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Wong RWC, Cheung ANY. Predictive and prognostic biomarkers in female genital tract tumours: an update highlighting their clinical relevance and practical issues. Pathology 2024; 56:214-227. [PMID: 38212229 DOI: 10.1016/j.pathol.2023.10.013] [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: 08/31/2023] [Revised: 10/24/2023] [Accepted: 10/29/2023] [Indexed: 01/13/2024]
Abstract
The evaluation of biomarkers by molecular techniques and immunohistochemistry has become increasingly relevant to the treatment of female genital tract tumours as a consequence of the greater availability of therapeutic options and updated disease classifications. For ovarian cancer, mutation testing for BRCA1/2 is the standard predictive biomarker for poly(ADP-ribose) polymerase inhibitor therapy, while homologous recombination deficiency testing may allow the identification of eligible patients among cases without demonstrable BRCA1/2 mutations. Clinical recommendations are available which specify how these predictive biomarkers should be applied. Mismatch repair (MMR) protein and folate receptor alpha immunohistochemistry may also be used to guide treatment in ovarian cancer. In endometrial cancer, MMR immunohistochemistry is the preferred test for predicting benefit from immune checkpoint inhibitor (ICI) therapy, but molecular testing for microsatellite instability may have a supplementary role. HER2 testing by immunohistochemistry and in situ hybridisation is applicable to endometrial serous carcinomas to assess trastuzumab eligibility. Immunohistochemistry for oestrogen receptor and progesterone receptor expression may be used for prognostication in endometrial cancer, but its predictive value for hormonal therapy is not yet proven. POLE mutation testing and p53 immunohistochemistry (as a surrogate for TP53 mutation status) serve as prognostic markers for favourable and adverse outcomes, respectively, in endometrial cancer, especially when combined with MMR testing for molecular subtype designation. For cervical cancer, programmed death ligand 1 immunohistochemistry may be used to predict benefit from ICI therapy although its predictive value is under debate. In vulvar cancer, p16 and p53 immunohistochemistry has established prognostic value, stratifying patients into three groups based on the human papillomavirus and TP53 mutation status of the tumour. Awareness of the variety and pitfalls of expression patterns for p16 and p53 in vulvar carcinomas is crucial for accurate designation. It is hoped that collaborative efforts in standardising and optimising biomarker testing for gynaecological tumours will contribute to evidence-based therapeutic decisions.
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Affiliation(s)
- Richard Wing-Cheuk Wong
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong Special Administrative Region of China.
| | - Annie N Y Cheung
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
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Scaglione GL, Pignata S, Pettinato A, Paolillo C, Califano D, Scandurra G, Lombardo V, Di Gaudio F, Pecorino B, Mereu L, Scollo P, Capoluongo ED. Homologous Recombination Deficiency (HRD) Scoring, by Means of Two Different Shallow Whole-Genome Sequencing Pipelines (sWGS), in Ovarian Cancer Patients: A Comparison with Myriad MyChoice Assay. Int J Mol Sci 2023; 24:17095. [PMID: 38069422 PMCID: PMC10707691 DOI: 10.3390/ijms242317095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
High-grade serous ovarian cancer (HGSOC) patients carrying the BRCA1/2 mutation or deficient in the homologous recombination repair system (HRD) generally benefit from treatment with PARP inhibitors. Some international recommendations suggest that BRCA1/2 genetic testing should be offered for all newly diagnosed epithelial ovarian cancer, along with HRD assessment. Academic tests (ATs) are continuously under development, in order to break down the barriers patients encounter in accessing HRD testing. Two different methods for shallow whole-genome sequencing (sWGS) were compared to the reference assay, Myriad. All these three assays were performed on 20 retrospective HGSOC samples. Moreover, HRD results were correlated with the progression-free survival rate (PFS). Both sWGS chemistries showed good correlation with each other and a complete agreement, even when compared to the Myriad score. Our academic HRD assay categorized patients as HRD-Deficient, HRM-Mild and HRN-Negative. These three groups were matched with PFS, providing interesting findings in terms of HRD scoring and months of survival. Both our sWGS assays and the Myriad test correlated with the patient's response to treatments. Finally, our AT confirms its capability of determining HRD status, with the advantage of being faster, cheaper, and easier to carry out. Our results showed a prognostic value for the HRD score.
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Affiliation(s)
- Giovanni L. Scaglione
- Laboratory of Molecular Oncology, IDI-IRCCS, Via dei Monti di Creta, 104, 00167 Rome, Italy;
| | - Sandro Pignata
- Department of Urology and Gynecology, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Via Mariano Semmola, 53, 80131 Naples, Italy;
| | - Angela Pettinato
- Department of Pathological Anatomy, A.O.E. Cannizzaro, Via Messina, 829, 95126 Catania, Italy;
| | - Carmela Paolillo
- Department of Clinical and Experimental Medicine, University of Foggia, Viale Luigi Pinto, 71122 Foggia, Italy;
| | - Daniela Califano
- Functional Genomic Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Via Mariano Semmola, 53, 80131 Naples, Italy;
| | - Giuseppa Scandurra
- Department of Medical Oncology, A.O.E. Cannizzaro, Via Messina, 829, 95126 Catania, Italy; (G.S.); (V.L.)
| | - Valentina Lombardo
- Department of Medical Oncology, A.O.E. Cannizzaro, Via Messina, 829, 95126 Catania, Italy; (G.S.); (V.L.)
| | | | - Basilio Pecorino
- Department of Obstetrics and Gynecology, A.O.E. Cannizzaro, Via Messina, 829, 95126 Catania, Italy; (B.P.); (P.S.)
| | - Liliana Mereu
- Division of Obstetrics and Gynecology, Department of General Surgery and Medical-Surgical Specialism, University of Catania, P.O. “G Rodolico”, Via Santa Sofia, 78, 95123 Catania, Italy;
| | - Paolo Scollo
- Department of Obstetrics and Gynecology, A.O.E. Cannizzaro, Via Messina, 829, 95126 Catania, Italy; (B.P.); (P.S.)
- Faculty of Medicine, “Kore” University, Cittadella Universitaria, 94100 Enna, Italy
| | - Ettore D. Capoluongo
- Department of Clinical Pathology and Genomics, A.O.E. Cannizzaro, Via Messina 829, 95126 Catania, Italy
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Via Pansini, 5, 80131 Naples, Italy
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Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer. Genes (Basel) 2022; 13:genes13091583. [PMID: 36140751 PMCID: PMC9498802 DOI: 10.3390/genes13091583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
The goal of biomarker testing, in the field of personalized medicine, is to guide treatments to achieve the best possible results for each patient. The accurate and reliable identification of everyone’s genome variants is essential for the success of clinical genomics, employing third-generation sequencing. Different variant calling techniques have been used and recommended by both Oxford Nanopore Technologies (ONT) and Nanopore communities. A thorough examination of the variant callers might give critical guidance for third-generation sequencing-based clinical genomics. In this study, two reference genome sample datasets (NA12878) and (NA24385) and the set of high-confidence variant calls provided by the Genome in a Bottle (GIAB) were used to allow the evaluation of the performance of six variant calling tools, including Human-SNP-wf, Clair3, Clair, NanoCaller, Longshot, and Medaka, as an integral step in the in-house variant detection workflow. Out of the six variant callers understudy, Clair3 and Human-SNP-wf that has Clair3 incorporated into it achieved the highest performance rates in comparison to the other variant callers. Evaluation of the results for the tool was expressed in terms of Precision, Recall, and F1-score using Hap.py tools for the comparison. In conclusion, our findings give important insights for identifying accurate variants from third-generation sequencing of personal genomes using different variant detection tools available for long-read sequencing.
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