Person: DOĞAN, BERKCAN
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DOĞAN
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BERKCAN
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Publication Hsa-miR-584-5p as a novel candidate biomarker in Turkish men with severe coronary artery disease(Springer, 2019-12-21) Çoban, Neslihan; Pirim, Dilek; Erkan, Ayçan Fahri; Doğan, Berkcan; Ekici, Berkay; PİRİM, DİLEK; DOĞAN, BERKCAN; Tıp Fakültesi; Tıbbi Genetik Ana Bilim Dalı; 0000-0002-0522-9432; 0000-0001-8061-8131; HTP-6233-2023; AAD-5249-2020; ABA-4957-2020Coronary artery disease (CAD) is still the preliminary cause of mortality and morbidity in the developed world. Identification of novel predictive and therapeutic biomarkers is crucial for accurate diagnosis, prognosis and treatment of the CAD. The aim of this study was to detect novel candidate miRNA biomarker that may be used in the management of CAD. We performed miRNA profiling in whole blood samples of angiographically confirmed Turkish men with CAD and non-CAD controls with insignificant coronary stenosis. Validation of microarray results was performed by qRT-PCR in a larger cohort of 62 samples. We subsequently assessed the diagnostic value of the miRNA and correlations of miRNA with clinical parameters. miRNA-target identification and network analyses were conducted by Ingenuity Pathway Analysis (IPA) software. Hsa-miR-584-5p was one of the top significantly dysregulated miRNA observed in miRNA microarray. Men-specific down-regulation (p = 0.040) of hsa-miR-584-5p was confirmed by qRT-PCR. ROC curve analysis highlighted the potential diagnostic value of hsa-miR-584-5p with a power area under the curve (AUC) of 0.714 and 0.643 in men and in total sample, respectively. The expression levels of hsa-miR-584-5p showed inverse correlation with stenosis and Gensini scores. IPA revealed CDH13 as the only CAD related predicted target for the miRNA with biological evidence of its involvement in CAD. This study suggests that hsa-miR-584-5p, known to be tumor suppressor miRNA, as a candidate biomarker for CAD and highlighted its putative role in the CAD pathogenesis. The validation of results in larger samples incorporating functional studies warrant further research.Publication BRCA variations risk assessment in breast cancers using different artificial intelligence models(Mdpi, 2021-11-08) Şentürk, Niyazi; Tuncel, Gülten; Doğan, Berkcan; Aliyeva, Lamiya; Dündar, Mehmet Sait; Özemri Sağ, Şebnem; Mocan, Gamze; Temel, Şehime Gülsün; Dündar, Munis; Ergoren, Mahmut Çerkez; DOĞAN, BERKCAN; ALIYEVA, LAMIYA; ÖZEMRİ SAĞ, ŞEBNEM; TEMEL, ŞEHİME GÜLSÜN; Tıp Fakültesi; Histoloji ve Embriyoloji Ana Bilim Dalı; 0000-0001-8061-8131; CCG-4609-2022 ; AAH-8355-2021 ; AAD-5249-2020; AAG-8385-2021Artificial intelligence provides modelling on machines by simulating the human brain using learning and decision-making abilities. Early diagnosis is highly effective in reducing mortality in cancer. This study aimed to combine cancer-associated risk factors including genetic variations and design an artificial intelligence system for risk assessment. Data from a total of 268 breast cancer patients have been analysed for 16 different risk factors including genetic variant classifications. In total, 61 BRCA1, 128 BRCA2 and 11 both BRCA1 and BRCA2 genes associated breast cancer patients' data were used to train the system using Mamdani's Fuzzy Inference Method and Feed-Forward Neural Network Method as the model softwares on MATLAB. Sixteen different tests were performed on twelve different subjects who had not been introduced to the system before. The rates for neural network were 99.9% for training success, 99.6% for validation success and 99.7% for test success. Despite neural network's overall success was slightly higher than fuzzy logic accuracy, the results from developed systems were similar (99.9% and 95.5%, respectively). The developed models make predictions from a wider perspective using more risk factors including genetic variation data compared with similar studies in the literature. Overall, this artificial intelligence models present promising results for BRCA variations' risk assessment in breast cancers as well as a unique tool for personalized medicine software.Publication Investigation of putative roles of smoking-associated salivary microbiome alterations on carcinogenesis by integrative in silico analysis(Elsevier Sci Ltd, 2022-12-30) DOĞAN, BERKCAN; Pirim, Dilek; PİRİM, DİLEK; Ayar, Berna; Sağlık Bilimleri Enstitüsü Fakültesi; Moleküler Biyoloji ve Genetik Ana Bilim Dalı; 0000-0001-8061-8131; HTP-6233-2023; AAD-5249-2020Growing evidence suggests that cigarette smoking alters the salivary microbiome composition and affects the risk of various complex diseases including cancer. However, the potential role of the smoking-associated microbiome in cancer development remains unexplained. Here, the putative roles of smoking-related microbiome alterations in carcinogenesis were investigated by in silico analysis and suggested evidence can be further explored by experimental methodologies. The Disbiome database was used to extract smoking-associated microbial taxa in saliva and taxon set enrichment analysis (TSEA) was conducted to identify the gene sets associated with extracted microbial taxa. We further analyzed the expression profiles of identified genes by using RNA-sequencing data from TCGA and GTEx projects. Associations of the genes with smoking-related phenotypes in cancer datasets were analyzed to prioritize genes for their interplay between smoking-related microbiome and carcinogenesis. Thirty-eight microbial taxa associated with smoking were included in the TSEA and this revealed sixteen genes that were significantly associated with smoking-associated microbial taxa. All genes were found to be differentially expressed in at least one cancer dataset, yet the ELF3 and CTSH were the most common differentially expressed genes giving significant results for several cancer types. Moreover, C2CD3, CTSH, DSC3, ELF3, RHOT2, and WSB2 showed statistically significant associations with smoking-related phenotypes in cancer datasets. This study provides in silico evidence for the potential roles of the salivary microbiome on carcino-genesis. The results shed light on the importance of smoking cessation strategies for cancer management and interventions to stratify smokers for their risk of smoking-induced carcinogenesis.Publication Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium(Springer Heidelberg, 2022-01-31) Dundar, Munis; Fahrioglu, Umut; Yildiz, Saliha Handan; Bakir-Gungor, Burcu; Temel, Sehime Gulsun; Akin, Haluk; Artan, Sevilhan; Cora, Tulin; Sahin, Feride Iffet; Dursun, Ahmet; Sezer, Ozlem; Gurkan, Hakan; Erdogan, Murat; Gunduz, C. Nur Semerci; Bisgin, Atil; Ozdemir, Ozturk; Ulgenalp, Ayfer; Percin, E. Ferda; Yildirim, Malik Ejder; Tekes, Selahaddin; Bagis, Haydar; Yuce, Huseyin; Duman, Nilgun; Bozkurt, Gokay; Yararbas, Kanay; Yildirim, Mahmut Selman; Arman, Ahmet; Mihci, Ercan; Eraslan, Serpil; Altintas, Zuhal Mert; Aymelek, Huri Sema; Ruhi, Hatice Ilgin; Tatar, Abdulgani; Ergoren, Mahmut Cerkez; Cetin, G. Ozan; Altunoglu, Umut; Caglayan, Ahmet Okay; Yuksel, Berrin; Ozkul, Yusuf; Saatci, Cetin; Kenanoglu, Sercan; Karasu, Nilgun; Dundar, Bilge; Ozcelik, Firat; Demir, Mikail; Siniksaran, Betul Seyhan; Kulak, Hande; Kiranatlioglu, Kubra; Baysal, Kubra; Kazimli, Ulviyya; Akalin, Hilal; Dundar, Ayca; Boz, Mehmet; Bayram, Arslan; Subasioglu, Asli; Colak, Fatma Kurt; Karaduman, Neslihan; Gunes, Meltem Cerrah; Kandemir, Nefise; Aynekin, Busra; Emekli, Rabia; Sahin, Izem Olcay; Ozdemir, Sevda Yesim; Onal, Muge Gulcihan; Senel, Abdurrahman Soner; Poyrazoglu, Muammer Hakan; Kisaarslan, Ayse Nur Pac; Gursoy, Sebnem; Baskol, Mevlut; Calis, Mustafa; Demir, Huseyin; Zararsiz, Gozde Erturk; Erdogan, Mujgan Ozdemir; Elmas, Muhsin; Solak, Mustafa; Ulu, Memnune Sena; Thahir, Adam; Aydin, Zafer; Atasever, Umut; Sag, Sebnem Ozemri; Aliyeva, Lamiya; Alemdar, Adem; Dogan, Berkcan; Erguzeloglu, Cemre Ornek; Kaya, Niyazi; Ozkinay, Ferda; Cogulu, Ozgur; Durmaz, Asude; Onay, Huseyin; Karaca, Emin; Durmaz, Burak; Aykut, Ayca; Cilingir, Oguz; Aras, Beyhan Durak; Gokalp, Ebru Erzurumluoglu; Arslan, Serap; Temena, Arda; Haziyeva, Konul; Kocagil, Sinem; Bas, Hasan; Susam, Ezgi; Keklikci, Ali Riza; Sarac, Elif; Kocak, Nadir; Nergiz, Suleyman; Terzi, Yunus Kasim; Dincer, Selin Akad; Baskin, Esra Sidika; Genc, Gunes Cakmak; Bahadir, Oguzhan; Sanri, Aslihan; Yigit, Serbulent; Tozkir, Hilmi; Yalcintepe, Sinem; Ozkayin, Nese; Kiraz, Aslihan; Balta, Burhan; Gonen, Gizem Akinci; Kurt, E. Emre; Ceylan, Gulay Gulec; Ceylan, Ahmet Cevdet; Erten, Sukran; Bozdogan, Sevcan Tug; Boga, Ibrahim; Yilmaz, Mustafa; Silan, Fatma; Kocabey, Mehmet; Koc, Altug; Cankaya, Tufan; Bora, Elcin; Bozkaya, Ozlem Giray; Ercal, Derya; Ergun, Mehmet Ali; Ergun, Sezen Guntekin; Duman, Yesim Sidar; Beyazit, Serife Busra; Uzel, Veysiye Hulya; Em, Serda; Cevik, Muhammer Ozgur; Eroz, Recep; Demirtas, Mercan; Firat, Cem Koray; Kabayegit, Zehra Manav; Altan, Mustafa; Mardan, Lamiya; Sayar, Ceyhan; Tumer, Sait; Turkgenc, Burcu; Karakoyun, Hilal Keskin; Tunc, Betul; Kuru, Seda; Zamani, Aysegul; Geckinli, Bilgen Bilge; Ates, Esra Arslan; Clark, Ozden Altiok; Toylu, Asli; Coskun, Mert; Nur, Banu; Bilge, Ilmay; Bayramicli, Oya Uygur; Emmungil, Hakan; Komesli, Zeynep; Zeybel, Mujdat; Gurakan, Figen; Tasdemir, Mehmet; Kebudi, Rejin; Karabulut, Halil Gurhan; Tuncali, Timur; Kutlay, Nuket Yurur; Kahraman, Cigdem Yuce; Onder, Nerin Bahceciler; Beyitler, Ilke; Kavukcu, Salih; Tulay, Pinar; Tosun, Ozgur; Tuncel, Gulten; Mocan, Gamze; Kale, Hamdi; Uyguner, Zehra Oya; Acar, Aynur; Altinay, Mert; Erdem, Levent; TEMEL, ŞEHİME GÜLSÜN; ÖZEMRİ SAĞ, ŞEBNEM; ALIYEVA, LAMIYA; ALEMDAR, ADEM; DOĞAN, BERKCAN; Ergüzeloğlu, Cemre Örnek; Kaya, Niyazi; Sağlık Bilimleri Enstitüsü; Tıbbi Genetik Ana Bilim Dalı; 0000-0001-8061-8131; AAG-8385-2021; AAH-8355-2021; CCG-4609-2022; HIZ-7332-2022; AAD-5249-2020; EXQ-7887-2022; FEL-0562-2022Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever, abdominal pain, serositis, articular manifestations, erysipelas-like erythema, and renal complications as its main features. Caused by the mutations in the MEditerranean FeVer (MEFV) gene, it mainly affects people of Mediterranean descent with a higher incidence in the Turkish, Jewish, Arabic, and Armenian populations. As our understanding of FMF improves, it becomes clearer that we are facing with a more complex picture of FMF with respect to its pathogenesis, penetrance, variant type (gain-of-function vs. loss-of-function), and inheritance. In this study, MEFV gene analysis results and clinical findings of 27,504 patients from 35 universities and institutions in Turkey and Northern Cyprus are combined in an effort to provide a better insight into the genotype-phenotype correlation and how a specific variant contributes to certain clinical findings in FMF patients. Our results may help better understand this complex disease and how the genotype may sometimes contribute to phenotype. Unlike many studies in the literature, our study investigated a broader symptomatic spectrum and the relationship between the genotype and phenotype data. In this sense, we aimed to guide all clinicians and academicians who work in this field to better establish a comprehensive data set for the patients. One of the biggest messages of our study is that lack of uniformity in some clinical and demographic data of participants may become an obstacle in approaching FMF patients and understanding this complex disease.Publication Different perspectives on translational genomics in personalized medicine(Galenos Publ House, 2022-12-01) Çelik, Hale Göksever; Küçükkaya, Reyhan Diz; Acar, Ece Gümüşoğlu; Günel, Tuba; Doğan, Berkcan; DOĞAN, BERKCAN; Tıp Fakültesi; Tıbbi Genetik Ana Bilim Dalı; 0000-0001-8061-8131; 0000-0002-5162-3262; 0000-0001-5814-7118; 0000-0003-3807-0330; A-8941-2018; AAD-5249-2020Personalized medicine is a relatively new and interesting concept in the medical and healthcare industries. New approaches in current research have supported the search for biomarkers, based on the genomic, epigenomic and proteomic profile of individuals, using new technological tools. This perspective involves the potential to determine optimal medical interventions and provide the optimal benefit-risk balance for treatment, whilst it also takes a patient's personal situation into consideration. Translational genomics, a subfield of personalized medicine, is changing medical practice, by facilitating clinical or non-clinical screening tests, informing diagnoses and therapeutics, and routinely offering personalized health-risk assessments and personalized treatments. Further research into translational genomics will play a critical role in creating a new approach to cancer, pharmacogenomics, and women's health. Our current knowledge may be used to develop new solutions that can be used to minimize, improve, manage, and delay the symptoms of diseases in real-time and maintain a healthy lifestyle. In this review, we define and discuss the current status of translational genomics in some special areas including integration into research and health care.Publication A multicenter study of genotype variation/demographic patterns in 2475 individuals including 1444 cases with breast cancer in Turkey(Galenos Yayınevi, 2023-07-01) Boğa, İbrahim; Sağ, Şebnem Özemri; Duman, Nilgün; Özdemir, Sevda Yeşim; Ergören, Mahmut Çerkez; Dalcı, Kubilay; Mujde, Cem; Parsak, Cem Kaan; Rencuzoğullari, Çağla; Sönmezler, Özge; Yalav, Orçun; Alemdar, Adem; Aliyeva, Lamiya; Bozkurt, Özlem; Çetintaş, Sibel; Çubukcu, Erdem; Deligönül, Adem; Doğan, Berkcan; Ergüzeloğlu, Cemre Örnek; Evrensel, Türkkan; Gökgöz, Şehsuvar; Şenol, Kazım; Tolunay, Şahsine; Akyürek, Esra; Başgöz, Neslihan; Gökçe, Nuriye; Dündar, Bilge; Öztürk, Figen; Taşkın, Duygu; Demirtaş, Mercan; Çağ, Murat; Diker, Ömer; Olgun, Polat; Bozdoğan, Sevcan Tuğ; Dündar, Munis; Bişgin, Atıl; Temel, Şehime Gülsün; ÖZEMRİ SAĞ, ŞEBNEM; ALIYEVA, LAMIYA; DOĞAN, BERKCAN; TEMEL, ŞEHİME GÜLSÜN; ALEMDAR, ADEM; Ergüzeloğlu, Cemre Örnek; EVRENSEL, TÜRKKAN; BOZKURT, ÖZLEM; TOLUNAY, ŞAHSİNE; ÇETİNTAŞ, SİBEL; ÇUBUKÇU, ERDEM; DELİGÖNÜL, ADEM; GÖKGÖZ, MUSTAFA ŞEHSUVAR; ŞENOL, KAZIM; Tıp Fakültesi; Tıbbi Onkoloji Ana Bilim Dalı; 0000-0001-8061-8131 ; IYV-1877-2023; CCG-4609-2022; AAD-5249-2020; IRT-7350-2023; HIZ-7332-2022; EXQ-7887-2022; EXZ-0745-2022; IJL-9778-2023; AAI-1612-2021; EOI-5652-2022; ETP-1691-2022; ESM-4544-2022; EXK-4525-2022; KGQ-4411-2024; GZC-2526-2022Objective: Breast cancer (BC) is the most common cancer type in women and may be inherited, mostly in an autosomal dominant pattern. The clinical diagnosis of BC relies on the published diagnostic criteria, and analysis of two genes, BRCA1 and BRCA2, which are strongly associated with BC, are included in these criteria. The aim of this study was to compare BC index cases with non-BC individuals in terms of genotype and diagnostic features to investigate the genotype/demographic information association. Materials and Methods: Mutational analyses for the BRCA1/BRCA2 genes was performed in 2475 individuals between 2013-2022 from collaborative centers across Turkey, of whom 1444 with BC were designated as index cases.Results: Overall, mutations were identified in 17% (421/2475), while the percentage of mutation carriers in cases of BC was similar, 16.6% (239/1444). BRCA1/BRCA2 gene mutations were detected in 17.8% (131/737) of familial cases and 12% (78/549) of sporadic cases. Mutations in BRCA1 were found in 4.9%, whereas 12% were in BRCA2 (p<0.05). Meta-analyses were performed to compare these results with other studies of Mediterranean-region populations.Conclusion: Patients with BRCA2 mutations were significantly more common than those with BRCA1 mutations. In sporadic cases, there was a lower proportion with BRCA1/BRCA2 variants, as expected, and these results were consistent with the data of Mediterranean-region populations. However, the present study, because of the large sample size, revealed more robust findings than previous studies. These findings may be helpful in facilitating the clinical management of BC for both familial and non-familial cases.Publication Metabolic pathways of potential mirna biomarkers derived from liquid biopsy in epithelial ovarian cancer(Spandidos, 2023-04-01) Gümüşoğlu-Acar, Ece; Günel, Tuba; Hosseini, Mohammad Kazem; Doğan, Berkcan; Tekarslan, Efnan Elif; Gürdamar, Berk; Çevik, Nazife; Sezerman, Uğur; Topuz, Samet; Aydınlı, Kılıç; DOĞAN, BERKCAN; Tıp Fakültesi; Tıbbi Genetik Ana Bilim Dalı; AAD-5249-2020Epithelial ovarian cancer (EOC) is the type of OC with the highest mortality rate. Due to the asymptomatic nature of the disease and few available diagnostic tests, it is mostly diagnosed at the advanced stage. Therefore, the present study aimed to discover predictive and/or early diagnostic novel circulating microRNAs (miRNAs or miRs) for EOC. Firstly, microarray analysis of miRNA expression levels was performed on 32 samples of female individuals: Eight plasma samples from patients with pathologically confirmed EOC (mean age, 45 (30-54) years), eight plasma samples from matched healthy individuals (HIs) (mean age, 44 (30-65) years), eight EOC tissue samples (mean age, 45 (30-54) years) and eight benign ovarian (mean age, 35 (17-70) years) neoplastic tissue samples A total of 31 significantly dysregulated miRNAs in serum and three miRNAs in tissue were identified by microarray. The results were validated using reverse transcription-quantitative PCR on samples from 10 patients with pathologically confirmed EOC (mean age, 47(30-54) years), 10 matched His (mean age, 40(26-65) years], 10 EOC tissue samples (mean age, 47(30-54) years) and 10 benign ovarian neoplastic tissue samples (mean age, 40(17-70) years). The 'Kyoto Encyclopedia of Genes and Genomes' (KEGG) database was used for target gene and pathway analysis. A total of three miRNAs from EOC serum (hsa-miR-1909-5p, hsa-miR-885-5p and hsa-let-7d-3p) and one microRNA from tissue samples (hsa-miR-200c-3p) were validated as significant to distinguish patients with EOC from HIs. KEGG pathway enrichment analysis showed seven significant pathways, which included 'prion diseases', 'proteoglycans in cancer', 'oxytocin signaling pathway', 'hippo signaling pathway', 'adrenergic signaling in cardiomyocytes', 'oocyte meiosis' and 'thyroid hormone signaling pathway', in which the validated miRNAs served a role. This supports the hypothesis that four validated miRNAs, have the potential to be a biomarker of EOC diagnosis and target for treatment.