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Tuncer SB, Celik B, Erciyas SK, Erdogan OS, Gültaslar BK, Odemis DA, Avsar M, Sen F, Saip PM, Yazici H. Germline mutational variants of Turkish ovarian cancer patients suspected of Hereditary Breast and Ovarian Cancer (HBOC) by next-generation sequencing. Pathol Res Pract 2024; 254:155075. [PMID: 38219492 DOI: 10.1016/j.prp.2023.155075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 01/16/2024]
Abstract
Hereditary Breast and Ovarian Cancer (HBOC) syndrome is characterized by an increased risk of developing breast cancer (BC) and ovarian cancer (OC) due to inherited genetic mutations. Understanding the genetic variants associated with HBOC is crucial for identifying individuals at high risk and implementing appropriate preventive measures. The study included 630 Turkish OC patients with confirmed diagnostic criteria of The National Comprehensive Cancer Network (NCCN) concerning HBOC. Genomic DNA was extracted from peripheral blood samples, and targeted Next-generation sequencing (NGS) was performed. Bioinformatics analysis and variant interpretation were conducted to identify pathogenic variants (PVs). Our analysis revealed a spectrum of germline pathogenic variants associated with HBOC in Turkish OC patients. Notably, several pathogenic variants in BRCA1, BRCA2, and other DNA repair genes were identified. Specifically, we observed germline PVs in 130 individuals, accounting for 20.63% of the total cohort. 76 distinct PVs in genes, BRCA1 (40 PVs), BRCA2 (29 PVs), ATM (1 PV), CHEK2 (2 PVs), ERCC2 (1 PV), MUTYH (1 PV), RAD51C (1 PV), and TP53 (1PV) and also, two different PVs (i.e., c.135-2 A>G p.? in BRCA1 and c.6466_6469delTCTC in BRCA2) were detected in a 34-year-old OC patient. In conclusion, our study contributes to a better understanding of the genetic variants underlying HBOC in Turkish OC patients. These findings provide valuable insights into the genetic architecture of HBOC in the Turkish population and shed light on the potential contribution of specific germline PVs to the increased risk of OC.
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Affiliation(s)
- Seref Bugra Tuncer
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Betul Celik
- Erzincan Binali Yıldırım University, Department of Molecular Biology, Erzincan, Türkiye
| | - Seda Kilic Erciyas
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Ozge Sukruoglu Erdogan
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Busra Kurt Gültaslar
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Demet Akdeniz Odemis
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Mukaddes Avsar
- Health Services Vocational of Higher Education, T.C. Istanbul Aydın University, Istanbul, Türkiye
| | - Fatma Sen
- Clinic of Medical Oncology, Avrasya Hospital, Istanbul, Türkiye
| | - Pınar Mualla Saip
- Department of Medical Oncology, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Hulya Yazici
- Istanbul Arel University, Arel Medical Faculty, Department of Medical Biology and Genetics, Istanbul, Türkiye
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Svyatova G, Berezina G, Urazbayeva G, Murtazaliyeva A. Frequencies of Diagnostically Significant Polymorphisms of Hereditary Breast Cancer Forms in BRCA1 and BRCA2 Genes in the Kazakh Population. Asian Pac J Cancer Prev 2023; 24:3899-3907. [PMID: 38019249 PMCID: PMC10772761 DOI: 10.31557/apjcp.2023.24.11.3899] [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: 07/24/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023] Open
Abstract
OBJECTIVE Breast cancer is the most common form of cancer in women in the world with more than 400,000 deaths each year worldwide. The aim of this study is to compare population frequencies of alleles and genotypes of polymorphic variants of BRCA1 and BRCA2 genes associated with breast cancer risk in an ethnically homogenous Kazakh population with previously studied world populations. The material of the study was DNA isolated from peripheral blood of the enrolled population control group, represented by 1800 conditionally healthy individuals of Kazakh ethnicity. METHODS The DNA extraction was possible with the use of M-PVA magnetic particle separation method on the Prepito (PerkinElmer) automatic analyser for extraction of Chemagic Prepito (Wallac, Finland) nucleic acids using the PrepitoDNACytoPure reagent kit. Statistical calculations of allele and genotype frequencies, significance tests, and non-parametric χ2 analysis were carried out using PLINK software. RESULTS The results favour for the high genetic heterogeneity of the studied polymorphisms, which reflects the specifics of the Kazakh population structure resulted from complex evolutionary and migration processes, as well as the median geographic location between the populations of Asia and Europe. CONCLUSION Knowledge of the spectrum and frequency of mutations in BRCA1 and BRCA2 genes predisposing to breast cancer, which are present in varying frequencies in the Kazakh population, will provide a more effective approach to the screening protocol and allow for a faster, less expensive and more accessible genetic testing strategy for the Kazakhstan citizens.
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Affiliation(s)
- Gulnara Svyatova
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Republic of Kazakhstan.
| | - Galina Berezina
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Republic of Kazakhstan.
| | - Gulfairuz Urazbayeva
- Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Republic of Kazakhstan.
| | - Alexandra Murtazaliyeva
- Republican Medical Genetic Consultation, Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Republic of Kazakhstan.
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Germline variants associated with breast cancer in Khakass women of North Asia. Mol Biol Rep 2023; 50:2335-2341. [PMID: 36577833 DOI: 10.1007/s11033-022-08215-1] [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: 08/04/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Variants in the BRCA1/2 genes are responsible for familial breast cancer. Numerous studies showed a different spectrum of BRCA variants among breast cancer patients of different Ethnicity origin. In the available literature, no previous research has focused on breast cancer-associated variants among the Khakass people (the indigenous people of the Russian Federation). METHODS Twenty-six Khakass breast cancer patients were enrolled in the study. Genomic DNA was isolated from blood samples and used to prepare libraries using a Hereditary Cancer Solution kit. Next-generation sequencing (NGS) was performed using the MiSeq System (Illumina, USA). RESULTS In our study, 12% of patients (3/26) carried a single pathogenic variant; 54% of patients (14/26) carried variants of uncertain significance (VUS) or conflicting variants; and 35% of patients (9/26) did not carry any clinically significant variants. Germline pathogenic variant in the ATM gene (rs780619951, NC_000011.10:g.108259022C > T) was identified in two unrelated patients with a family history of cancer (7.6%, 2/26). The pathogenic truncating variant in the ATM gene (p. R805* or c.2413C > T) leads to the nonfunctional version of the protein. This variant has been earlier reported in individuals with a family history of breast cancer. CONCLUSIONS Our pilot study describes the germline variant in the ATM gene associated with breast cancer in Khakass women of North Asia.
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Bisgin A, Sag SO, Dogan ME, Yildirim MS, Gumus AA, Akkus N, Balasar O, Durmaz CD, Eroz R, Altiner S, Alemdar A, Aliyeva L, Boga I, Cam FS, Dogan B, Esbah O, Hanta A, Mujde C, Ornek C, Ozer S, Rencuzogullari C, Sonmezler O, Bozdogan ST, Dundar M, Temel SG. Germline landscape of BRCAs by 7-site collaborations as a BRCA consortium in Turkey. Breast 2022; 65:15-22. [PMID: 35753294 PMCID: PMC9249944 DOI: 10.1016/j.breast.2022.06.005] [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: 01/19/2022] [Revised: 05/26/2022] [Accepted: 06/17/2022] [Indexed: 11/12/2022] Open
Abstract
BRCA1/2 mutations play a significant role in cancer pathogenesis and predisposition particularly in breast, ovarian and prostate cancers. Thus, germline analysis of BRCA1 and BRCA2 is essential for clinical management strategies aiming at the identification of recurrent and novel mutations that could be used as a first screening approach. We analyzed germline variants of BRCA1/2 genes for 2168 individuals who had cancer diagnosis or high risk assessment due to BRCAs related cancers, referred to 10 health care centers distributed across 7 regions covering the Turkish landscape. Overall, 68 and 157 distinct mutations were identified in BRCA1 and BRCA2, respectively. Twenty-two novel variants were reported from both genes while BRCA2 showed higher mutational heterogeneity. We herein report the collective data as BRCA Turkish consortium that confirm the molecular heterogeneity in BRCAs among Turkish population, and also as the first study presenting the both geographical, demographical and gene based landscape of all recurrent and novel mutations which some might be a founder effect in comparison to global databases. This wider perspective leads to the most accurate variant interpretations which pave the way for the more precise and efficient management affecting the clinical and molecular aspects. A similar percentage of clinically unaffected individuals were also identified with potentially pathogenic variants. Based on the geographic examinations, Eastern Anatolian and the Mediterranean region had the lowest positivity rates. The Southeastern Anatolian region showed the lowest density of both patients and clinically relevant genetic changes.
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Hu J, Xu Z, Ye Z, Li J, Hao Z, Wang Y. The association between single nucleotide polymorphisms and ovarian cancer risk: A systematic review and network meta-analysis. Cancer Med 2022; 12:541-556. [PMID: 35637613 PMCID: PMC9844622 DOI: 10.1002/cam4.4891] [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: 03/29/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The relationship between single nucleotide polymorphisms (SNPs) and ovarian cancer (OC) risk remains controversial. This systematic review and network meta-analysis was aimed to determine the association between SNPs and OC risk. METHODS Several databases (PubMed, EMBASE, China National Knowledge Infrastructure, Wanfang databases, China Science and Technology Journal Database, and China Biology Medicine disc) were searched to summarize the association between SNPs and OC published throughout April 2021. Direct meta-analysis was used to identify SNPs that could predict the incidence of OC. Ranking probability resulting from network meta-analysis and the Thakkinstian's algorithm was used to select the most appropriate gene model. The false positive report probability (FPRP) and Venice criteria were further tested for credible relationships. Subgroup analysis was also carried out to explore whether there are racial differences. RESULTS A total of 63 genes and 92 SNPs were included in our study after careful consideration. Fok1 rs2228570 is likely a dominant risk factor for the development of OC compared to other selected genes. The dominant gene model of Fok1 rs2228570 (pooled OR = 1.158, 95% CI: 1.068-1.256) was determined to be the most suitable model with a FPRP <0.2 and moderate credibility. CONCLUSIONS Fok1 rs2228570 is closely linked to OC risk, and the dominant gene model is likely the most appropriate model for estimating OC susceptibility.
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Affiliation(s)
- Jia Hu
- Department of GastroenterologyThe Second Xiangya Hospital, Central South UniversityChangshaChina,Research Center of Digestive DiseaseThe Second Xiangya Hospital, Central South UniversityChangshaChina
| | - Zhe Xu
- Department of Pharmacy, Xiangya HospitalCentral South UniversityChangshaChina
| | - Zhuomiao Ye
- Department of Oncology, Xiangya HospitalCentral South UniversityChangshaChina
| | - Jin Li
- Xiangya School of MedicineCentral South UniversityChangshaChina
| | - Zhinan Hao
- Department of Gastrointestinal SurgeryHebei General HospitalShijiazhuangChina
| | - Yongjun Wang
- Department of GastroenterologyThe Second Xiangya Hospital, Central South UniversityChangshaChina,Research Center of Digestive DiseaseThe Second Xiangya Hospital, Central South UniversityChangshaChina
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Al-Khatib SM, Abdo N, Al-Eitan LN, Al-Mistarehi AHW, Zahran DJ, Al Ajlouni M, Kewan TZ. The Impact of the Genetic Polymorphism in DNA Repair Pathways on Increased Risk of Glioblastoma Multiforme in the Arab Jordanian Population: A Case-Control Study. APPLICATION OF CLINICAL GENETICS 2020; 13:115-126. [PMID: 32606887 PMCID: PMC7295542 DOI: 10.2147/tacg.s248994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 05/22/2020] [Indexed: 01/06/2023]
Abstract
Introduction Among the Jordanian population, brain tumors are the tenth most common type of cancers in both males and females, comprising 2.8% of all newly diagnosed neoplasms. Diffuse gliomas are the most prevalent and the most aggressive primary brain tumors in adults. The incidence of diffuse gliomas varies among different populations; this variation is partially linked to genetic polymorphisms. The purpose of the study is to examine the association between (BRCA1 rs799917G>A, rs1799966T>C, EXO1 rs1047840G>A, EME1 rs12450550T>C, ERCC2 rs13181T>G, rs1799793C>T, and XRCC1 rs1799782G>A) DNA repair gene polymorphisms and glioblastoma multiforme (GBM) susceptibility, and survival in the Jordanian Arab population. Methods Eighty-four patients diagnosed with glioblastoma multiforme at the King Abdullah University Hospital (KAUH) between 2013 and 2018 and 225 healthy cancer-free control subjects with similar geographic and ethnic backgrounds to the patients were included in the study. Genomic DNA was extracted from the formalin-fixed paraffin-embedded tissues of the subjects. The Sequenom MassARRAY® sequencer system (iPLEX GOLD) was used. The analyses included assessments of population variability and survival. Results This study is the first to address the relationship between BRCA1 rs1799966 and rs799917 SNP, and the risk of GBM among the Arab Jordanian population. The findings of the study show that BRCA1 rs799917 is associated with decreased risk of GBM in the recessive model (AA vs G/G-A/G: OR, 0.46, 95% CI, 0.26-0.82, p=0.01) and the same SNP is associated with increased risk of GBM in the overdominant model (AG vs G/G-A/A: OR, 1.72, 95% CI, 1.02-2.89, p=0.04).
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Affiliation(s)
- Sohaib M Al-Khatib
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Nour Abdo
- Department of Public Health, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Laith N Al-Eitan
- Department of Biotechnology and Genetic Engineering, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Abdel-Hameed W Al-Mistarehi
- Department of Family Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Deeb Jamil Zahran
- Department of Internal Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Marwan Al Ajlouni
- Department of Public Health, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Tariq Zuheir Kewan
- Department of Internal Medicine, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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Zhou Z, Ou X, Zou Q, Chu L, Quan X, Chen Y, Liu Y. Functional polymorphisms in FOXC2 gene and Epithelial ovarian Cancer susceptibility in Chinese population. J Ovarian Res 2020; 13:34. [PMID: 32222147 PMCID: PMC7103066 DOI: 10.1186/s13048-020-00634-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Background Epithelial ovarian cancer (EOC) is highly lethal gynecological cancer. Forkhead Box Protein C2 (FOXC2) promotes occurrence and development of various malignant tumors. The present study is aimed at exploring the correlation between the polymorphism of FOXC2 and epithelial ovarian cancer susceptibility in Chinese Han population. Methods A case-control design was used to verify the association between FOXC2 polymorphisms and epithelial ovarian cancer. The genotyping was performed using Taqman® SNP Genotyping kit by qRT-PCR. The genetic variants including rs3751794 C > T, rs1035550 A > G, rs4843163 C > G and rs4843396 C > T in FOXC2 gene were analyzed. The strength of the associations was detected using odds ratios and 95% confidence intervals. Stratification analyses showed the association between the FOXC2 gene polymorphisms rs3751794 C > T, rs4843163 C > G and rs4843396 C > T with epithelial ovarian cancer susceptibility in terms of age, metastasis status, clinical stage, pathological grade, pregnant times, pausimenia, and the expression of ER, PR, wild p53 and mutant p53. Results Rs3751794 C > T (P = 0.0016), rs4843163 C > G (P < 0.0001) and rs4843396 C > T (P < 0.0001) were significantly associated with increased epithelial ovarian cancer risk. In stratification analyses,rs3751794 C > T, was identified to be dominant in no metastasis patients, clinical stage 4 group, middle grade pathological stage, pregnant time over 3 patients, post-menopause women, strong wild type p53 expression; rs4843163 C > G was dominant in high grade clinical stage, high grade pathological stage, post-menopause women, strong ER expression group and no mutant p53 expression group; rs4843396 C > T was dominant in high grade clinical stage, high grade pathological stage, strong ER expression group. The rs1035550 A > G was not related to epithelial ovarian cancer susceptibility. Conclusions The results of the current study verified that FOXC2 gene polymorphisms were associated with increased epithelial ovarian cancer risk and suggested that FOXC2 gene polymorphisms might be a potential biomarker for epithelial ovarian cancer susceptibility.
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Affiliation(s)
- Zhijiao Zhou
- Department of Pathology, Third Xiangya Hospital,Central South University, Changsha, 410013, Hunan, China
| | - Xiang Ou
- Department of Endocrinology, The First Hospital of Changsha, Changsha, Hunan, China
| | - Qiong Zou
- Department of Pathology, Third Xiangya Hospital,Central South University, Changsha, 410013, Hunan, China
| | - Ling Chu
- Department of Pathology, Third Xiangya Hospital,Central South University, Changsha, 410013, Hunan, China
| | - Xiyun Quan
- Department of Pathology, Zhuzhou Central Hospital, Zhuzhou, Hunan, China
| | - Yong Chen
- Department of Clinical Laboratory, The First Hospital of Changsha, Changsha, Hunan, China
| | - Yang Liu
- Department of Pathology, Third Xiangya Hospital,Central South University, Changsha, 410013, Hunan, China.
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Cecener G, Sabour Takanlou L, Sabour Takanlou M, Egeli U, Eskiler GG, Aksoy S, Unal U, Tezcan H, Eryilmaz IE, Gokgoz MS, Tunca B, Cubukcu E, Evrensel T, Cetintas S, Tasdelen I. Clinicopathologic features and genetic characteristics of the BRCA1/2 mutation in Turkish breast cancer patients. Cancer Genet 2020; 240:23-32. [DOI: 10.1016/j.cancergen.2019.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/14/2019] [Indexed: 12/29/2022]
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