Person: ÖZEMRİ SAĞ, ŞEBNEM
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ÖZEMRİ SAĞ
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ŞEBNEM
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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 Birt-hogg-dube syndrome: Diagnostic journey of three cases from skin to gene(Korean Dermatological Assoc, 2022-02-01) Gül, Şeref; Dilektaşlı, Aslı Görek; GÖREK DİLEKTAŞLI, ASLI; Temel, Şehime Gülsün; TEMEL, ŞEHİME GÜLSÜN; Hasal, Eda; Başkan, Emel Bülbül; BÜLBÜL BAŞKAN, EMEL; Sag, Şebnem Özemri; ÖZEMRİ SAĞ, ŞEBNEM; Adım, Şaduman Balaban; BALABAN ADIM, ŞADUMAN; Tıp Fakültesi; Tıbbi Genetik Ana Bilim Dalı; 0000-0001-6310-5107; 0000-0001-7099-9647; 0000-0002-9802-0880; AAG-8385-2021; AAH-8355-2021Birt-Hogg-Dube syndrome (BHDS) is a rare disorder characterized by the triad of cutaneous lesions, renal tumors, lung cysts and inactivation of the gene folliculin (FLCN). Here, we present three female patients diagnosed with BHDS. First case a 55-year-old female had flesh moles histopathology compatible with angiofibroma, multiple cysts in the lung and kidneys, FLCN gene mutations ('c.1285dupC [p.His429Profs*]' 11th exon and 'c.653G>A [p.Arg258His]' 7th exon). The second case a 76-year-old female had trichodiscoma on her skin, multiple cysts in the lung, spontaneous pneumothorax, FLCN gene mutation 'c.1285dupC (p.His429Profs*27) 11th exon' and, her son had renal carcinoma history under 50 years of age. Our third case, also the daughter of case 2, had dermal papules histopathology compatible with trichodiscoma, spontaneous pneumothorax, FLCN gene mutation 'c.1285dupC (p.His429Profs*27) 11th exon' and, parotid oncocytoma. Through our cases, we document the first case of two mutations ('c.1285dupC [p.His429Profs*]' 11th exon and 'c.653G>A [p.Arg258His]' 7th exon) in the same FLCN gene and the 11th known case of parotid oncocytoma associated with BHDS in the light of the literature.Publication Clinical management and quality of life in patients with homozygous familial hypercholesterolemia undergoing lipid-apheresis in turkey: First results of a nation-wide survey (a-hit registry)(Elsevier Ireland Ltd, 2016-09-01) Kayıkçıoğlu, M.; Tokgozoglu, L.; Pırıldar, S.; Yılmaz, M.; Kaynar, L.; Aktan, M.; Durmuş, R.; Temizhan, A.; Özcebe, O.; Akyol, T.; Okutan, H.; Altunkeser, B.; Yenercağ, M.; Kurtoglu, E.; Demircioğlu, S.; Salcıoğlu, O.; Demir, M.; Yılmaz, H.; Sağ, S.; ÖZEMRİ SAĞ, ŞEBNEM; Tıp FakültesiPublication Novel homozygous missense mutation in NARS1 gene: A new neurodevelopmental disorder with microcephaly(Springernature, 2022-04-01) Temel, Sehime Gülsün; Sağ, Şebnem Özemri; Eren, Erdal; Deniz, Engin; TEMEL, ŞEHİME GÜLSÜN; ÖZEMRİ SAĞ, ŞEBNEM; EREN, ERDAL; Tıp Fakültesi; 0000-0002-9802-0880; 0000-0002-1684-1053; JPK-3909-2023; AAG-8385-2021; AAH-8355-2021Publication Diagnostic efficiency of clinical exome solution panel in patients with hearing loss/hereditary deafness by using next generation sequencing(Springernature, 2020-12-01) ; Sağ, Şebnem Özemri; ÖZEMRİ SAĞ, ŞEBNEM; Alemdar, A.; ALEMDAR, ADEM; Yılmaz, M.; Aliyeva, L.; ALIYEVA, LAMIYA; Temel Şehime Gülsün; TEMEL, ŞEHİME GÜLSÜN; Tıp Fakültesi; Genetik Top Ana Bilim Dalı; 0000-0002-9802-0880; HIZ-7332-2022; AAH-8355-2021; AAG-8385-2021Publication Multiple congenital anomalies in a child with 47,XY,+der(8;9)(p10;p10): A case report(Medecine Et Hygiene, 2015-01-01) Görükmez, O.; Görükmez, Orhan; Sağ, Şebnem Özemri; Yakut, T.; Gülten, Tuna; Görükmez, Orhan; ÖZEMRİ SAĞ, ŞEBNEM; Yakut, T.; Gülten, Tuna; Tıp Fakültesi; Genetik Bölümü; 0000-0002-9241-0896; 0000-0002-9241-0896; AAH-8355-2021; AFZ-0764-2022; GIS-1493-2022; EYU-9227-2022Multiple congenital anomalies in a child with 47,XY,+der(8;9)(p10;p10): a case report: Complex small supernumerary marker chromosomes (sSMC) constitute one of the smallest subgroups of sSMC in general. Complex sSMC consist of chromosomal material derived from more than one chromosome. We report a complex sSMC derived from chromosomes 9 and 8, characterized as der(8;9)(p10;p10) resulting from unbalanced transition of maternal balanced translocation. Besides dysmorphic face and mental-motor retardation, the patient had Dandy-Walker malformation (DWM) in cranial MR also. As far as we are concerned, this is the first complex sSMC case comprising short arms of 8th and 9th chromosomes.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 A rare case of fructose-1,6-bisphosphatase deficiency: A delayed diagnosis story(Walter De Gruyter Gmbh, 2020-10-01) Tuncel, Gulten; Ergören, Mahmut Çerkez; Sag, Sebnem Ozemri; ÖZEMRİ SAĞ, ŞEBNEM; Temel, Sehime Gulsun; TEMEL, ŞEHİME GÜLSÜN; Tıp Fakültesi; Genetik Tıp Ana Bilim Dalı; 0000-0002-9802-0880; AAH-8355-2021; AAG-8385-2021Objectives: Fructose-1,6-bisphosphatase deficiency (FBPase deficiency, OMIM 229700) is an early-onset rare genetic disorder caused by mutations in the FBP1 gene.Case presentation: Our patient was 17-years-old when she was diagnosed with the disease. Initial sequencing analysis with Ion Torrent technology failed to detect the gross deletion that covered complete exon 2 (c.-24-26_170 + 5192del) of FBP1 gene and caused the delay in diagnosis. Deletion was then detected when sequencing was performed in an Illumina MiSeq platform.Conclusions: This case emphasizes the importance of sequencing data analysis for precise diagnosis of rare diseases and therapy planning.Publication Association between p16(cdkn2a) c540g polymorphism and tumor behavior in prolactinoma: A single-center study(Spandidos Publ Ltd, 2014-07-01) Karkucak, Mutlu; Gül, Özen Öz; ÖZ GÜL, ÖZEN; Yakut, Tahsin; Sağ, Şebnem Özemri; ÖZEMRİ SAĞ, ŞEBNEM; Ersoy, Canan; ERSOY, CANAN; Tuncel, Ercan; Ertürk, Erdinç; ERTÜRK, ERDİNÇ; Cander, Soner; Tıp Fakültesi; Genetik Ana Bilim Dalı; AAJ-6536-2021; AAH-8861-2021; AAI-1005-2021; ABI-5648-2022; AAH-8355-2021Pituitary tumors usually originate as benign sporadic adenomas and develop into invasive and aggressive tumors such as prolactinomas, which are common functioning pituitary adenomas. The aim of the present study was to examine the association between the tumor behavior in prolactinomas and the p16(CDKN2A) gene polymorphism occurring at the 3'-untranslated region of exon 3 (C540G). A total of 104 patients with prolactinoma were included and assigned to two groups based on invasive vs. non-invasive tumor behavior. Ki67 indices were recorded according to histopathology results. Genotypic analysis of the p16( CDKN2A) C540G polymorphism was carried out using a modified polymerase chain reaction-restriction fragment length polymorphism assay. The corresponding frequencies for CC, CG and GG genotypes in non-invasive vs. invasive tumors were 61.5, 30.8, 7.7 and 64.1, 28.2, 7.7%, respectively ( not significant). The observed CG genotype frequency was higher compared with previous studies. In addition, the patients with giant adenomas or a high Ki67 index had a higher frequency of the CG genotype as compared with the other subgroups, although the differences were not significant (46.2 and 42.9%, respectively). In conclusion, a higher frequency of the C540G CG genotype of the CDKN2A gene was found among patients with prolactinoma in comparison with previous studies. These frequencies were also higher in the subgroups with elevated Ki67 or giant adenomas. Further studies are required to improve the definition of the role of the CG genotype in the development and progression of tumors in prolactinomas.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.