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Kilicaslan DY, Cumaogullari O, Emiral E, Tezer N, Oncu B, Ozdag H, Canturk N, Tufan NLS. Investigation of polymorphic variants of SLC6A4, TPH-1, and TPH-2 genes in cases of completed suicide. J Mens Health 2022. [DOI: 10.31083/jomh.2021.116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Dastouri M, Ozdag H, Akar AR, Can A. Differentiation and molecular characterization of endothelial progenitor and vascular smooth muscle cells from induced pluripotent stem cells. Bioimpacts 2022; 13:289-300. [PMID: 37645025 PMCID: PMC10460769 DOI: 10.34172/bi.2022.24132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 08/31/2023]
Abstract
Introduction Pluripotent stem cells have been used by various researchers to differentiate and characterize endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) for the clinical treatment of vascular injuries. Studies continue to differentiate and characterize the cells with higher vascularization potential and low risk of malignant transformation to the recipient. Unlike previous studies, this research aimed to differentiate induced pluripotent stem (iPS) cells into endothelial progenitor cells (EPCs) and VSMCs using a step-wise technique. This was achieved by elucidating the spatio-temporal expressions of the stage-specific genes and proteins during the differentiation process. The presence of highly expressed oncogenes in iPS cells was also investigated during the differentiation period. Methods Induced PS cells were differentiated into lateral mesoderm cells (Flk1+). The Flk1+ populations were isolated on day 5.5 of the mesodermal differentiation period. Flk1+ cells were further differentiated into EPCs and VSMCs using VEGF165 and platelet-derived growth factor-BB (PDGF-BB), respectively, and then characterized using gene expression levels, immunocytochemistry (ICC), and western blot (WB) methods. During the differentiation steps, the expression levels of the marker genes and proto-oncogenic Myc and Klf4 genes were simultaneously studied. Results The optimal time for the isolation of Flk1+ cells was on day 5.5. EPCs and VSMCs were differentiated from Flk1+ cells and characterized with EPC-specific markers, including Kdr, Pecam1, CD133, Cdh5, Efnb2, Vcam1; and VSMC-specific markers, including Acta2, Cnn1, Des, and Myh11. Differentiated cells were validated based on their temporal gene expressions, protein synthesis, and localization at certain time points. Significant decreases in Myc and Klf4 gene expression levels were observed during the EPCs and VSMC differentiation period. Conclusion EPCs and VSMCs were successfully differentiated from iPS cells and characterized by gene expression levels, ICC, and WB. We observed significant decreases in oncogene expression levels in the differentiated EPCs and VSMCs. In terms of safety, the described methodology provided a better safety margin. EPCs and VSMC obtained using this method may be good candidates for transplantation and vascular regeneration.
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Affiliation(s)
- Mohammadreza Dastouri
- Ankara University Biotechnology Institute and SISBIYOTEK Advanced Research Unit, Gumusdere Yerleskesi, Kecioren Ankara, 06135, Turkey
| | - Hilal Ozdag
- Ankara University Biotechnology Institute and SISBIYOTEK Advanced Research Unit, Gumusdere Yerleskesi, Kecioren Ankara, 06135, Turkey
| | - Ahmet Ruchan Akar
- Ankara University School of Medicine, Department of Cardiovascular Surgery, Heart Center Dikimevi, Ankara, 06340, Turkey
| | - Alp Can
- Ankara University School of Medicine, Department of Histology and Embryology, Laboratories for Stem Cells and Reproductive Medicine, Sihhiye, Ankara, 06410, Turkey
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Omidvar N, Tekin N, Conget P, Bruna F, Timar B, Gagyi E, Basak R, Auewarakul C, Sritana N, Cerci JJ, Dimamay MP, Gyorke T, Redondo F, Nair R, Gorospe C, Paez D, Fanti S, Ozdag H, Padua RA, Carr R. Identification of a Patient Cohort with Relapsing Diffuse Large B-Cell Lymphoma with a Low International Prognostic Index in PET/CT Using a 2-Gene (LMO2/TNFRSF9) Scoring System. Acta Haematol 2020; 143:600-602. [PMID: 32187599 DOI: 10.1159/000505605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/25/2019] [Indexed: 11/19/2022]
MESH Headings
- Adaptor Proteins, Signal Transducing/metabolism
- Adult
- Aged
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Cyclophosphamide/administration & dosage
- Doxorubicin/administration & dosage
- Female
- Humans
- LIM Domain Proteins/metabolism
- Lymphoma, Large B-Cell, Diffuse/diagnostic imaging
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/mortality
- Male
- Middle Aged
- Positron Emission Tomography Computed Tomography
- Prednisone/administration & dosage
- Proto-Oncogene Proteins/metabolism
- Rituximab/administration & dosage
- Tumor Necrosis Factor Receptor Superfamily, Member 9/metabolism
- Vincristine/administration & dosage
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Affiliation(s)
- Nader Omidvar
- Department of Haematology, Cardiff University School of Medicine, Cardiff, United Kingdom,
| | - Nilgun Tekin
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Paulette Conget
- Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Flavia Bruna
- Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Botond Timar
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Eva Gagyi
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ranjan Basak
- Department of Medical Oncology and Pathology, Tata Memorial Hospital, Mumbai, India
| | - Chirayu Auewarakul
- Chulabhorn Cancer Centre and Faculty of Medicine, Siriraj Hospital, Bangkok, Thailand
| | - Narongrit Sritana
- Chulabhorn Cancer Centre and Faculty of Medicine, Siriraj Hospital, Bangkok, Thailand
| | - Juliano Julio Cerci
- Department of Nuclear Medicine, Quanta - Diagnóstico e Terapia, Curitiba, Brazil
| | - Mark Pierre Dimamay
- Research and Biotechnology Division, St Luke's Medical Center, Manila, Philippines
| | - Tamas Gyorke
- Department of Nuclear Medicine, Semmelweis University, Budapest, Hungary
| | | | - Reena Nair
- Department of Medical Oncology and Pathology, Tata Memorial Hospital, Mumbai, India
| | - Charity Gorospe
- Research and Biotechnology Division, St Luke's Medical Center, Manila, Philippines
| | - Diana Paez
- Department of Nuclear Sciences and Application, International Atomic Energy Agency, Vienna, Austria
| | - Stefano Fanti
- Metropolitan Nuclear Medicine, Policlinico S. Orsola, University of Bologna, Bologna, Italy
| | - Hilal Ozdag
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | | | - Robert Carr
- Department of Haematology, Guy's and St. Thomas' Hospital, London, United Kingdom
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Tekin N, Omidvar N, Morris TP, Conget P, Bruna F, Timar B, Gagyi E, Basak R, Naik O, Auewarakul C, Sritana N, Levy D, Cerci JJ, Bydlowski SP, Pereira J, Dimamay MP, Natividad F, Chung JK, Belder N, Kuzu I, Paez D, Dondi M, Carr R, Ozdag H, Padua RA. Protocol for qRT-PCR analysis from formalin fixed paraffin embedded tissue sections from diffuse large b-cell lymphoma: Validation of the six-gene predictor score. Oncotarget 2016; 7:83319-83329. [PMID: 27825111 PMCID: PMC5347772 DOI: 10.18632/oncotarget.13066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 09/24/2016] [Indexed: 11/28/2022] Open
Abstract
As a part of an international study on the molecular analysis of Diffuse Large B-cell Lymphoma (DLBCL), a robust protocol for gene expression analysis from RNA extraction to qRT-PCR using Formalin Fixed Paraffin Embedded tissues was developed. Here a study was conducted to define a strategy to validate the previously reported 6-gene (LMO2, BCL6, FN1, CCND2, SCYA3 and BCL2) model as predictor of prognosis in DLBCL. To avoid variation, all samples were tested in a single centre and single platform. This study comprised 8 countries (Brazil, Chile, Hungary, India, Philippines, S. Korea, Thailand and Turkey). Using the Kaplan-Meier and log rank test on patients (n=162) and two mortality risk groups (with those above and below the mean representing high and low risk groups) confirmed that the 6-gene predictor score correlates significantly with overall survival (OS, p<0.01) but not with event free survival (EFS, p=0.18). Adding the International Prognostic Index (IPI) shows that the 6-gene predictor score correlates significantly with high IPI scores for OS (p<0.05), whereas those with low IPI scores show a trend not reaching significance (p=0.08). This study defined an effective and economical qRT-PCR strategy and validated the 6-gene score as a predictor of OS in an international setting.
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Affiliation(s)
- Nilgun Tekin
- Ankara University, Biotechnology Institute, Ankara, Turkey
| | - Nader Omidvar
- Department of Hematology, University of Cardiff School of Medicine, UK
| | - Tim Peter Morris
- Medical Research Council (MRC) Clinical Trials Unit at University College (UCL), London, UK
| | - Paulette Conget
- Facultad de Medicina Clínica Alemana - Universidad del Desarrollo Santiago, Chile
| | - Flavia Bruna
- Facultad de Medicina Clínica Alemana - Universidad del Desarrollo Santiago, Chile
| | - Botond Timar
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Eva Gagyi
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ranjan Basak
- Departments of Medical Oncology & Pathology, Tata Memorial Hospital, Mumbai, India
| | - Omkar Naik
- Departments of Medical Oncology & Pathology, Tata Memorial Hospital, Mumbai, India
| | - Chirayu Auewarakul
- Chulabhorn Cancer Centre and Faculty of Medicine Siriraj Hospital, Bangkok, Thailand
| | - Narongrit Sritana
- Chulabhorn Cancer Centre and Faculty of Medicine Siriraj Hospital, Bangkok, Thailand
| | - Debora Levy
- Laboratory of Genetics and Molecular Hematology (LIM31), University of São Paulo School of Medicine, São Paulo/SP, Brazil
| | - Juliano Julio Cerci
- Department of Nuclear Medicine, Quanta - Diagnóstico e Terapia, Curitiba, Brazil
| | - Sergio Paulo Bydlowski
- Laboratory of Genetics and Molecular Hematology (LIM31), University of São Paulo School of Medicine, São Paulo/SP, Brazil
| | - Juliana Pereira
- Laboratory of Genetics and Molecular Hematology (LIM31), University of São Paulo School of Medicine, São Paulo/SP, Brazil
| | - Mark Pierre Dimamay
- Research and Biotechnology Division, St Luke's Medical Centre, Manila, Philippines
| | - Filipinas Natividad
- Research and Biotechnology Division, St Luke's Medical Centre, Manila, Philippines
| | - June-Key Chung
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Nevin Belder
- Ankara University, Biotechnology Institute, Ankara, Turkey
| | - Isinsu Kuzu
- Department of Pathology, Ankara University School of Medicine, Ankara, Turkey
| | - Diana Paez
- Department of Nuclear Sciences and Application, Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - Maurizio Dondi
- Department of Nuclear Sciences and Application, Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - Robert Carr
- Department of Haematology, Guy's & St Thomas' Hospital, King's College, London, UK
| | - Hilal Ozdag
- Ankara University, Biotechnology Institute, Ankara, Turkey
| | - Rose Ann Padua
- Institut National de la Sante et de la Recherche Médicale (INSERM) Unité 1131, Université Paris-Diderot, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
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Carr R, Ozdag H, Tekin N, Morris T, Conget P, Bruna F, Timar B, Gagyi E, Basak R, Naik O, Auewarakul C, Srithana N, Dimamay MP, Natividad F, Chung JK, Belder N, Kuzu I, Omidvar N, Paez D, Padua RA. The effect of biological heterogeneity on R-CHOP treatment outcome in diffuse large B-cell lymphoma across five international regions. Leuk Lymphoma 2016; 58:1178-1183. [PMID: 27724056 DOI: 10.1080/10428194.2016.1231308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Addressing the global burden of cancer, understanding its diverse biology, and promoting appropriate prevention and treatment strategies around the world has become a priority for the United Nations and International Atomic Energy Agency (IAEA), the WHO, and International Agency for Research on Cancer (IARC). The IAEA sponsored an international prospective cohort study to better understand biology, treatment response, and outcomes of diffuse large B-cell lymphoma (DLBCL) in low and middle-income countries across five UN-defined geographical regions. We report an analysis of biological variation in DLBCL across seven ethnic and environmentally diverse populations. In this cohort of 136 patients treated to a common protocol, we demonstrate significant biological differences between countries, characterized by a validated prognostic gene expression score (p < .0001), but International Prognostic Index (IPI)-adjusted survivals in all participating countries were similar. We conclude that DLBCL treatment outcomes in these populations can be benchmarked to international standards, despite biological heterogeneity.
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Affiliation(s)
- Robert Carr
- a Department of Haematology , Guy's & St. Thomas' Hospital, King's College , London , UK
| | - Hilal Ozdag
- b Biotechnology Institute, Ankara University , Ankara , Turkey
| | - Nilgun Tekin
- b Biotechnology Institute, Ankara University , Ankara , Turkey
| | - Timothy Morris
- c Medical Research Council Clinical Trials Unit , University College London , London , UK
| | - Paulette Conget
- d Facultad de Medicina Clínica Alemana, Universidad del Desarrollo , Santiago , Chile
| | - Flavia Bruna
- d Facultad de Medicina Clínica Alemana, Universidad del Desarrollo , Santiago , Chile
| | - Botond Timar
- e 1st Department of Pathology and Experimental Cancer Research , Semmelweis University , Budapest , Hungary
| | - Eva Gagyi
- e 1st Department of Pathology and Experimental Cancer Research , Semmelweis University , Budapest , Hungary
| | - Ranjan Basak
- f Department of Medical Oncology and Pathology , Tata Memorial Hospital , Mumbai , India
| | - Omkar Naik
- f Department of Medical Oncology and Pathology , Tata Memorial Hospital , Mumbai , India
| | | | | | - Mark Pierre Dimamay
- h Research and Biology Division , St. Luke's Medical Centre , Manila , Philippines
| | - Filipinas Natividad
- h Research and Biology Division , St. Luke's Medical Centre , Manila , Philippines
| | - June-Key Chung
- i Oncology Clinic , Seoul National University Hospital , Seoul , Republic of Korea
| | - Nevin Belder
- b Biotechnology Institute, Ankara University , Ankara , Turkey
| | - Isinsu Kuzu
- j Department of Pathology , Ankara University , Ankara , Turkey
| | - Nader Omidvar
- k Department of Haematology , University of Cardiff , Cardiff , UK
| | - Diana Paez
- l Nuclear Medicine Section, International Atomic Energy Agency , Vienna , Austria
| | - Rose Ann Padua
- m INSERM 1131 , University Paris-Diderot, Hôpital Saint-Louis , Paris , France
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Sucularli C, Shehwana H, Kuscu C, Dungul DC, Ozdag H, Konu O. Functionally conserved effects of rapamycin exposure on zebrafish. Mol Med Rep 2016; 13:4421-30. [PMID: 27035657 DOI: 10.3892/mmr.2016.5059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/22/2016] [Indexed: 11/06/2022] Open
Abstract
Mechanistic target of rapamycin (mTOR) is a conserved serine/threonine kinase important in cell proliferation, growth and protein translation. Rapamycin, a well‑known anti‑cancer agent and immunosuppressant drug, inhibits mTOR activity in different taxa including zebrafish. In the present study, the effect of rapamycin exposure on the transcriptome of a zebrafish fibroblast cell line, ZF4, was investigated. Microarray analysis demonstrated that rapamycin treatment modulated a large set of genes with varying functions including protein synthesis, assembly of mitochondrial and proteasomal machinery, cell cycle, metabolism and oxidative phosphorylation in ZF4 cells. A mild however, coordinated reduction in the expression of proteasomal and mitochondrial ribosomal subunits was detected, while the expression of numerous ribosomal subunits increased. Meta‑analysis of heterogeneous mouse rapamycin microarray datasets enabled the comparison of zebrafish and mouse pathways modulated by rapamycin, using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology pathway analysis. The analyses demonstrated a high degree of functional conservation between zebrafish and mice in response to rapamycin. In addition, rapamycin treatment resulted in a marked dose‑dependent reduction in body size and pigmentation in zebrafish embryos. The present study is the first, to the best of our knowledge, to evaluate the conservation of rapamycin‑modulated functional pathways between zebrafish and mice, in addition to the dose‑dependent growth curves of zebrafish embryos upon rapamycin exposure.
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Affiliation(s)
- Ceren Sucularli
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Huma Shehwana
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | - Cem Kuscu
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
| | | | - Hilal Ozdag
- Biotechnology Institute, Ankara University, Ankara 06010, Turkey
| | - Ozlen Konu
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara 06800, Turkey
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Yildiz G, Arslan-Ergul A, Bagislar S, Konu O, Yuzugullu H, Gursoy-Yuzugullu O, Ozturk N, Ozen C, Ozdag H, Erdal E, Karademir S, Sagol O, Mizrak D, Bozkaya H, Ilk HG, Ilk O, Bilen B, Cetin-Atalay R, Akar N, Ozturk M. Genome-wide transcriptional reorganization associated with senescence-to-immortality switch during human hepatocellular carcinogenesis. PLoS One 2013; 8:e64016. [PMID: 23691139 PMCID: PMC3655073 DOI: 10.1371/journal.pone.0064016] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/07/2013] [Indexed: 01/11/2023] Open
Abstract
Senescence is a permanent proliferation arrest in response to cell stress such as DNA damage. It contributes strongly to tissue aging and serves as a major barrier against tumor development. Most tumor cells are believed to bypass the senescence barrier (become “immortal”) by inactivating growth control genes such as TP53 and CDKN2A. They also reactivate telomerase reverse transcriptase. Senescence-to-immortality transition is accompanied by major phenotypic and biochemical changes mediated by genome-wide transcriptional modifications. This appears to happen during hepatocellular carcinoma (HCC) development in patients with liver cirrhosis, however, the accompanying transcriptional changes are virtually unknown. We investigated genome-wide transcriptional changes related to the senescence-to-immortality switch during hepatocellular carcinogenesis. Initially, we performed transcriptome analysis of senescent and immortal clones of Huh7 HCC cell line, and identified genes with significant differential expression to establish a senescence-related gene list. Through the analysis of senescence-related gene expression in different liver tissues we showed that cirrhosis and HCC display expression patterns compatible with senescent and immortal phenotypes, respectively; dysplasia being a transitional state. Gene set enrichment analysis revealed that cirrhosis/senescence-associated genes were preferentially expressed in non-tumor tissues, less malignant tumors, and differentiated or senescent cells. In contrast, HCC/immortality genes were up-regulated in tumor tissues, or more malignant tumors and progenitor cells. In HCC tumors and immortal cells genes involved in DNA repair, cell cycle, telomere extension and branched chain amino acid metabolism were up-regulated, whereas genes involved in cell signaling, as well as in drug, lipid, retinoid and glycolytic metabolism were down-regulated. Based on these distinctive gene expression features we developed a 15-gene hepatocellular immortality signature test that discriminated HCC from cirrhosis with high accuracy. Our findings demonstrate that senescence bypass plays a central role in hepatocellular carcinogenesis engendering systematic changes in the transcription of genes regulating DNA repair, proliferation, differentiation and metabolism.
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Affiliation(s)
- Gokhan Yildiz
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
- INSERM - Université Joseph Fourrier, CRI U823, Grenoble, France
| | - Ayca Arslan-Ergul
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Sevgi Bagislar
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
- INSERM - Université Joseph Fourrier, CRI U823, Grenoble, France
| | - Ozlen Konu
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Haluk Yuzugullu
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
- INSERM - Université Joseph Fourrier, CRI U823, Grenoble, France
| | - Ozge Gursoy-Yuzugullu
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
- INSERM - Université Joseph Fourrier, CRI U823, Grenoble, France
| | - Nuri Ozturk
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Cigdem Ozen
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Hilal Ozdag
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Esra Erdal
- Department of Medical Biology, Dokuz Eylul University Medical School, Izmir, Turkey
| | - Sedat Karademir
- Department of Surgery, Dokuz Eylul University Medical School, Izmir, Turkey
| | - Ozgul Sagol
- Department of Pathology, Dokuz Eylul University Medical School, Izmir, Turkey
| | - Dilsa Mizrak
- Department of Gastroenterology, Ankara University, Ankara, Turkey
| | - Hakan Bozkaya
- Department of Gastroenterology, Ankara University, Ankara, Turkey
| | - Hakki Gokhan Ilk
- Department of Electronic Engineering, Ankara University, Ankara, Turkey
| | - Ozlem Ilk
- Department of Statistics, Middle East Technical University, Ankara, Turkey
| | - Biter Bilen
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Rengul Cetin-Atalay
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Nejat Akar
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Mehmet Ozturk
- BilGen Genetics and Biotechnology Center, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
- INSERM - Université Joseph Fourrier, CRI U823, Grenoble, France
- * E-mail:
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Ilk O, Rajabli F, Dungul DC, Ozdag H, Ilk HG. A novel approach for small sample size family-based association studies: sequential tests. Eur J Hum Genet 2011; 19:915-20. [PMID: 21427757 PMCID: PMC3172932 DOI: 10.1038/ejhg.2011.51] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 02/15/2011] [Accepted: 02/25/2011] [Indexed: 02/08/2023] Open
Abstract
In this paper, we propose a sequential probability ratio test (SPRT) to overcome the problem of limited samples in studies related to complex genetic diseases. The results of this novel approach are compared with the ones obtained from the traditional transmission disequilibrium test (TDT) on simulated data. Although TDT classifies single-nucleotide polymorphisms (SNPs) to only two groups (SNPs associated with the disease and the others), SPRT has the flexibility of assigning SNPs to a third group, that is, those for which we do not have enough evidence and should keep sampling. It is shown that SPRT results in smaller ratios of false positives and negatives, as well as better accuracy and sensitivity values for classifying SNPs when compared with TDT. By using SPRT, data with small sample size become usable for an accurate association analysis.
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Affiliation(s)
- Ozlem Ilk
- Department of Statistics, Faculty of Arts and Sciences, Middle East Technical University, Ankara, Turkey.
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Mesci L, Ozdag H, Yel L, Ozgur TT, Tan C, Sanal Ö. H2AX gene does not have a modifier effect on ataxia-telangiectasia phenotype. Int J Immunogenet 2011; 38:209-13. [DOI: 10.1111/j.1744-313x.2010.00989.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Duman D, Sirmaci A, Cengiz FB, Ozdag H, Tekin M. Screening of 38 genes identifies mutations in 62% of families with nonsyndromic deafness in Turkey. Genet Test Mol Biomarkers 2010; 15:29-33. [PMID: 21117948 DOI: 10.1089/gtmb.2010.0120] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
More than 60% of prelingual deafness is genetic in origin, and of these up to 95% are monogenic autosomal recessive traits. Causal mutations have been identified in 1 of 38 different genes in a subset of patients with nonsyndromic autosomal recessive deafness. In this study, we screened 49 unrelated Turkish families with at least three affected children born to consanguineous parents. Probands from all families were negative for mutations in the GJB2 gene, two large deletions in the GJB6 gene, and the 1555A>G substitution in the mitochondrial DNA MTRNR1 gene. Each family was subsequently screened via autozygosity mapping with genomewide single-nucleotide polymorphism arrays. If the phenotype cosegregated with a haplotype flanking one of the 38 genes, mutation analysis of the gene was performed. We identified 22 different autozygous mutations in 11 genes, other than GJB2, in 26 of 49 families, which overall explains deafness in 62% of families. Relative frequencies of genes following GJB2 were MYO15A (9.9%), TMIE (6.6%), TMC1 (6.6%), OTOF (5.0%), CDH23 (3.3%), MYO7A (3.3%), SLC26A4 (1.7%), PCDH15 (1.7%), LRTOMT (1.7%), SERPINB6 (1.7%), and TMPRSS3 (1.7%). Nineteen of 22 mutations are reported for the first time in this study. Unknown rare genes for deafness appear to be present in the remaining 23 families.
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Affiliation(s)
- Duygu Duman
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Dikimevi, Ankara, Turkey
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Uz E, Alanay Y, Aktas D, Vargel I, Gucer S, Tuncbilek G, von Eggeling F, Yilmaz E, Deren O, Posorski N, Ozdag H, Liehr T, Balci S, Alikasifoglu M, Wollnik B, Akarsu NA. Disruption of ALX1 causes extreme microphthalmia and severe facial clefting: expanding the spectrum of autosomal-recessive ALX-related frontonasal dysplasia. Am J Hum Genet 2010; 86:789-96. [PMID: 20451171 DOI: 10.1016/j.ajhg.2010.04.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/05/2010] [Accepted: 04/09/2010] [Indexed: 01/01/2023] Open
Abstract
We present an autosomal-recessive frontonasal dysplasia (FND) characterized by bilateral extreme microphthalmia, bilateral oblique facial cleft, complete cleft palate, hypertelorism, wide nasal bridge with hypoplasia of the ala nasi, and low-set, posteriorly rotated ears in two distinct families. Using Affymetrix 250K SNP array genotyping and homozygosity mapping, we mapped this clinical entity to chromosome 12q21. In one of the families, three siblings were affected, and CNV analysis of the critical region showed a homozygous 3.7 Mb deletion containing the ALX1 (CART1) gene, which encodes the aristaless-like homeobox 1 transcription factor. In the second family we identified a homozygous donor-splice-site mutation (c.531+1G > A) in the ALX1 gene, providing evidence that complete loss of function of ALX1 protein causes severe disruption of early craniofacial development. Unlike loss of its murine ortholog, loss of human ALX1 does not result in neural-tube defects; however, it does severely affect the orchestrated fusion between frontonasal, nasomedial, nasolateral, and maxillary processes during early-stage embryogenesis. This study further expands the spectrum of the recently recognized autosomal-recessive ALX-related FND phenotype in humans.
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Affiliation(s)
- Elif Uz
- Gene Mapping Laboratory, Department of Medical Genetics, Hacettepe University Medical Faculty, Sihhiye, Ankara, Turkey
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13
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Orbey B, Cuhruk H, Tulunay M, Oral M, Unal N, Ozdag H. Can plasma-free DNA concentration be a diagnostic tool in critically ill septic patients? Crit Care 2007. [PMCID: PMC4095102 DOI: 10.1186/cc5208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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14
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Mesci L, Ozdag H, Turul T, Ersoy F, Tezcan I, Sanal O. A novel mutation leading to a deletion in the SH3 domain of Bruton's tyrosine kinase. Turk J Pediatr 2006; 48:362-4. [PMID: 17290574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
X-linked agammaglobulinemia (XLA) is a primary B cell immunodeficiency disorder, caused by a defect in the Bruton tyrosine kinase (BTK) gene. Here, we describe a novel four base pair mutation (838delGAGT) in intron 9 of the BTK gene leading to the skipping of exon 9 in a 2.5-year-old boy with this disorder.
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Affiliation(s)
- Lütfiye Mesci
- Immunology Unit, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
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15
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Ozdag H, Egin Y, Akar N. Prothrombin gene 20209 C >T along with the first description of a homozygous polymorphism at the 3' downstream region +4 C >T in the Turkish population. Lab Hematol 2006; 12:131-3. [PMID: 16950672 DOI: 10.1532/lh96.06013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mutation screening studies related with thrombosis revealed that prothrombin 20210A allele of the prothrombin gene leads to an increase in plasma prothrombin levels. The G20210A mutation screening has become a routine analysis in patients with thrombosis. For the detection of the mutation, several molecular techniques have been defined. Real-time polymerase chain reaction is an easy and feasible way to monitor this mutation according to the melting point analysis. Here we report a different pattern in the LightCycler melting point analysis of 2 patients with thrombosis. DNA sequencing of the prothrombin gene showed that these patients with an atypical melting point profile carry a 20209 C >T mutation along with a novel homozygous polymorphism at the 3' downstream region, +4 C >T.
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Affiliation(s)
- Hilal Ozdag
- Department of Ankara University, Pediatric Molecular Genetics, Cayyolu 06810, Ankara, Turkey
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16
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Garcia MJ, Pole JCM, Chin SF, Teschendorff A, Naderi A, Ozdag H, Vias M, Kranjac T, Subkhankulova T, Paish C, Ellis I, Brenton JD, Edwards PAW, Caldas C. A 1 Mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes. Oncogene 2005; 24:5235-45. [PMID: 15897872 DOI: 10.1038/sj.onc.1208741] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amplification of 8p11-12 is a well-known alteration in human breast cancers but the driving oncogene has not been identified. We have developed a high-resolution comparative genomic hybridization array covering 8p11-12 and analysed 33 primary breast tumors, 20 primary ovarian tumors and 27 breast cancer cell lines. Expression analysis of the genes in the region was carried out by using real-time quantitative PCR and/or oligo-microarray profiling. In all, 24% (8/33) of the breast tumors, 5% (1/20) of the ovary tumors and 15% (4/27) of the cell lines showed 8p11-12 amplification. We identified a 1 Mb segment of common amplification that excludes previously proposed candidate genes. Some of the amplified genes did not show overexpression, whereas for others, overexpression was not specifically attributable to amplification. The genes FLJ14299, C8orf2, BRF2 and RAB11FIP, map within the 8p11-12 minimal amplicon, two have a putative function consistent with an oncogenic role, these four genes showed a strong correlation between amplification and overexpression and are therefore the best candidate driver oncogenes at 8p12.
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Affiliation(s)
- Maria J Garcia
- Department of Oncology, Hutchison/MRC Research Centre, Cancer Genomics Program, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK
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17
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Grigorova M, Staines JM, Ozdag H, Caldas C, Edwards PAW. Possible causes of chromosome instability: comparison of chromosomal abnormalities in cancer cell lines with mutations in BRCA1, BRCA2, CHK2 and BUB1. Cytogenet Genome Res 2004; 104:333-40. [PMID: 15162061 DOI: 10.1159/000077512] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2004] [Accepted: 02/02/2004] [Indexed: 11/19/2022] Open
Abstract
A large proportion of epithelial cancers show the chromosome-instability phenotype, in which they have many chromosome abnormalities. This is thought to be the result of mutations that disrupt chromosome maintenance, but the causative mutations are not known. We identified cell lines known to have mutations that might cause chromosome instability, and examined their karyotypes. Two cell lines, the breast cancer line HCC1937 and the pancreatic cancer line CAPAN-1, that have mutations respectively in BRCA1 and BRCA2, had very abnormal karyotypes, with many structural and numerical chromosome changes and substantial variation between metaphases. However, two colorectal cancer lines with mutations in BUB1, a spindle checkpoint protein involved in chromosome segregation, had rather simple near-tetraploid karyotypes, with minimal loss or gain of chromosomes other than the endoreduplication event, and minimal structural change. Apart from tetraploidy, these karyotypes were typical of colorectal lines considered to be chromosomally stable. Two lines derived from the same tumour, DLD-1 and HCT-15, with bi-allelic mutation of CHK2, had karyotypes that were typical of near-diploid colorectal lines considered chromosomally stable. The karyotypes observed supported the proposed role for BRCA1 and BRCA2 mutations in chromosomal instability, but showed that the tested mutations in BUB1 and CHK2 did not result in karyotypes that would have been predicted if they were sufficient for chromosomal instability.
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Affiliation(s)
- M Grigorova
- Cancer Genomics Program, Department of Pathology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK
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18
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Abstract
p300 and cyclic AMP response element-binding protein (CBP) are adenoviral E1A-binding proteins involved in multiple cellular processes, and function as transcriptional co-factors and histone acetyltransferases. Germline mutation of CBP results in Rubinstein-Taybi syndrome, which is characterized by an increased predisposition to childhood malignancies. Furthermore, somatic mutations of p300 and CBP occur in a number of malignancies. Chromosome translocations target CBP and, less commonly, p300 in acute myeloid leukemia and treatment-related hematological disorders. p300 mutations in solid tumors result in truncated p300 protein products or amino-acid substitutions in critical protein domains, and these are often associated with inactivation of the second allele. A mouse model confirms that p300 and CBP function as suppressors of hematological tumor formation. The involvement of these proteins in critical tumorigenic pathways (including TGF-beta, p53 and Rb) provides a mechanistic route as to how their inactivation could result in cancer.
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Affiliation(s)
- Narayanan Gopalakrishna Iyer
- Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge CB2 2XZ, UK
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19
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Iyer NG, Chin SF, Ozdag H, Daigo Y, Hu DE, Cariati M, Brindle K, Aparicio S, Caldas C. p300 regulates p53-dependent apoptosis after DNA damage in colorectal cancer cells by modulation of PUMA/p21 levels. Proc Natl Acad Sci U S A 2004; 101:7386-91. [PMID: 15123817 PMCID: PMC409928 DOI: 10.1073/pnas.0401002101] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Activation of the tumor suppressor p53 by DNA damage induces either cell cycle arrest or apoptosis, but what determines the choice between cytostasis and death is not clear. In this report, we show that the E1A-binding p300 nucleoprotein is a key determinant of p53-dependent cell fate in colorectal cancer cells: absence of p300 increases apoptosis in response to DNA damage. In addition, p300-deficient (p300(-)) cells fail to undergo G(1)/S arrest after UV irradiation. These abnormalities are associated with prolongation of p53 stability, reduced p53-acetylation, blunting of MDM2 activation, failure to transactivate p21, and a disproportionate increase in PUMA levels. When xenografted, p300(-) cells are more sensitive to chemotherapy with doxorubicin. These results show that p300 is a key regulator of the p53 response and suggest that p300 inhibition could be used to modulate chemotherapy.
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Affiliation(s)
- N Gopalakrishna Iyer
- Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
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20
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Hughes-Davies L, Huntsman D, Ruas M, Fuks F, Bye J, Chin SF, Milner J, Brown LA, Hsu F, Gilks B, Nielsen T, Schulzer M, Chia S, Ragaz J, Cahn A, Linger L, Ozdag H, Cattaneo E, Jordanova ES, Schuuring E, Yu DS, Venkitaraman A, Ponder B, Doherty A, Aparicio S, Bentley D, Theillet C, Ponting CP, Caldas C, Kouzarides T. EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer. Cell 2004; 115:523-35. [PMID: 14651845 DOI: 10.1016/s0092-8674(03)00930-9] [Citation(s) in RCA: 346] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The BRCA2 gene is mutated in familial breast and ovarian cancer, and its product is implicated in DNA repair and transcriptional regulation. Here we identify a protein, EMSY, which binds BRCA2 within a region (exon 3) deleted in cancer. EMSY is capable of silencing the activation potential of BRCA2 exon 3, associates with chromatin regulators HP1beta and BS69, and localizes to sites of repair following DNA damage. EMSY maps to chromosome 11q13.5, a region known to be involved in breast and ovarian cancer. We show that the EMSY gene is amplified almost exclusively in sporadic breast cancer (13%) and higher-grade ovarian cancer (17%). In addition, EMSY amplification is associated with worse survival, particularly in node-negative breast cancer, suggesting that it may be of prognostic value. The remarkable clinical overlap between sporadic EMSY amplification and familial BRCA2 deletion implicates a BRCA2 pathway in sporadic breast and ovarian cancer.
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Affiliation(s)
- Luke Hughes-Davies
- Cancer Research UK/Wellcome Trust Institute and Department of Pathology, Tennis Court Road, Cambridge CB2 1QR, United Kingdom.
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21
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Ozdag H, Tez M, Sayek I, Müslümanoglu M, Tarcan O, Içli F, Oztürk M, Ozçelik T. Germ line BRCA1 and BRCA2 gene mutations in Turkish breast cancer patients. Eur J Cancer 2000; 36:2076-82. [PMID: 11044644 DOI: 10.1016/s0959-8049(00)00277-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Germ line BRCA1 and/or BRCA2 mutations were screened in 50 Turkish breast and/or ovarian cancer patients composed of hereditary, familial, early onset and male cancer groups. Genomic DNA samples were tested by heteroduplex analysis and DNA sequencing. Two truncating BRCA2 mutations, one novel (6880 insG) and one previously reported (3034 delAAAC), were found in two out of six (33%) hereditary breast and/or ovarian cancer patients. A novel truncating (1200 insA) and a missense (2080A-->G) BRCA1 mutation was found in two of 27 (7%) individuals in the early onset group. A total of four (8%) disease-causing mutations in 50 breast cancer patients were identified in BRCA1 and BRCA2 genes. In addition, five BRCA1 sequence variants have been identified in 23 patients. These results indicate that BRCA1 and BRCA2 genes are involved in some, but not all, forms of hereditary predisposition to breast cancer in the Turkish population.
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Affiliation(s)
- H Ozdag
- Department of Molecular Biology and Genetics, Bilkent University, 06533, Ankara, Turkey
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