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Nechifor-Boilă A, Zahan A, Bănescu C, Moldovan V, Piciu D, Voidăzan S, Borda A. Impact of BRAFV600E Mutation on Event-Free Survival in Patients with Papillary Thyroid Carcinoma: A Retrospective Study in a Romanian Population. Cancers (Basel) 2023; 15:4053. [PMID: 37627081 PMCID: PMC10452493 DOI: 10.3390/cancers15164053] [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: 06/23/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
We aimed to evaluate the prognostic value of BRAFV600E mutation in a series of 127 papillary thyroid carcinoma (PTC) cases as a single factor, and in synergic interaction with other standard risk factors. BRAFV600E mutation was assessed by real-time PCR. Event-free survival (EFS) was calculated between the date of the first evaluation and the date of occurrence of an adverse event or the date of the last known status. The prevalence of BRAFV600E mutation was 57.2%. The Kaplan-Meier analysis showed a significant reduction of EFS among cases harboring BRAFV600E mutation compared to non-mutated cases (p = 0.010). In addition, BRAFV600E mutation was found to better predict adverse outcomes when associated with the following risk factors: age ≥ 55 years old (p < 0.001), male gender (p < 0.001), conventional (p = 0.005) and tall cell (p = 0.014) histology, tumor size > 40 mm (p = 0.001), extrathyroidal extension (p = 0.001), multifocality (p = 0.001) and lymph node metastasis (p < 0.001). In univariate analysis, a 3.74-fold increased risk for a reduced EFS (p = 0.018) was found for BRAFV600E-mutated cases, but no increased risk was further confirmed by multivariate analysis. Our results highlight that BRAFV600E mutation cannot be used alone as an independent predictive factor in PTC patients, but is prognostically valuable if integrated in the context of other clinicopathological risk factors.
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Affiliation(s)
- Adela Nechifor-Boilă
- Department of Histology, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu-Mureș, 38th Gh. Marinescu Street, 540139 Targu Mures, Romania; (A.Z.); (A.B.)
- Department of Pathology, Targu-Mures Clinical County Hospital, 28 First December 1918 Street, 540061 Targu Mures, Romania
| | - Ancuţa Zahan
- Department of Histology, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu-Mureș, 38th Gh. Marinescu Street, 540139 Targu Mures, Romania; (A.Z.); (A.B.)
| | - Claudia Bănescu
- Department of Genetics, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu-Mureș, 38th Gh. Marinescu Street, 540139 Targu Mures, Romania; (C.B.); (V.M.)
| | - Valeriu Moldovan
- Department of Genetics, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu-Mureș, 38th Gh. Marinescu Street, 540139 Targu Mures, Romania; (C.B.); (V.M.)
| | - Doina Piciu
- Department of Nuclear Medicine, “Ion Chiricuţă” Institute of Oncology, 400015 Cluj-Napoca, Romania;
| | - Septimiu Voidăzan
- Department of Epidemiology, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu-Mureș, 38th Gh. Marinescu Street, 540139 Targu Mures, Romania;
| | - Angela Borda
- Department of Histology, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu-Mureș, 38th Gh. Marinescu Street, 540139 Targu Mures, Romania; (A.Z.); (A.B.)
- Department of Pathology, Targu-Mureș Emergency County Hospital, 50 Gh. Marinescu Street, 540139 Targu Mures, Romania
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Chromosomal Junction Detection from Whole-Genome Sequencing on Formalin-Fixed, Paraffin-Embedded Tumors. J Mol Diagn 2020; 23:375-388. [PMID: 33387698 DOI: 10.1016/j.jmoldx.2020.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/20/2020] [Accepted: 12/14/2020] [Indexed: 11/22/2022] Open
Abstract
DNA junctions (DNAJs) frequently impact clinically relevant genes in tumors and are important for diagnostic and therapeutic purposes. Although routinely screened through fluorescence in situ hybridization assays, such testing only allows the interrogation of single-gene regions or known fusion partners. Comprehensive assessment of DNAJs present across the entire genome can only be determined from whole-genome sequencing. Structural variance analysis from whole-genome paired-end sequencing data is, however, frequently restricted to copy number changes without DNAJ detection. Through optimized whole-genome sequencing and specialized bioinformatics algorithms, complete structural variance analysis is reported, including DNAJs, from formalin-fixed DNA. Selective library assembly from larger fragments (>500 bp) and economical sequencing depths (300 to 400 million reads) provide representative genomic coverage profiles and increased allelic coverage to levels compatible with DNAJ calling (40× to 60×). Although consistently fragmented, more recently formalin-fixed, specimens (<2 years' storage) revealed consistent populations of larger DNA fragments. Optimized bioinformatics efficiently detected >90% of DNAJs in two prostate tumors (approximately 60% tumor) previously analyzed by mate-pair sequencing on fresh frozen tissue, with evidence of at least one spanning-read in 99% of DNAJs. Rigorous masking with data from unrelated formalin-fixed tissue progressively eliminated many false-positive DNAJs, without loss of true positives, resulting in low numbers of false-positive passing current filters. This methodology enables more comprehensive clinical genomics testing on formalin-fixed clinical specimens.
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Nechifor-Boilă A, Banescu C, Zahan AE, Moldovan V, Szasz E, Borda A. DNA isolation from achieved formalin-fixed paraffin-embedded tissues in a series of 212 thyroid carcinoma cases: the influence of preanalytical factors on DNA quantity and purity. J Investig Med 2019; 68:792-798. [PMID: 31801793 DOI: 10.1136/jim-2019-001134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2019] [Indexed: 11/03/2022]
Abstract
OBJECTIVE The present study aimed to investigate the influence of several important preanalytical factors (storage period of the tumor block, maximal diameter of the tumor circled area, tumor volume and tumor fraction) on the isolated DNA from formalin-fixed paraffin-embedded (FFPE) tissues in a series of thyroid carcinomas. DESIGN Our study included 212 FFPE blocks, archived in the Department of Pathology, Târgu-Mureș Emergency County Hospital for up to 10 years. DNA isolation was performed using a commercially available kit (MasterPure DNA purification kit, Epicentre). The DNA parameters (concentration and purity) were determined using a spectrophotometer and the Qubit 2.0 Fluorometer (Thermo Fisher Scientific) for an accurate and sensitive DNA quantification. RESULTS The mean DNA concentration and purity for the study cases were 489.3±372.6 ng/µl and 1.667±0.1912, respectively. The DNA concentration was correlated with the maximal diameter of the tumor circled area (p<0.0001), the tumor volume (p<0.0001) and tumor fraction (p=0.0462). No statistically significant differences both in terms of DNA concentration (p=0.374) and purity (p=0.125) in relation with the storage period of the tumor blocks were observed. When using a fluorometric quantification method, the DNA concentration was lower (mean DNA concentration: 47.15±32.85 ng/µl), but similar correlations with the morphological factors were observed. Apart for three cases, the real-time PCR amplification of the BRAF gene was successfully assessed in all cases. CONCLUSION The maximal diameter of the tumor circled area, tumor volume and tumor fraction are important morphological factors that correlate with the DNA concentration and should be carefully assessed in routine practice prior to performing DNA isolation from FFPE tissues.
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Affiliation(s)
- Adela Nechifor-Boilă
- Department of Histology, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
| | - Claudia Banescu
- Department of Genetics, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
| | - Ancuta Elena Zahan
- Department of Histology, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
| | - Valeriu Moldovan
- Department of Genetics, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
| | - Emoke Szasz
- Department of Histology, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
| | - Angela Borda
- Department of Histology, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
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