing mechanism of VUS identified in different functional domains of BRCA1 is still challenging. The current study uses a multidisciplinary approach to assess the structural impact of BRCA1 Arg866Cys mutation discovered in the central domain of BRCA1. The structural alterations have been characterized using Circular-Dichroism spectroscopy, nano-DSF, and molecular-dynamics simulations. BRCA1 Arg866Cys mutant demonstrated more flexibility and lesser affinity to DNA than the wild-type protein. The BRCA1(759-1064) wild-type protein was shown to be a βII-rich protein with an induced D-O transition in the presence of DNA and 2,2,2-Trifluoroethanol (TFE). The protein's alpha-helical composition did not significantly change in the presence of TFE, besides an increase in β-turns and loops. Under Transmission Electron Microscopes (TEM), amyloid-like fibrils structure was detected for Arg866Cys mutant whereas the wild-type protein showed amorphous aggregates. An increased ThT fluorescence indicated β-rich composition and aggregation-prone behaviour for BRCA1 wild-type protein, while the fluorescence intensity was significantly quenched in the Arg866Cys mutant. Furthermore, increased conformational flexibility in the Arg866Cys variant was observed by principal component analysis. This work aims to comprehend the inherently disordered region of BRCA1 as well as the impact of missense mutations on folding patterns and binding to DNA for functional aspects.
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Affiliation(s)
- Neha Mishra
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, Maharashtra 400094, India
| | - Suchita Dubey
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, Maharashtra 400094, India
| | - Anchala Kumari
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - M Quadir Siddiqui
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - Ekaterina Kuligina
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, RU-197758, Pesochny-2, St.-Petersburg, Russia
| | - Ashok K Varma
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, Maharashtra 400094, India.
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18
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Duarte CAB, Dos Santos CA, de Oliveira CDD, Spautz CC, Sumita LM, Nakatani SM. Hereditary breast cancer next-generation sequencing (NGS) panel evaluation in the south region of Brazil: a novel BRCA2 candidate pathogenic variant is reported. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.08.24302195. [PMID: 38370791 PMCID: PMC10871466 DOI: 10.1101/2024.02.08.24302195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
In this article, we delineate a loosely selected cohort comprising patients with a history of early-onset breast cancer and/or a familial occurrence of cancer. The aim of this study was to gain insights into the presence of breast cancer-related gene variants in a population from a micro-region in southern Brazil, specifically the Metropolitan Region of Curitiba. This area exhibits a highly genetically mixed population, mirroring the general characteristics of the Brazilian people. Comprehensive next-generation sequencing (NGS) multigene panel testing was conducted, involving the evaluation of twelve patients. Two pathogenic variants and one candidate pathogenic variant were identified: BRCA2:c.8878C>T, p.Gln2960Ter; CHEK2:c.1100delAG>A, p.Thr367Metfs*15 and BRCA2:c.3482dupG>GA, p.Asp1161Glufs*3, a novel variant, previously unpublished, is reported.
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Affiliation(s)
- Cesar Augusto B Duarte
- Research and Development Division, Genoprimer Diagnóstico Molecular, Curitiba, Paraná, Brazil
| | | | | | | | - Laura Masami Sumita
- Clinimol Diagnóstico Molecular, Molecular Biology Clinical Laboratory, São Paulo, São Paulo, Brazil
| | - Sueli Massumi Nakatani
- Research and Development Division, Genoprimer Diagnóstico Molecular, Curitiba, Paraná, Brazil
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19
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Barili V, Ambrosini E, Bortesi B, Minari R, De Sensi E, Cannizzaro IR, Taiani A, Michiara M, Sikokis A, Boggiani D, Tommasi C, Serra O, Bonatti F, Adorni A, Luberto A, Caggiati P, Martorana D, Uliana V, Percesepe A, Musolino A, Pellegrino B. Genetic Basis of Breast and Ovarian Cancer: Approaches and Lessons Learnt from Three Decades of Inherited Predisposition Testing. Genes (Basel) 2024; 15:219. [PMID: 38397209 PMCID: PMC10888198 DOI: 10.3390/genes15020219] [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: 12/30/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Germline variants occurring in BRCA1 and BRCA2 give rise to hereditary breast and ovarian cancer (HBOC) syndrome, predisposing to breast, ovarian, fallopian tube, and peritoneal cancers marked by elevated incidences of genomic aberrations that correspond to poor prognoses. These genes are in fact involved in genetic integrity, particularly in the process of homologous recombination (HR) DNA repair, a high-fidelity repair system for mending DNA double-strand breaks. In addition to its implication in HBOC pathogenesis, the impairment of HR has become a prime target for therapeutic intervention utilizing poly (ADP-ribose) polymerase (PARP) inhibitors. In the present review, we introduce the molecular roles of HR orchestrated by BRCA1 and BRCA2 within the framework of sensitivity to PARP inhibitors. We examine the genetic architecture underneath breast and ovarian cancer ranging from high- and mid- to low-penetrant predisposing genes and taking into account both germline and somatic variations. Finally, we consider higher levels of complexity of the genomic landscape such as polygenic risk scores and other approaches aiming to optimize therapeutic and preventive strategies for breast and ovarian cancer.
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Affiliation(s)
- Valeria Barili
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Enrico Ambrosini
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Beatrice Bortesi
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Roberta Minari
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Erika De Sensi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Antonietta Taiani
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Maria Michiara
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Angelica Sikokis
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Daniela Boggiani
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Chiara Tommasi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Olga Serra
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Francesco Bonatti
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Alessia Adorni
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Anita Luberto
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Antonio Percesepe
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Antonino Musolino
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Benedetta Pellegrino
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
- Breast Unit, University Hospital of Parma, 43126 Parma, Italy
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20
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Gandhi H, Kumar K. Artificial Intelligence for the Management of Breast Cancer: An Overview. Curr Drug Discov Technol 2024; 21:e031123223115. [PMID: 38047362 DOI: 10.2174/0115701638262066231030052520] [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: 06/15/2023] [Revised: 08/22/2023] [Accepted: 08/30/2023] [Indexed: 12/05/2023]
Abstract
Breast cancer is a severe global health problem, and early detection, accurate diagnosis, and personalized treatment is the key to improving patient outcomes. Artificial intelligence (AI) and machine learning (ML) have emerged as promising breast cancer research and clinical practice tools in recent years. Various projects are underway in early detection, diagnosis, prognosis, drug discovery, advanced image analysis, precision medicine, predictive modeling, and personalized treatment planning using artificial intelligence and machine learning. These projects use different algorithms, including convolutional neural networks (CNNs), support vector machines (SVMs), decision trees, and deep learning methods, to analyze and improve different types of data, such as clinical, genomic, and imaging data for breast cancer management. The success of these projects has the potential to transform breast cancer care, and continued research and development in this area is likely to lead to more accurate and personalized breast cancer diagnosis, treatment, and outcomes.
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Affiliation(s)
- Harshita Gandhi
- School of Pharmaceutical Sciences, Apeejay Stya University, Gurugram, Haryana 122103, India
| | - Kapil Kumar
- School of Pharmaceutical Sciences, Apeejay Stya University, Gurugram, Haryana 122103, India
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21
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Tsimberidou AM, Kahle M, Vo HH, Baysal MA, Johnson A, Meric-Bernstam F. Molecular tumour boards - current and future considerations for precision oncology. Nat Rev Clin Oncol 2023; 20:843-863. [PMID: 37845306 DOI: 10.1038/s41571-023-00824-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2023] [Indexed: 10/18/2023]
Abstract
Over the past 15 years, rapid progress has been made in developmental therapeutics, especially regarding the use of matched targeted therapies against specific oncogenic molecular alterations across cancer types. Molecular tumour boards (MTBs) are panels of expert physicians, scientists, health-care providers and patient advocates who review and interpret molecular-profiling results for individual patients with cancer and match each patient to available therapies, which can include investigational drugs. Interpretation of the molecular alterations found in each patient is a complicated task that requires an understanding of their contextual functional effects and their correlations with sensitivity or resistance to specific treatments. The criteria for determining the actionability of molecular alterations and selecting matched treatments are constantly evolving. Therefore, MTBs have an increasingly necessary role in optimizing the allocation of biomarker-directed therapies and the implementation of precision oncology. Ultimately, increased MTB availability, accessibility and performance are likely to improve patient care. The challenges faced by MTBs are increasing, owing to the plethora of identifiable molecular alterations and immune markers in tumours of individual patients and their evolving clinical significance as more and more data on patient outcomes and results from clinical trials become available. Beyond next-generation sequencing, broader biomarker analyses can provide useful information. However, greater funding, resources and expertise are needed to ensure the sustainability of MTBs and expand their outreach to underserved populations. Harmonization between practice and policy will be required to optimally implement precision oncology. Herein, we discuss the evolving role of MTBs and current and future considerations for their use in precision oncology.
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Affiliation(s)
- Apostolia M Tsimberidou
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Michael Kahle
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Henry Hiep Vo
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mehmet A Baysal
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amber Johnson
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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22
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Gebhart P, Tan Y, Muhr D, Stein C, Singer C. A de Novo BRCA1 Pathogenic Variant in a 29-Year-Old Woman with Triple-Negative Breast Cancer. Breast Care (Basel) 2023; 18:412-416. [PMID: 37901051 PMCID: PMC10601672 DOI: 10.1159/000531612] [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: 04/18/2023] [Accepted: 06/14/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Germline pathogenic variants in the BRCA1 and BRCA2 genes lead to a highly increased lifetime risk for breast and ovarian cancer. These variants are usually inherited and reports of de novo occurrences are a very rare phenomenon. Case Presentation We report on a breast cancer patient with a de novo BRCA1 variant c.121C>T (p.His41Tyr). The pathogenic variant was detected in leukocyte DNA of a patient with negative family history who had developed early onset, triple-negative breast cancer. The variant was not found in any of the maternal and paternal tissues tested, but it was detected in multiple samples representing all three germ layers of the affected carrier, which renders somatic mosaicism unlikely. Conclusion This case highlights the importance of including early onset of disease and triple negativity of the tumor as criteria for genetic testing, even in patients without family history. Considering the availability of effective breast cancer treatments in patients with pathogenic variants in the BRCA genes, this finding underscores the importance of genetic testing in breast cancer patients.
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Affiliation(s)
- Paulina Gebhart
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Yen Tan
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Daniela Muhr
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Christina Stein
- Center for Forensic Medicine, DNA Central Laboratory, Medical University of Vienna, Vienna, Austria
| | - Christian Singer
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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23
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Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL. The status of the human gene catalogue. Nature 2023; 622:41-47. [PMID: 37794265 PMCID: PMC10575709 DOI: 10.1038/s41586-023-06490-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/27/2023] [Indexed: 10/06/2023]
Abstract
Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.
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Affiliation(s)
- Paulo Amaral
- INSPER Institute of Education and Research, Sao Paulo, Brazil
| | | | - Francisco M De La Vega
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Tempus Labs, Chicago, IL, USA
| | | | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas Gingeras
- Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jennifer L Harrow
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Royston, UK
| | - Artemis G Hatzigeorgiou
- Department of Computer Science and Biomedical Informatics, Universithy of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens, Greece
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Christine A Wells
- Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Yandell
- Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Human Technopole, Milan, Italy.
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
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Sahu S, Sullivan TL, Mitrophanov AY, Galloux M, Nousome D, Southon E, Caylor D, Mishra AP, Evans CN, Clapp ME, Burkett S, Malys T, Chari R, Biswas K, Sharan SK. Saturation genome editing of 11 codons and exon 13 of BRCA2 coupled with chemotherapeutic drug response accurately determines pathogenicity of variants. PLoS Genet 2023; 19:e1010940. [PMID: 37713444 PMCID: PMC10529611 DOI: 10.1371/journal.pgen.1010940] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 09/27/2023] [Accepted: 08/28/2023] [Indexed: 09/17/2023] Open
Abstract
The unknown pathogenicity of a significant number of variants found in cancer-related genes is attributed to limited epidemiological data, resulting in their classification as variant of uncertain significance (VUS). To date, Breast Cancer gene-2 (BRCA2) has the highest number of VUSs, which has necessitated the development of several robust functional assays to determine their functional significance. Here we report the use of a humanized-mouse embryonic stem cell (mESC) line expressing a single copy of the human BRCA2 for a CRISPR-Cas9-based high-throughput functional assay. As a proof-of-principle, we have saturated 11 codons encoded by BRCA2 exons 3, 18, 19 and all possible single-nucleotide variants in exon 13 and multiplexed these variants for their functional categorization. Specifically, we used a pool of 180-mer single-stranded donor DNA to generate all possible combination of variants. Using a high throughput sequencing-based approach, we show a significant drop in the frequency of non-functional variants, whereas functional variants are enriched in the pool of the cells. We further demonstrate the response of these variants to the DNA-damaging agents, cisplatin and olaparib, allowing us to use cellular survival and drug response as parameters for variant classification. Using this approach, we have categorized 599 BRCA2 variants including 93-single nucleotide variants (SNVs) across the 11 codons, of which 28 are reported in ClinVar. We also functionally categorized 252 SNVs from exon 13 into 188 functional and 60 non-functional variants, demonstrating that saturation genome editing (SGE) coupled with drug sensitivity assays can enhance functional annotation of BRCA2 VUS.
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Affiliation(s)
- Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Teresa L. Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Alexander Y. Mitrophanov
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland, United States of America
| | | | - Darryl Nousome
- CCR Bioinformatics Resource, Leidos Biomedical Sciences, Inc. Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Dylan Caylor
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Arun Prakash Mishra
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Christine N. Evans
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Michelle E. Clapp
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Sandra Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Tyler Malys
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland, United States of America
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Shyam K. Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
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25
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Rădoi VE, Țurcan M, Maioru OV, Dan A, Bohîlțea LC, Dumitrescu EA, Gheorghe AS, Stănculeanu DL, Thodi G, Loukas YL, Săbău ID. Homologous Recombination Deficiency Score Determined by Genomic Instability in a Romanian Cohort. Diagnostics (Basel) 2023; 13:1896. [PMID: 37296748 PMCID: PMC10252278 DOI: 10.3390/diagnostics13111896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/02/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The Homologous Recombination Deficiency (HRD) Score, determined by evaluating genomic instability through the assessment of loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transitions (LST), serves as a crucial biomarker for identifying patients who might benefit from targeted therapies, such as PARP inhibitors (PARPi). This study aimed to investigate the efficacy of HRD testing in high-grade serous ovarian carcinoma, tubal, and peritoneal cancer patients who are negative for somatic BRCA1 and BRCA2 mutations and to evaluate the impact of HRD status on Bevacizumab and PARPi therapy response. A cohort of 100 Romanian female patients, aged 42-77, was initially selected. Among them, 30 patients had unsuitable samples for HRD testing due to insufficient tumor content or DNA integrity. Using the OncoScan C.N.V. platform, HRD testing was successfully performed on the remaining 70 patients, with 20 testing negative and 50 testing positive for HRD. Among the HRD-positive patients, 35 were eligible for and benefited from PARPi maintenance therapy, resulting in a median progression-free survival (PFS) increase from 4 months to 8.2 months. Our findings support the importance of HRD testing in ovarian cancer patients, demonstrating the potential therapeutic advantage of PARPi therapy in HRD-positive patients without somatic BRCA1/2 mutations.
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Affiliation(s)
- Viorica-Elena Rădoi
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
- “Alessandrescu-Rusescu” National Institute for Maternal and Child Health, 20382 Bucharest, Romania
- Independent Researcher, 010987 Bucharest, Romania
- Sanador, 011026 Bucharest, Romania
| | - Mihaela Țurcan
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
- Independent Researcher, 010987 Bucharest, Romania
| | - Ovidiu Virgil Maioru
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
| | - Andra Dan
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
| | - Laurentiu Camil Bohîlțea
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
- “Alessandrescu-Rusescu” National Institute for Maternal and Child Health, 20382 Bucharest, Romania
| | - Elena Adriana Dumitrescu
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.A.D.); (D.L.S.)
| | - Adelina Silvana Gheorghe
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.A.D.); (D.L.S.)
- Department of Medical Oncology I, Institute of Oncology “Prof. Dr. Al. Trestioreanu” Bucharest, 022328 Bucharest, Romania
| | - Dana Lucia Stănculeanu
- Department of Oncology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.A.D.); (D.L.S.)
- Department of Medical Oncology I, Institute of Oncology “Prof. Dr. Al. Trestioreanu” Bucharest, 022328 Bucharest, Romania
| | - Georgia Thodi
- Neoscreen Diagnostic Laboratory, Voreiou Ipeirou, 15235 Athens, Greece;
| | - Yannis L. Loukas
- School of Pharmacy, University of Athens, Panepistimiolopis, 15771 Zografou, Greece;
| | - Ileana-Delia Săbău
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-E.R.); (O.V.M.); (A.D.); (L.C.B.); (I.-D.S.)
- Independent Researcher, 010987 Bucharest, Romania
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26
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Berga-Švītiņa E, Maksimenko J, Miklaševičs E, Fischer K, Vilne B, Mägi R. Polygenic Risk Score Predicts Modified Risk in BRCA1 Pathogenic Variant c.4035del and c.5266dup Carriers in Breast Cancer Patients. Cancers (Basel) 2023; 15:cancers15112957. [PMID: 37296919 DOI: 10.3390/cancers15112957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
The aim of this study was to assess the power of the polygenic risk score (PRS) in estimating the overall genetic risk of women carrying germline BRCA1 pathogenic variants (PVs) c.4035del or c.5266dup to develop breast (BC) or ovarian cancer (OC) due to additional genetic variations. In this study, PRSs previously developed from two joint models using summary statistics of age-at-onset (BayesW model) and case-control data (BayesRR-RC model) from a genome-wide association analysis (GWAS) were applied to 406 germline BRCA1 PV (c.4035del or c.5266dup) carriers affected by BC or OC, compared with unaffected individuals. A binomial logistic regression model was used to assess the association of PRS with BC or OC development risk. We observed that the best-fitting BayesW PRS model effectively predicted the individual's BC risk (OR = 1.37; 95% CI = 1.03-1.81, p = 0.02905 with AUC = 0.759). However, none of the applied PRS models was a good predictor of OC risk. The best-fitted PRS model (BayesW) contributed to assessing the risk of developing BC for germline BRCA1 PV (c.4035del or c.5266dup) carriers and may facilitate more precise and timely patient stratification and decision-making to improve the current BC treatment or even prevention strategies.
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Affiliation(s)
- Egija Berga-Švītiņa
- Bioinformatics Lab, Rīga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia
- Institute of Oncology, Rīga Stradiņš University, Pilsoņu Street 13, Block 13, LV-1002 Riga, Latvia
| | - Jeļena Maksimenko
- Institute of Oncology, Rīga Stradiņš University, Pilsoņu Street 13, Block 13, LV-1002 Riga, Latvia
- Pauls Stradiņš Clinical University Hospital, Pilsoņu Street 13, LV-1002 Riga, Latvia
| | - Edvīns Miklaševičs
- Institute of Oncology, Rīga Stradiņš University, Pilsoņu Street 13, Block 13, LV-1002 Riga, Latvia
- Department of Biology and Microbiology, Rīga Stradiņš University, LV-1007 Riga, Latvia
| | - Krista Fischer
- Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Narva mnt 18, 51009 Tartu, Estonia
| | - Baiba Vilne
- Bioinformatics Lab, Rīga Stradiņš University, Dzirciema Street 16, LV-1007 Riga, Latvia
| | - Reedik Mägi
- Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
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Margioula-Siarkou C, Almperis A, Papanikolaou A, Laganà AS, Mavromatidis G, Guyon F, Dinas K, Petousis S. HIPEC for gynaecological malignancies: A last update (Review). MEDICINE INTERNATIONAL 2023; 3:25. [PMID: 37205988 PMCID: PMC10189421 DOI: 10.3892/mi.2023.85] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Advanced-stage gynaecological cancer represents a clinical entity with challenging surgical treatment in an effort to optimize prognosis. Hyperthermic intraperitoneal chemotherapy (HIPEC) following cytoreductive surgery (CRS) has been reported as a method potentially eligible to improve prognosis. However, no definitive conclusions have yet been made on which types of cancer and which context HIPEC may actually have a beneficial impact. The present review discusses the efficacy and safety of HIPEC as a treatment option for patients with primary/recurrent ovarian, endometrial and cervix cancer, as well as peritoneal sarcomatosis. A literature search was conducted using MeSH terms for each topic in the PubMed database and supplemented with a manual search to retrieve additional articles eligible for inclusion/fulfilling the inclusion criteria. The implementation of HIPEC appears to be beneficial in terms of survival in patients with epithelial ovarian carcinoma (EOC) following neoadjuvant chemotherapy, as well as in patients with recurrent EOC. Statistical superiority is not justified by current studies regarding other gynaecological malignancies with peritoneal dissemination. Furthermore, as regards safety, HIPEC following CRS does not appear to significantly increase the mortality and morbidity rates compared to the use of CRS alone. The rationale for using HIPEC and CRS in the treatment of ovarian cancer, particularly in the neoadjuvant setting, as well as for recurrences, is adequately evidenced, with acceptable safety and post-operative complication rate profiles. Its current place in the multimodal strategy for patients with peritoneal metastases remains uncertain, however. Randomized clinical trials are warranted to further examine the use of HIPEC and establish the optimal regimen and temperature settings. The role of optimal cytoreduction and no residual disease, as well as the proper patient selection remain basic parameters for maximizing survival parameters.
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Affiliation(s)
- Chrysoula Margioula-Siarkou
- 2nd Department of Obstetrics and Gynaecology, Gynaecologic Oncology Unit, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece
- Gynaeocologic Oncology Unit Institute Bergonie, 33076 Bordeaux, France
| | - Aristarchos Almperis
- 2nd Department of Obstetrics and Gynaecology, Gynaecologic Oncology Unit, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece
- Correspondence to: Dr Aristarchos Almperis, 2nd Department of Obstetrics and Gynaecology, Gynaecologic Oncology Unit, Aristotle University of Thessaloniki, Konstantinoupoleos 49, 54642 Thessaloniki, Greece
| | - Alexios Papanikolaou
- 2nd Department of Obstetrics and Gynaecology, Gynaecologic Oncology Unit, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece
| | - Antonio Simone Laganà
- Unit of Gynecologic Oncology, ARNAS ‘Civico-Di Cristina-Benfratelli’, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, I-90121 Palermo, Italy
| | - George Mavromatidis
- 2nd Department of Obstetrics and Gynaecology, Gynaecologic Oncology Unit, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece
| | - Frederic Guyon
- Gynaeocologic Oncology Unit Institute Bergonie, 33076 Bordeaux, France
| | - Konstantinos Dinas
- 2nd Department of Obstetrics and Gynaecology, Gynaecologic Oncology Unit, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece
| | - Stamatios Petousis
- 2nd Department of Obstetrics and Gynaecology, Gynaecologic Oncology Unit, Aristotle University of Thessaloniki, 54642 Thessaloniki, Greece
- Gynaeocologic Oncology Unit Institute Bergonie, 33076 Bordeaux, France
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28
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Kerr SM, Cowan E, Klaric L, Bell C, O'Sullivan D, Buchanan D, Grzymski JJ, van Hout CV, Tzoneva G, Shuldiner AR, Wilson JF, Miedzybrodzka Z. Clinical case study meets population cohort: identification of a BRCA1 pathogenic founder variant in Orcadians. Eur J Hum Genet 2023; 31:588-595. [PMID: 36927983 PMCID: PMC10172333 DOI: 10.1038/s41431-023-01297-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/20/2022] [Accepted: 01/18/2023] [Indexed: 03/18/2023] Open
Abstract
We multiply ascertained the BRCA1 pathogenic missense variant c.5207T > C; p.Val1736Ala (V1736A) in clinical investigation of breast and ovarian cancer families from Orkney in the Northern Isles of Scotland, UK. We sought to investigate the frequency and clinical relevance of this variant in those of Orcadian ancestry as an exemplar of the value of population cohorts in clinical care, especially in isolated populations. Oral history and birth, marriage and death registrations indicated genealogical linkage of the clinical cases to ancestors from the Isle of Westray, Orkney. Further clinical cases were identified through targeted testing for V1736A in women of Orcadian ancestry attending National Health Service (NHS) genetic clinics for breast and ovarian cancer family risk assessments. The variant segregates with female breast and ovarian cancer in clinically ascertained cases. Separately, exome sequence data from 2088 volunteer participants with three or more Orcadian grandparents, in the ORCADES research cohort, was interrogated to estimate the population prevalence of V1736A in Orcadians. The effects of the variant were assessed using Electronic Health Record (EHR) linkage. Twenty out of 2088 ORCADES research volunteers (~1%) carry V1736A, with a common haplotype around the variant. This allele frequency is ~480-fold higher than in UK Biobank participants. Cost-effectiveness of population screening for BRCA1 founder pathogenic variants has been demonstrated at a carrier frequency below the ~1% observed here. Thus we suggest that Orcadian women should be offered testing for the BRCA1 V1736A founder pathogenic variant, starting with those with known Westray ancestry.
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Affiliation(s)
- Shona M Kerr
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Cancer, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Emma Cowan
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, AB25 2ZA, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Cancer, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Christine Bell
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, AB25 2ZA, UK
| | - Dawn O'Sullivan
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, AB25 2ZA, UK
| | - David Buchanan
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Cancer, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Joseph J Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, USA
- Renown Health, Reno, NV, USA
| | - Cristopher V van Hout
- Regeneron Genetics Center, Tarrytown, NY, USA
- Laboratorio Internacional de Investigatión sobre el Genoma Humano, Campus Juriquilla de la Universidad Nacional Autónoma de México, Querétaro, Querétaro, 76230, México
| | | | | | - James F Wilson
- MRC Human Genetics Unit, University of Edinburgh, Institute of Genetics and Cancer, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Zosia Miedzybrodzka
- Department of Medical Genetics, Ashgrove House, NHS Grampian, Aberdeen, AB25 2ZA, UK.
- Medical Genetics Group, School of Medicine, Medical Sciences, Nutrition and Dentistry, University of Aberdeen, Polwarth Building, Aberdeen, AB25 2ZD, UK.
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29
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Liu Y, Jin B, Shen C, Gao X, Qi X, Ma M, Li H, Hao H, Tang Q, Yang K, Mi Y, Guan J, Feng X, He Z, Li H, Yu W. Somatic and germline aberrations in homologous recombination repair genes in Chinese prostate cancer patients. Front Oncol 2023; 13:1086517. [PMID: 37064136 PMCID: PMC10091863 DOI: 10.3389/fonc.2023.1086517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Simple summarySomatic and germline aberrations in homologous recombinant repair (HHR) genes are associated with increased incidence and poor prognosis for prostate cancer. Through next-generation sequencing of prostate cancer patients across all clinical states from north China, here the authors identified a somatic mutational rate of 3% and a germline mutational rate of 3.9% for HRR genes using 200 tumor tissues and 714 blood specimens. Thus, mutational rates in HRR genes were lower compared with previous studies.BackgroundHomologous recombination repair deficiency is associated with higher risk and poorer prognosis for prostate cancer. However, the landscapes of somatic and germline mutations in these genes remain poorly defined in Chinese patients, especially for those with localized disease and those from north part of China. In this study, we explore the genomic profiles of these patients.MethodsWe performed next-generation sequencing with 200 tumor tissues and 714 blood samples from prostate cancer patients at Peking University First Hospital, using a 32 gene panel including 19 homologous recombination repair genes.ResultsTP53, PTEN, KRAS were the most common somatic aberrations; BRCA2, NBN, ATM were the most common germline aberrations. In terms of HRR genes, 3% (6/200) patients harbored somatic aberrations, and 3.8% (28/714) patients harbored germline aberrations. 98.0% (196/200) somatic-tested and 72.7% (519/714) germline tested patients underwent prostatectomy, of which 28.6% and 42.0% had Gleason scores ≥8 respectively. Gleason scores at either biopsy or prostatectomy were predictive for somatic aberrations in general and in TP53; while age of onset <60 years old, PSA at diagnosis, and Gleason scores at biopsy were clinical factors associated with positive germline aberrations in BRCA2/ATM.ConclusionsOur results showed a distinct genomic profile in homologous recombination repair genes for patients with prostate cancer across all clinical states from north China. Clinicians may consider to expand the prostate cancer patients receiving genetic tests to include more individuals due to the weak guiding role by the clinical factors currently available.
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Affiliation(s)
- Yixiao Liu
- Department of Urology, Peking University First Hospital, Peking University, Beijing, China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Bo Jin
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Cheng Shen
- Department of Urology, Peking University First Hospital, Peking University, Beijing, China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Xianshu Gao
- Department of Radiation Therapy, Peking University First Hospital, Beijing, China
| | - Xin Qi
- Department of Radiation Therapy, Peking University First Hospital, Beijing, China
| | - Mingwei Ma
- Department of Radiation Therapy, Peking University First Hospital, Beijing, China
| | - Hongzhen Li
- Department of Radiation Therapy, Peking University First Hospital, Beijing, China
| | - Han Hao
- Department of Urology, Peking University First Hospital, Peking University, Beijing, China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Qi Tang
- Department of Urology, Peking University First Hospital, Peking University, Beijing, China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Kaiwei Yang
- Department of Urology, Peking University First Hospital, Peking University, Beijing, China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Yue Mi
- Department of Urology, Peking University First Hospital, Peking University, Beijing, China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Jie Guan
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Xuero Feng
- Department of Geriatrics, Peking University First Hospital, Beijing, China
| | - Zhisong He
- Department of Urology, Peking University First Hospital, Peking University, Beijing, China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
| | - Haixia Li
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
- *Correspondence: Wei Yu, ; Haixia Li,
| | - Wei Yu
- Department of Urology, Peking University First Hospital, Peking University, Beijing, China
- Institute of Urology, Peking University, Beijing, China
- National Urological Cancer Center, Beijing, China
- *Correspondence: Wei Yu, ; Haixia Li,
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30
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Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL. The status of the human gene catalogue. ARXIV 2023:arXiv:2303.13996v1. [PMID: 36994150 PMCID: PMC10055485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the estimated number has shrunk to fewer than 20,000, although the number of distinct protein-coding isoforms has expanded dramatically. The invention of high-throughput RNA sequencing and other technological breakthroughs have led to an explosion in the number of reported non-coding RNA genes, although most of them do not yet have any known function. A combination of recent advances offers a path forward to identifying these functions and towards eventually completing the human gene catalogue. However, much work remains to be done before we have a universal annotation standard that includes all medically significant genes, maintains their relationships with different reference genomes, and describes clinically relevant genetic variants.
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Affiliation(s)
- Paulo Amaral
- INSPER Institute of Education and Research, São Paulo, SP, Brasil
| | - Silvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Francisco M. De La Vega
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA; Tempus Labs, Inc., Chicago, IL
| | | | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Gingeras
- Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Jennifer L Harrow
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Da Vinci Building. Melbourn Science Park, Royston UK SG8 6HB
| | - Artemis G. Hatzigeorgiou
- Universithy of Thessaly, Department of Computer Science and Biomedical Informatics, Lamia, Greece; Hellenic Pasteur Institute, Athens, Greece
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, D04 V1W8 Dublin, Ireland; Conway Institute of Biomedical and Biomolecular Research, University College Dublin, D04 V1W8 Dublin, Ireland; Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Terence D. Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kim D. Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama Kanagawa 230-0045 Japan
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ales Varabyou
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Christine A. Wells
- Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville 3010 Vic Australia
| | - Mark Yandell
- Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Piero Carninci
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Human Technopole, via Rita Levi Montalcini 1, Milan 20157 Italy
| | - Steven L. Salzberg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Immunology and Regenerative Biology; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
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Qin Z, Li J, Tam B, Sinha S, Zhao B, Bhaskaran SP, Huang T, Wu X, Chian JS, Guo M, Kou SH, Lei H, Zhang L, Wang X, Lagniton PNP, Xiao F, Jiang X, Wang SM. Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population. Int J Cancer 2023; 152:1159-1173. [PMID: 36385461 PMCID: PMC10098510 DOI: 10.1002/ijc.34359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
Pathogenic variation in BRCA1 and BRCA2 (BRCA) causes high risk of breast and ovarian cancer, and BRCA variation data are important markers for BRCA-related clinical cancer applications. However, comprehensive BRCA variation data are lacking from the Asian population despite its large population size, heterogenous genetic background and diversified living environment across the Asia continent. We performed a systematic study on BRCA variation in Asian population including extensive data mining, standardization, annotation and characterization. We identified 7587 BRCA variants from 685 592 Asian individuals in 40 Asia countries and regions, including 1762 clinically actionable pathogenic variants and 4915 functionally unknown variants (https://genemutation.fhs.um.edu.mo/Asian-BRCA/). We observed the highly ethnic-specific nature of Asian BRCA variants between Asian and non-Asian populations and within Asian populations, highlighting that the current European descendant population-based BRCA data is inadequate to reflect BRCA variation in the Asian population. We also provided archeological evidence for the evolutionary origin and arising time of Asian BRCA variation. We further provided structural-based evidence for the deleterious variants enriched within the functionally unknown Asian BRCA variants. The data from our study provide a current view of BRCA variation in the Asian population and a rich resource to guide clinical applications of BRCA-related cancer for the Asian population.
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Affiliation(s)
- Zixin Qin
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Siddharth Sinha
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Shanmuga Priya Bhaskaran
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Teng Huang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xiaobing Wu
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jia Sheng Chian
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Maoni Guo
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Li Zhang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xiaoyu Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Philip Naderev P Lagniton
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xinyang Jiang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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Wang SM. A global perspective on the ethnic-specific BRCA variation and its implication in clinical application. JOURNAL OF THE NATIONAL CANCER CENTER 2023; 3:14-20. [PMID: 39036311 PMCID: PMC11256725 DOI: 10.1016/j.jncc.2022.12.001] [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: 09/03/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Pathogenic BRCA1 and BRCA2 (BRCA) variation is the genetic predisposition for high cancer risk affecting mostly breast and ovarian. BRCA variation information is widely used in clinical diagnosis, treatment, and prevention of BRCA-related cancer. The positive selection imposed on human BRCA leads to highly ethnic-specific BRCA variation to adapt different living environment on earth. Most of the human BRCA variants identified so far were from the European descendant populations and used as the standard reference for global human populations, whereas BRCA variation in other ethnic populations remains poorly characterized. This review addresses the origin of ethnic-specific BRCA variation, the importance of ethnic-specific BRCA variation in clinical application, the limitation of current BRCA variation data, and potential solutions to fill the gap.
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Affiliation(s)
- San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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Casaletto J, Cline M, Shirts B. Modeling the impact of data sharing on variant classification. J Am Med Inform Assoc 2023; 30:466-474. [PMID: 36451272 PMCID: PMC9933054 DOI: 10.1093/jamia/ocac232] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/10/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
OBJECTIVE Many genetic variants are classified, but many more are variants of uncertain significance (VUS). Clinical observations of patients and their families may provide sufficient evidence to classify VUS. Understanding how long it takes to accumulate sufficient patient data to classify VUS can inform decisions in data sharing, disease management, and functional assay development. MATERIALS AND METHODS Our software models the accumulation of clinical evidence (and excludes all other types of evidence) to measure their unique impact on variant interpretation. We illustrate the time and probability for VUS classification when laboratories share evidence, when they silo evidence, and when they share only variant interpretations. RESULTS Using conservative assumptions for frequencies of observed clinical evidence, our models show the probability of classifying rare pathogenic variants with an allele frequency of 1/100 000 increases from less than 25% with no data sharing to nearly 80% after one year when labs share data, with nearly 100% classification after 5 years. Conversely, our models found that extremely rare (1/1 000 000) variants have a low probability of classification using only clinical data. DISCUSSION These results quantify the utility of data sharing and demonstrate the importance of alternative lines of evidence for interpreting rare variants. Understanding variant classification circumstances and timelines provides valuable insight for data owners, patients, and service providers. While our modeling parameters are based on our own assumptions of the rate of accumulation of clinical observations, users may download the software and run simulations with updated parameters. CONCLUSIONS The modeling software is available at https://github.com/BRCAChallenge/classification-timelines.
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Affiliation(s)
- James Casaletto
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Melissa Cline
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Brian Shirts
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
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Musacchio L, Boccia S, Marchetti C, Minucci A, Camarda F, Cassani C, Ventriglia J, Salutari V, Ghizzoni V, Giudice E, Perri MT, Carbone MV, Ricci C, Pignata S, Fagotti A, Scambia G, Lorusso D. Survival outcomes in patients with BRCA mutated, variant of unknown significance, and wild type ovarian cancer treated with PARP inhibitors. Int J Gynecol Cancer 2023:ijgc-2022-003903. [PMID: 36759000 DOI: 10.1136/ijgc-2022-003903] [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: 02/11/2023] Open
Abstract
OBJECTIVE Correlation between BRCA1/2 (BRCA) pathogenic variants and the response to poly (ADP-ribose) polymerase inhibitors (PARPi) has been recognized in patients with ovarian cancer. Moreover, data on the clinical implications of variants of unknown significance are lacking. The aim of this study was to evaluate differences in survival outcomes in patients with BRCA variants of unknown significance, mutated, and wild type relapsed ovarian cancer treated with PARPi. METHODS Patients with ovarian cancer whose somatic BRCA testing was available and who were receiving PARPi as maintenance treatment at the first recurrence between January 2014 and January 2021 were included in the present study and analyzed. Patients were divided into three groups according to BRCA mutational status (variant of unknown significance, mutated, and wild type). Progression-free survival was assessed in each study group. RESULTS Of 67 patients identified, 20 (29.9%), 24 (35.8%), and 23 (34.3%) had BRCA variant of unknown significance, mutated, and wild type, respectively. Patients received PARPi as maintenance treatment at the time of the first relapse after a complete response or partial response to platinum-based chemotherapy without differences in the previous platinum-free interval among the analyzed groups. The median progression-free survival of patients with BRCA mutation was significantly longer than for those with BRCA wild type or variant of unknown significance (not reached vs 4 months vs 7 months, respectively; p<0.001). Additionally, no significant difference was found between patients with BRCA wild type and BRCA variant of unknown significance (p=0.50). CONCLUSION Our study suggests that carriers of BRCA variant of unknown significance have survival outcomes comparable to patients with BRCA wild type and shorter progression-free survival than women harboring BRCA pathogenic variants.
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Affiliation(s)
- Lucia Musacchio
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Serena Boccia
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Claudia Marchetti
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Angelo Minucci
- Departmental Unit of Molecular and Genomic Diagnostic, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Floriana Camarda
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Chiara Cassani
- Fondazione IRCCS Policlinico San Matteo, Pavia, Lombardia, Italy
| | - Jole Ventriglia
- Department of Urology and Gynecology, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Naples, Italy
| | - Vanda Salutari
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Viola Ghizzoni
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Elena Giudice
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Maria Teresa Perri
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Maria Vittoria Carbone
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Caterina Ricci
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy
| | - Sandro Pignata
- Department of Urology and Gynecology, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Naples, Italy
| | - Anna Fagotti
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy.,Department of Life Science and Public Health, Catholic University of Sacred Heart Agostino Gemelli, Rome, Italy
| | - Giovanni Scambia
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy.,Department of Life Science and Public Health, Catholic University of Sacred Heart Agostino Gemelli, Rome, Italy
| | - Domenica Lorusso
- Department of Women and Child Health, Division of Gynecologic Oncology, Fondazione Policlinico Universitario A.Gemelli IRCCS, Rome, Italy .,Department of Life Science and Public Health, Catholic University of Sacred Heart Agostino Gemelli, Rome, Italy
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Consent Codes: Maintaining Consent in an Ever-expanding Open Science Ecosystem. Neuroinformatics 2023; 21:89-100. [PMID: 36520344 PMCID: PMC9931855 DOI: 10.1007/s12021-022-09577-4] [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] [Accepted: 02/23/2022] [Indexed: 12/23/2022]
Abstract
We previously proposed a structure for recording consent-based data use 'categories' and 'requirements' - Consent Codes - with a view to supporting maximum use and integration of genomic research datasets, and reducing uncertainty about permissible re-use of shared data. Here we discuss clarifications and subsequent updates to the Consent Codes (v4) based on new areas of application (e.g., the neurosciences, biobanking, H3Africa), policy developments (e.g., return of research results), and further practical considerations, including developments in automated approaches to consent management.
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36
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Li C, Zhang L, Zhuo Z, Su F, Li H, Xu S, Liu Y, Zhang Z, Xie Y, Yu X, Bian L, Xiao F. Artificial intelligence-based recognition for variant pathogenicity of BRCA1 using AlphaFold2-predicted structures. Theranostics 2023; 13:391-402. [PMID: 36593954 PMCID: PMC9800725 DOI: 10.7150/thno.79362] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022] Open
Abstract
With the surge of the high-throughput sequencing technologies, many genetic variants have been identified in the past decade. The vast majority of these variants are defined as variants of uncertain significance (VUS), as their significance to the function or health of an organism is not known. It is urgently needed to develop intelligent models for the clinical interpretation of VUS. State-of-the-art artificial intelligence (AI)-based variant effect predictors only learn features from primary amino acid sequences, leaving out information about the most important three-dimensional structure that is more related to its function. Methods: We proposed a deep convolutional neural network model named variant effect recognition network for BRCA1 (vERnet-B) to recognize the clinical pathogenicity of missense single-nucleotide variants in the BRCT domain of BRCA1. vERnet-B learned features associated with the pathogenicity from the tertiary protein structures of variants predicted by AlphaFold2. Results: After performing a series of validation and analyses on vERnet-B, we discovered that it exhibited significant advances over previous works. Recognizing the phenotypic consequences of VUS is one of the most daunting challenges in genetic informatics; however, we achieved 85% accuracy in recognizing disease BRCA1 variants with an ideal balance of false-positive and true-positive detection rates. vERnet-B correctly recognized the pathogenicity of variant A1708E, which was poorly predicted by AlphaFold2 as previously described. The vERnet-B web server is freely available from URL: http://ai-lab.bjrz.org.cn/vERnet. Conclusions: We applied protein tertiary structures to successfully recognize the pathogenic missense SNVs, which were difficult to be addressed by classical approaches based on sequences. Our work demonstrated that AlphaFold2-predicted structures were expected to be used for rich feature learning and revealed unique insights into the clinical interpretation of VUS in disease-related genes, using vERnet-B as a discovery tool.
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Affiliation(s)
- Chang Li
- Peking University Fifth School of Clinical Medicine, Beijing, China.,Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhongling Zhuo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Siyuan Xu
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Zaifeng Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yibo Xie
- Information Center, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xue Yu
- Department of Cardiology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,✉ Corresponding authors: Prof. Xue Yu, Department of Cardiology, Beijing Hospital, Beijing, China, ; Prof. Liheng Bian, Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China, ; Prof. Fei Xiao, Peking University Fifth School of Clinical Medicine, Beijing, China, Phone: (86)10-58115083,
| | - Liheng Bian
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China.,✉ Corresponding authors: Prof. Xue Yu, Department of Cardiology, Beijing Hospital, Beijing, China, ; Prof. Liheng Bian, Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China, ; Prof. Fei Xiao, Peking University Fifth School of Clinical Medicine, Beijing, China, Phone: (86)10-58115083,
| | - Fei Xiao
- Peking University Fifth School of Clinical Medicine, Beijing, China.,Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,✉ Corresponding authors: Prof. Xue Yu, Department of Cardiology, Beijing Hospital, Beijing, China, ; Prof. Liheng Bian, Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China, ; Prof. Fei Xiao, Peking University Fifth School of Clinical Medicine, Beijing, China, Phone: (86)10-58115083,
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Offit K, Sharkey CM, Green D, Wu X, Trottier M, Hamilton JG, Walsh MF, Dandiker S, Belhadj S, Lipkin SM, Sugrañes TA, Caggana M, Stadler ZK. Regulation of Laboratory-Developed Tests in Preventive Oncology: Emerging Needs and Opportunities. J Clin Oncol 2023; 41:11-21. [PMID: 35944238 PMCID: PMC10409443 DOI: 10.1200/jco.22.00995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/19/2022] [Accepted: 06/27/2022] [Indexed: 12/27/2022] Open
Abstract
Cancer predictive or diagnostic assays, offered as Laboratory-Developed Tests (LDTs), have been subject to regulatory authority and enforcement discretion by the US Food and Drug Administration. Many LDTs enter the market without US Food and Drug Administration or any regulatory review. The Centers for Medicare & Medicaid Services under the Clinical Laboratory Improvement Amendments focuses on analytic performance, but has limited oversight of the quality or utility of LDTs, including whether patients have been harmed as a result of their use. Increasingly, LDTs for cancer risk or early detection have been marketed directly to consumers, with many LDT developers depicting these tests, requested by patients but ordered by personal or company-associated physicians, as procedures falling under the practice of medicine. This patchwork of regulation and enforcement uncertainty regarding LDTs and public concerns about accuracy of tests given emergency authorization during the COVID-19 pandemic led to the Verifying Accurate Leading-edge IVCT (in vitro clinical test) Development Act of 2021. This pending federal legislation represents an opportunity to harmonize regulatory policies and address growing concerns over quality, utility, and safety of LDTs for cancer genomics, including tests marketed directly to consumers. We review here questions regarding the potential benefits and harms of some cancer-related LDTs for cancer risk and presymptomatic molecular diagnosis, increasingly marketed to oncologists or directly to the worried well. We offer specific proposals to strengthen oversight of the accuracy and clinical utility of cancer genetic testing to ensure public safety.
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Affiliation(s)
- Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | | | - Dina Green
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiaohan Wu
- The University of California, Berkeley School of Law, Berkeley, CA
| | - Magan Trottier
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jada G. Hamilton
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Michael F. Walsh
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Sita Dandiker
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sami Belhadj
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Michele Caggana
- Wadsworth Center, New York State Department of Health, Albany, NY
| | - Zsofia K. Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
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38
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Sobahy TM, Motwalli O, Alazmi M. AllelePred: A Simple Allele Frequencies Ensemble Predictor for Different Single Nucleotide Variants. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:796-801. [PMID: 35239491 DOI: 10.1109/tcbb.2022.3155659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND & OBJECTIVE Genomic medicine stands to be revolutionized by understanding single nucleotide variants (SNVs) and their expression in single-gene disorders (Mendelian diseases). Computational tools can play a vital role in the exploration of such variations and their pathogenicity. Consequently, we developed the ensemble prediction tool AllelePred to identify deleterious SNVs and disease causative genes. RESULTS The model utilizes different population genetics backgrounds and restricted criteria for features selection to help generate high accuracy results. In comparison to other tools, such as Eigen, PROVEAN, and fathmm-MKL our classifier achieves higher accuracy (98%), precision (96%), F1 score (93%), and coverage (100%) for different types of coding variants. The new method was also compared against a bioinformatics analytical workflow, which uses gnomAD overall AFs (less than 1%) and CADD (scaled C-score of at least 15). Furthermore, this research highlights the stature of genetic variant sharing and curation. We accumulated a list of highly probable deleterious variants and recommended further experimental validation before medical diagnostic usage. CONCLUSIONS The ensemble prediction tool AllelePred enables increased accuracy in recognizing deleterious SNVs and the genetic determinants in real clinical data.
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Clinical Impact of Next-Generation Sequencing Multi-Gene Panel Highlighting the Landscape of Germline Alterations in Ovarian Cancer Patients. Int J Mol Sci 2022; 23:ijms232415789. [PMID: 36555431 PMCID: PMC9779064 DOI: 10.3390/ijms232415789] [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: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
BRCA1 and BRCA2 are the most frequently mutated genes in ovarian cancer (OC) crucial both for the identification of cancer predisposition and therapeutic choices. However, germline variants in other genes could be involved in OC susceptibility. We characterized OC patients to detect mutations in genes other than BRCA1/2 that could be associated with a high risk of developing OC and permit patients to enter the most appropriate treatment and surveillance program. Next-generation sequencing analysis with a 94-gene panel was performed on germline DNA of 219 OC patients. We identified 34 pathogenic/likely pathogenic variants in BRCA1/2 and 38 in other 21 genes. The patients with pathogenic/likely pathogenic variants in the non-BRCA1/2 genes mainly developed OC alone compared to the other groups that also developed breast cancer or other tumors (p = 0.001). Clinical correlation analysis showed that the low-risk patients were significantly associated with platinum sensitivity (p < 0.001). Regarding PARP inhibitors (PARPi) response, the patients with pathogenic mutations in the non-BRCA1/2 genes had worse PFS and OS. Moreover, a statistically significantly worse PFS was found for every increase of one thousand platelets before PARPi treatment. To conclude, knowledge about molecular alterations in genes beyond BRCA1/2 in OC could allow for more personalized diagnostic, predictive, prognostic, and therapeutic strategies for OC patients.
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Barua S, Goswami N, Mishra N, Sawant UU, Varma AK. In Silico and Structure-Based Assessment of Similar Variants Discovered in Tandem Repeats of BRCT Domains of BRCA1 and BARD1 To Characterize the Folding Pattern. ACS OMEGA 2022; 7:44772-44785. [PMID: 36530327 PMCID: PMC9753114 DOI: 10.1021/acsomega.2c04782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
BRCA1 and BARD1 are important proteins in the homologous DNA damage repair pathways. Different genetic variants identified in these proteins have been clinically correlated with the occurrence of hereditary breast and ovarian cancer (HBOC). Variants of unknown significance (VUS) reported in the BRCT domains of BRCA1 and BARD1 substantiate the importance of BRCT domain-containing proteins for genomic integrity. To classify the pathogenicity of variants, in silico, structural and molecular dynamics (MD)-based approaches were explored. Different variants reported in the BRCT region were retrieved from cBioPortal, LOVD3, BRCA Exchange, and COSMIC databases to evaluate the pathogenicity. Multiple sequence alignment and superimposition of the structures of BRCA1 BRCT and BARD1 BRCT domains were performed to compare alterations in folding patterns. From 11 in silico predictions servers, variants reported to be pathogenic by 70% of the servers were considered for structural analysis. To our observations, four residue pairs of both the proteins were reported, harboring 11 variants, H1686Y, W1718L, P1749L, P1749S, and W1837L variants for BRCA1 BRCT and H606D, H606N, W635L, P657L, P657S, and W762F for BARD1 BRCT. MD simulations of the BRCT repeat regions of these variants and wild-type proteins were performed to evaluate the differences of folding patterns. Root mean square deviation (RMSD), R g, solvent-accessible surface area (SASA), and root mean square fluctuation (RMSF) of variants showed slight differences in the folding patterns from the wild-type proteins. Furthermore, principal components analysis of H1686Y, P1749S, and W1718L variants of BRCA1 showed less flexibility than the wild type, whereas that of H606D, W635L, and W762F of BARD1 showed more flexibility than the wild type. Normal mode analysis of the energy minima from the simulation trajectories revealed that most of the variants do not show much differences in the flexibility compared to the wild-type proteins, except for the discrete regions in the BRCT repeats, most prominently in the 1798-1801 amino acid region of BRCA1 and at the residue 744 in BARD1.
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Affiliation(s)
- Siddhartha
A. Barua
- Advanced
Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
- Homi
Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, Maharashtra 400094, India
| | - Nabajyoti Goswami
- Advanced
Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - Neha Mishra
- Advanced
Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
- Homi
Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, Maharashtra 400094, India
| | - Ulka U. Sawant
- Advanced
Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
| | - Ashok K. Varma
- Advanced
Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India
- Homi
Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, Maharashtra 400094, India
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Dace P, Findlay GM. Reducing uncertainty in genetic testing with Saturation Genome Editing. MED GENET-BERLIN 2022; 34:297-304. [PMID: 38836089 PMCID: PMC11006300 DOI: 10.1515/medgen-2022-2159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Accurate interpretation of human genetic data is critical for optimizing outcomes in the era of genomic medicine. Powerful methods for testing genetic variants for functional effects are allowing researchers to characterize thousands of variants across disease genes. Here, we review experimental tools enabling highly scalable assays of variants, focusing specifically on Saturation Genome Editing (SGE). We discuss examples of how this technique is being implemented for variant testing at scale and describe how SGE data for BRCA1 have been clinically validated and used to aid variant interpretation. The initial success at predicting variant pathogenicity with SGE has spurred efforts to expand this and related techniques to many more genes.
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Affiliation(s)
- Phoebe Dace
- The Genome Function Laboratory, The Francis Crick Institute, 1 Midland Rd, London, United Kingdom
| | - Gregory M Findlay
- The Genome Function Laboratory, The Francis Crick Institute, 1 Midland Rd, London, United Kingdom
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Kohno T, Kato M, Kohsaka S, Sudo T, Tamai I, Shiraishi Y, Okuma Y, Ogasawara D, Suzuki T, Yoshida T, Mano H. C-CAT: The National Datacenter for Cancer Genomic Medicine in Japan. Cancer Discov 2022; 12:2509-2515. [PMID: 36321305 PMCID: PMC9762342 DOI: 10.1158/2159-8290.cd-22-0417] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SUMMARY Since June 2019, under the umbrella of the national health insurance system, Japan has started cancer genomic medicine (CGM) with comprehensive genomic profiling (CGP) tests. The Ministry of Health, Labour and Welfare (MHLW) of Japan constructed a network of CGM hospitals (a total of 233 institutes as of July 1, 2022) and established the Center for Cancer Genomics and Advanced Therapeutics (C-CAT), the national datacenter for CGM. Clinical information and genomic data from the CGP tests are securely transferred to C-CAT, which then generates "C-CAT Findings" reports containing information of clinical annotation and matched clinical trials based on the CGP data. As of June 30, 2022, a total of 36,340 datapoints of clinical/genomic information are aggregated in C-CAT, and the number is expected to increase swiftly. The data are now open for sharing with not only the CGM hospitals but also other academic institutions and industries.
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Affiliation(s)
- Takashi Kohno
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan
| | - Mamoru Kato
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan
| | - Shinji Kohsaka
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan
| | - Tomohisa Sudo
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan
| | - Ikuo Tamai
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan
| | - Yuichi Shiraishi
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan
| | - Yusuke Okuma
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan
| | - Daisuke Ogasawara
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan
| | - Tatsuya Suzuki
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan
| | - Teruhiko Yoshida
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan
| | - Hiroyuki Mano
- Center for Cancer Genomics and Advanced Therapeutics (C-CAT), National Cancer Center, Tokyo, Japan.,Corresponding Author: Hiroyuki Mano, C-CAT, National Cancer Center, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan. Phone: 813-3547-5241; E-mail:
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Hamamoto R, Koyama T, Kouno N, Yasuda T, Yui S, Sudo K, Hirata M, Sunami K, Kubo T, Takasawa K, Takahashi S, Machino H, Kobayashi K, Asada K, Komatsu M, Kaneko S, Yatabe Y, Yamamoto N. Introducing AI to the molecular tumor board: one direction toward the establishment of precision medicine using large-scale cancer clinical and biological information. Exp Hematol Oncol 2022; 11:82. [PMID: 36316731 PMCID: PMC9620610 DOI: 10.1186/s40164-022-00333-7] [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: 08/31/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
Since U.S. President Barack Obama announced the Precision Medicine Initiative in his New Year's State of the Union address in 2015, the establishment of a precision medicine system has been emphasized worldwide, particularly in the field of oncology. With the advent of next-generation sequencers specifically, genome analysis technology has made remarkable progress, and there are active efforts to apply genome information to diagnosis and treatment. Generally, in the process of feeding back the results of next-generation sequencing analysis to patients, a molecular tumor board (MTB), consisting of experts in clinical oncology, genetic medicine, etc., is established to discuss the results. On the other hand, an MTB currently involves a large amount of work, with humans searching through vast databases and literature, selecting the best drug candidates, and manually confirming the status of available clinical trials. In addition, as personalized medicine advances, the burden on MTB members is expected to increase in the future. Under these circumstances, introducing cutting-edge artificial intelligence (AI) technology and information and communication technology to MTBs while reducing the burden on MTB members and building a platform that enables more accurate and personalized medical care would be of great benefit to patients. In this review, we introduced the latest status of elemental technologies that have potential for AI utilization in MTB, and discussed issues that may arise in the future as we progress with AI implementation.
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Affiliation(s)
- Ryuji Hamamoto
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Takafumi Koyama
- grid.272242.30000 0001 2168 5385Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Nobuji Kouno
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.258799.80000 0004 0372 2033Department of Surgery, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8303 Japan
| | - Tomohiro Yasuda
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.417547.40000 0004 1763 9564Research and Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8601 Japan
| | - Shuntaro Yui
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.417547.40000 0004 1763 9564Research and Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8601 Japan
| | - Kazuki Sudo
- grid.272242.30000 0001 2168 5385Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.272242.30000 0001 2168 5385Department of Medical Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Makoto Hirata
- grid.272242.30000 0001 2168 5385Department of Genetic Medicine and Services, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Kuniko Sunami
- grid.272242.30000 0001 2168 5385Department of Laboratory Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Takashi Kubo
- grid.272242.30000 0001 2168 5385Department of Laboratory Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Ken Takasawa
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Satoshi Takahashi
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Hidenori Machino
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Kazuma Kobayashi
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Ken Asada
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Masaaki Komatsu
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Syuzo Kaneko
- grid.272242.30000 0001 2168 5385Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.509456.bCancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027 Japan
| | - Yasushi Yatabe
- grid.272242.30000 0001 2168 5385Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan ,grid.272242.30000 0001 2168 5385Division of Molecular Pathology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
| | - Noboru Yamamoto
- grid.272242.30000 0001 2168 5385Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045 Japan
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44
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Katsonis P, Wilhelm K, Williams A, Lichtarge O. Genome interpretation using in silico predictors of variant impact. Hum Genet 2022; 141:1549-1577. [PMID: 35488922 PMCID: PMC9055222 DOI: 10.1007/s00439-022-02457-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/17/2022] [Indexed: 02/06/2023]
Abstract
Estimating the effects of variants found in disease driver genes opens the door to personalized therapeutic opportunities. Clinical associations and laboratory experiments can only characterize a tiny fraction of all the available variants, leaving the majority as variants of unknown significance (VUS). In silico methods bridge this gap by providing instant estimates on a large scale, most often based on the numerous genetic differences between species. Despite concerns that these methods may lack reliability in individual subjects, their numerous practical applications over cohorts suggest they are already helpful and have a role to play in genome interpretation when used at the proper scale and context. In this review, we aim to gain insights into the training and validation of these variant effect predicting methods and illustrate representative types of experimental and clinical applications. Objective performance assessments using various datasets that are not yet published indicate the strengths and limitations of each method. These show that cautious use of in silico variant impact predictors is essential for addressing genome interpretation challenges.
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Affiliation(s)
- Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Kevin Wilhelm
- Graduate School of Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Department of Biochemistry, Human Genetics and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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45
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Khandakji MN, Mifsud B. Gene-specific machine learning model to predict the pathogenicity of BRCA2 variants. Front Genet 2022; 13:982930. [PMID: 36246618 PMCID: PMC9561395 DOI: 10.3389/fgene.2022.982930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Existing BRCA2-specific variant pathogenicity prediction algorithms focus on the prediction of the functional impact of a subtype of variants alone. General variant effect predictors are applicable to all subtypes, but are trained on putative benign and pathogenic variants and do not account for gene-specific information, such as hotspots of pathogenic variants. Local, gene-specific information have been shown to aid variant pathogenicity prediction; therefore, our aim was to develop a BRCA2-specific machine learning model to predict pathogenicity of all types of BRCA2 variants. Methods: We developed an XGBoost-based machine learning model to predict pathogenicity of BRCA2 variants. The model utilizes general variant information such as position, frequency, and consequence for the canonical BRCA2 transcript, as well as deleteriousness prediction scores from several tools. We trained the model on 80% of the expert reviewed variants by the Evidence-Based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium and tested its performance on the remaining 20%, as well as on an independent set of variants of uncertain significance with experimentally determined functional scores. Results: The novel gene-specific model predicted the pathogenicity of ENIGMA BRCA2 variants with an accuracy of 99.9%. The model also performed excellently on predicting the functional consequence of the independent set of variants (accuracy was up to 91.3%). Conclusion: This new, gene-specific model is an accurate method for interpreting the pathogenicity of variants in the BRCA2 gene. It is a valuable addition for variant classification and can prioritize unreviewed variants for functional analysis or expert review.
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Affiliation(s)
- Mohannad N. Khandakji
- College of Health and Life Sciences, Hamad Bin Khalifa University, Ar-Rayyan, Qatar
- Hamad Medical Corporation, Doha, Qatar
| | - Borbala Mifsud
- College of Health and Life Sciences, Hamad Bin Khalifa University, Ar-Rayyan, Qatar
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
- *Correspondence: Borbala Mifsud,
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Nepomuceno TC, Dos Santos APP, Fernandes VC, Elias ABR, Gomes TT, Suarez-Kurtz G, Iversen ES, Couch FJ, Monteiro ANA, Carvalho MA. Assessment of small in-frame indels and C-terminal nonsense variants of BRCA1 using a validated functional assay. Sci Rep 2022; 12:16203. [PMID: 36171434 PMCID: PMC9519549 DOI: 10.1038/s41598-022-20500-4] [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: 02/16/2022] [Accepted: 09/14/2022] [Indexed: 11/29/2022] Open
Abstract
BRCA1 (Breast Cancer 1, early onset) is linked to breast and ovarian cancer predisposition. Still, the risks conferred by a significant portion of BRCA1 variants identified in the population remains unknown. Most of these variants of uncertain significance are missense alterations. However, the functional implications of small in-frame deletions and/or insertions (indels) are also difficult to predict. Our group has previously evaluated the functional impact of 347 missense variants using an extensively validated transcriptional activity assay. Here we show a systematic assessment of 30 naturally occurring in-frame indels located at the C-terminal region of BRCA1. We identified positions sensitive and tolerant to alterations, expanding the knowledge of structural determinants of BRCA1 function. We further designed and assessed the impact of four single codon deletions in the tBRCT linker region and six nonsense variants at the C-terminus end of BRCA1. Amino acid substitutions, deletions or insertions in the disordered region do not significantly impact activity and are not likely to constitute pathogenic alleles. On the other hand, a sizeable fraction of in-frame indels at the BRCT domain significantly impact function. We then use a Bayesian integrative statistical model to derive the probability of pathogenicity for each variant. Our data highlights the importance of assessing the impact of small in-frame indels in BRCA1 to improve risk assessment and clinical decisions for carriers.
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Affiliation(s)
- Thales C Nepomuceno
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil.,Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Ana P P Dos Santos
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Vanessa C Fernandes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Anna B R Elias
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Thiago T Gomes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Guilherme Suarez-Kurtz
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC, 27708, USA
| | | | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
| | - Marcelo A Carvalho
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil. .,Laboratório de Genética Molecular, Instituto Federal Do Rio de Janeiro, Rua Senador Furtado, Campus Rio de Janeiro121, Rio de Janeiro, RJ, 20270-021, Brazil.
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47
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Ben Aim L, Maher ER, Cascon A, Barlier A, Giraud S, Ercolino T, Pigny P, Clifton-Bligh RJ, Mirebeau-Prunier D, Mohamed A, Favier J, Gimenez-Roqueplo AP, Schiavi F, Toledo RA, Dahia PL, Robledo M, Bayley JP, Burnichon N. International initiative for a curated SDHB variant database improving the diagnosis of hereditary paraganglioma and pheochromocytoma. J Med Genet 2022; 59:785-792. [PMID: 34452955 PMCID: PMC8882202 DOI: 10.1136/jmedgenet-2020-107652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 07/18/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND SDHB is one of the major genes predisposing to paraganglioma/pheochromocytoma (PPGL). Identifying pathogenic SDHB variants in patients with PPGL is essential to the management of patients and relatives due to the increased risk of recurrences, metastases and the emergence of non-PPGL tumours. In this context, the 'NGS and PPGL (NGSnPPGL) Study Group' initiated an international effort to collect, annotate and classify SDHB variants and to provide an accurate, expert-curated and freely available SDHB variant database. METHODS A total of 223 distinct SDHB variants from 737 patients were collected worldwide. Using multiple criteria, each variant was first classified according to a 5-tier grouping based on American College of Medical Genetics and NGSnPPGL standardised recommendations and was then manually reviewed by a panel of experts in the field. RESULTS This multistep process resulted in 23 benign/likely benign, 149 pathogenic/likely pathogenic variants and 51 variants of unknown significance (VUS). Expert curation reduced by half the number of variants initially classified as VUS. Variant classifications are publicly accessible via the Leiden Open Variation Database system (https://databases.lovd.nl/shared/genes/SDHB). CONCLUSION This international initiative by a panel of experts allowed us to establish a consensus classification for 223 SDHB variants that should be used as a routine tool by geneticists in charge of PPGL laboratory diagnosis. This accurate classification of SDHB genetic variants will help to clarify the diagnosis of hereditary PPGL and to improve the clinical care of patients and relatives with PPGL.
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Affiliation(s)
- Laurene Ben Aim
- Genetics Department, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Européen Georges Pompidou, Paris, France
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | | | - Anne Barlier
- Laboratory of Molecular Biology, La Conception Hospital, Marseille, France
| | - Sophie Giraud
- Department of Genetics, Hospices Civils de Lyon, Bron, France
| | - Tonino Ercolino
- Endocrinology Unit, Azienda Ospedaliero-Universitaria Careggi, Firenze, Italy
| | - Pascal Pigny
- Institut de Biochimie & Biologie Moléculaire, Lille University Hospital Center, Lille, France
| | - Roderick J Clifton-Bligh
- Department of Endocrinology, Royal North Shore Hospital, Kolling Institute, University of Sydney, Sydney, New South Wales, Australia
| | | | - Amira Mohamed
- Laboratory of Molecular Biology, La Conception Hospital, Marseille, France
| | - Judith Favier
- Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue contre le Cancer, Paris, France
| | - Anne-Paule Gimenez-Roqueplo
- Genetics Department, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Européen Georges Pompidou, Paris, France
- Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue contre le Cancer, Paris, France
| | - Francesca Schiavi
- Familial Cancer Clinic and Oncoendocrinology, IOV IRCCS, Padova, Italy
| | - Rodrigo A Toledo
- CIBERONC, Gastrointestinal and Endocrine Tumors, VHIO, Barcelona, Spain
| | - Patricia L Dahia
- Department of Medicine, Division of Hematology and Medical Oncology, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | | | | | - Nelly Burnichon
- Genetics Department, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Européen Georges Pompidou, Paris, France
- Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue contre le Cancer, Paris, France
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48
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Abreu RBV, Gomes TT, Nepomuceno TC, Li X, Fuchshuber-Moraes M, De Gregoriis G, Suarez-Kurtz G, Monteiro ANA, Carvalho MA. Functional Restoration of BRCA1 Nonsense Mutations by Aminoglycoside-Induced Readthrough. Front Pharmacol 2022; 13:935995. [PMID: 35837282 PMCID: PMC9273842 DOI: 10.3389/fphar.2022.935995] [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: 05/04/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
BRCA1 is a major tumor suppressor that functions in the accurate repair of DNA double-strand breaks via homologous recombination (HR). Nonsense mutations in BRCA1 lead to inactive truncated protein products and are associated with high risk of breast and ovarian cancer. These mutations generate premature termination codons (PTCs). Different studies have shown that aminoglycosides can induce PTC suppression by promoting stop codon readthrough and restoring full-length (FL) protein expression. The use of these compounds has been studied in clinical trials for genetic diseases such as cystic fibrosis and Duchenne muscular dystrophy, with encouraging results. Here we show proof-of-concept data demonstrating that the aminoglycoside G418 can induce BRCA1 PTC readthrough and restore FL protein synthesis and function. We first demonstrate that G418 treatment restores BRCA1 FL protein synthesis in HCC1395, a human breast tumor cell line carrying the R1751X mutation. HCC1395 cells treated with G418 also recover HR DNA repair and restore cell cycle checkpoint activation. A set of naturally occurring BRCA1 nonsense variants encoding different PTCs was evaluated in a GFP C-terminal BRCA1 construct model and BRCA1 PTC readthrough levels vary depending on the stop codon context. Because PTC readthrough could generate FL protein carrying pathogenic missense mutations, variants representing the most probable acquired amino acid substitutions in consequence of readthrough were functionally assessed by a validated transcription activation assay. Overall, this is the first study that evaluates the readthrough of PTC variants with clinical relevance in the breast and ovarian cancer-predisposing gene BRCA1.
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Affiliation(s)
- Renata B. V. Abreu
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Thiago T. Gomes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Thales C. Nepomuceno
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Xueli Li
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | | | | | | | - Alvaro N. A. Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Marcelo A. Carvalho
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Instituto Federal do Rio de Janeiro—IFRJ, Rio de Janeiro, Brazil
- *Correspondence: Marcelo A. Carvalho,
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49
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Rambla J, Baudis M, Ariosa R, Beck T, Fromont LA, Navarro A, Paloots R, Rueda M, Saunders G, Singh B, Spalding JD, Törnroos J, Vasallo C, Veal CD, Brookes AJ. Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond. Hum Mutat 2022; 43:791-799. [PMID: 35297548 PMCID: PMC9322265 DOI: 10.1002/humu.24369] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/07/2022] [Accepted: 03/12/2022] [Indexed: 11/05/2022]
Abstract
Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple "yes" or "no" responses to queries about the presence of a given variant in datasets hosted by Beacon providers. The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations. Particularly, rare disease genetics and cancer research will benefit from new case level and genomic variant level requests and the enabling of richer phenotype and clinical queries as well as support for fuzzy searches. Beacon is designed as a "lingua franca" to bridge data collections hosted in software solutions with different and rich interfaces. Beacon version 2 works alongside popular standards like Phenopackets, OMOP, or FHIR, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. The protocol is being explored by other research domains and is being tested in several international projects.
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Affiliation(s)
- Jordi Rambla
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of Experimental and Health SciencesUniversitat Pompeu Fabra (UPF), PRBBBarcelonaSpain
| | - Michael Baudis
- Department of Molecular Life SciencesUniversity of Zurich and Swiss Institute of BioinformaticsZurichSwitzerland
| | - Roberto Ariosa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Tim Beck
- Department of Genetics & Genome BiologyUniversity of LeicesterLeicesterUK
| | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of Experimental and Health Sciences, IBE, Institute of Evolutionary Biology (UPF‐CSIC)Universitat Pompeu Fabra. PRBBBarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Universitat Pompeu FabraBarcelonaSpain
- Barcelona Beta Brain Research Center, Pasqual Maragall FoundationBarcelonaSpain
| | - Rahel Paloots
- Department of Molecular Life SciencesUniversity of Zurich and Swiss Institute of BioinformaticsZurichSwitzerland
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Gary Saunders
- European Infrastructure for Translational Medicine, EATRISAmsterdamThe Netherlands
| | - Babita Singh
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | | | - Juha Törnroos
- ELIXIR Finland; CSC ‐ IT Center for Science LtdEspooFinland
| | - Claudia Vasallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Colin D. Veal
- Department of Genetics & Genome BiologyUniversity of LeicesterLeicesterUK
| | - Anthony J. Brookes
- Department of Genetics & Genome BiologyUniversity of LeicesterLeicesterUK
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50
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Combrink H, van der Merwe N, Katarya R, de Wet K, Motloung M. A South African Indian population group dataset for breast cancer and BRCA1/2 variants. Data Brief 2022; 42:108180. [PMID: 35496481 PMCID: PMC9048066 DOI: 10.1016/j.dib.2022.108180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/26/2022] Open
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