Browsing by Author "Ozbek, Ugur"
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Item Aberrant Hypermethylation of APC Tumor Supressor Gene in Acute Leukemia Patients(AKAD DOKTORLAR YAYINEVI, 2017-01-01) Hatirnaz, Ozden N. G.; Firtina, Sinem; Erbilgin, Yucel; Ozbek, Ugur; Sayitoglu, MugeWingless Type (WNT) signaling pathway is an evolutionarily conserved pathway that is crucial for the cell fate determination, survival and expansion of lymphocyte progenitors. It has been demonstrated that deregulated WNT signaling is one of the participating mechanism underlying lymphoid leukemogenesis. Inactivating mutations and methylation in Adenomatous Polyposis Coli (APC) gene, a negative regulator of WNT pathway, can cause ligand independent WNT pathway simulation. In this study, promoter methylation and expression of the APC gene is evaluated in childhood lymphoid and myeloid acute leukemia patients (n=118) and representative cell lines by using methylation specific PCR (MS-PCR) and real time quantitative PCR (QRT-PCR). APC gene promoter found hypermethylated in the 56\% of childhood acute leukemia patients {[}49.2\% of B-cell acute lymphoblastic leukemia (B-ALL), 62.5\% of T-cell acute lymphoblastic leukemia (T-ALL) and 64.1\% of Acute myeloid leukemia (AML)]. To evaluate the reflection of promoter methylation, APC mRNA levels were examined and found that all acute lymphoblastic leukemia subgroups have statistically lower APC expression levels compared to controls. Although there was no association with clinical parameters, promoter hypermethylation of APC gene seems to be a common epigenetic event in acute leukemia and leading to differential expression levels among different acute leukemia phenotypes.Item Aberrant Methylation Profile and Microsatellit Instability in Turkish Sporadic Colorectal Carcinoma(BEZMIALEM VAKIF UNIV, 2019-01-01) Ekmekci, Cumhur Gokhan; Gulluoglu, Mine; Kapran, Yersu; Dizdaroglu, Ferhunde; Ozbek, UgurObjective: Genomic DNA obtained from paraffin blocks of the intended colorectal cancer cases was evaluated for promoting colorectal cancer by investigating the promoter methylation of 6 different gene promoter regions and microsatellite instability. Methods: DNA was isolated from the paraffin tissue of 76 sporadic colorectal cancer patients by cross sections from the areas determined to be tumorous. The methylation specific PCR (MS-PCR) method was used for these DNA samples fo rmethlylation studies in promoter region of six different APC, hMLH1, p16INK4A, p15, p73 and DAPK1 genes. In the same samples, the presence of microsatellite instability (MSI). Results: The fequencey of methylation was 24\% for hMLH1, 31.5\% for APC, 19.6\% for DAPK1, 42.8\% for p16, 30\% for p15, 17\% for p73. We calculated a methylation index (MI=ratio between the number of genes methylated and the number of genes analyzed). MI was ranged from 0-0.83, with an average of 0.271 corresponding to 1.6 genes/sample and median was 0.225 and there were 15 samples which doesn't methylated in any loci. We analysed MSI in C-kit (21\%), hMSH2 (18\%) and APC (15\%), microsatellite region. Conclusion: We observed APC methylation was common then the other population for Turkish patient. P16 was the most commenest methylated loci among the 6 of gene and it seems storongly related with female patients. P73 was releated with left colorectal cancer and additionally it was related with the MSI.Item Anti-neuronal and stress-induced-phosphoprotein 1 antibodies in neuro-Behcet's disease(ELSEVIER SCIENCE BV, 2011-01-01) Vural, Burcak; Ugurel, Elif; Tuzun, Erdem; Kurtuncu, Murat; Zuliani, Luigi; Cavus, Filiz; Icoz, Sema; Erdag, Ece; Gul, Ahmet; Gure, Ali O.; Vincent, Angela; Ozbek, Ugur; Eraksoy, Mefkure; Akman-Demir, GulsenNo disease-specific neuronal antibodies have so far been defined in neuro-Behcet's disease (NBD). Immunohistochemistry and immunocytochemistry studies showed antibodies to hippocampal and cerebellar molecular layers and the surface antigens of cultured hippocampal neurons in sera and/or cerebrospinal fluids (CSF) of 13 of 20 NBD and 6 of 20 BD patients but not in multiple sclerosis or headache controls. Screening with a protein macroarray led to identification of stress-induced-phosphoprotein-1 (STIP-1) as an antigenic target. High-titer STIP-1-antibodies were detected in 6 NBD patients' sera but not in controls. These results suggest that neuronal antibodies could be useful as diagnostic biomarkers in NBD. (C) 2011 Elsevier B.V. All rights reserved.Item Cerebral Palsy and Genetics(TURKISH NEUROLOGICAL SOC, 2018-01-01) Akcakaya, Nihan Hande; Yapici, Zuhal; Ozbek, UgurItem Clinical and genetic spectrum of an orphan disease MPAN: a series with new variants and a novel phenotype(VIA MEDICA, 2019-01-01) Akcakaya, Nihan Hande; Haryanyan, Garen; Mercan, Sevcan; Sozer, Nejla; Ali, Asuman; Tombul, Temel; Ozbek, Ugur; Iseri, Sibel Aylin Ugur; Yapici, ZuhalIntroduction. Pathogenic variations in C19orf12 are responsible for two allelic diseases: mitochondrial membrane protein-associated neurodegeneration (MPAN)Item COMBINED ANALYSIS OF LINKAGE AND WHOLE EXOME SEQUENCING REVEALS CIC AS A CANDIDATE GENE FOR ISOLATED DYSTONIA(ISTANBUL UNIV, FAC MEDICINE, PUBL OFF, 2021-01-01) Salman, Baris; Yucesan, Emrah; Samanci, Bedia; Bilgic, Basar; Hanagasi, Hasmet; Gurvit, Ibrahim; Ozbek, Ugur; Ugur Iseri, SibelObjective: To explore the underlying genetic variations and mechanisms in a family affected by isolated dystonia. Material and Method: We employed whole genome Single Nu-cleotide Polymorphism (SNP) based linkage analysis along with whole exome sequencing (WES) in a consanguineous family pre -senting with isolated dystonia. An in-house pipeline compiled for WES analysis along with in-depth in silico prediction algo-rithms were used to assess the associated data produced in this study. Sanger sequencing was used for variant confirmation and segregation. Results: Data analysis included locus oriented WES variant prior-itization and cryptic splicing predictions. We detected a homo-zygous and synonymous variation rs748449895 (NM\_015125.4: c.4143C>TItem Copy-number variations in adult patients with chronic immune thrombocytopenia(TAYLOR \& FRANCIS LTD, 2020-01-01) Yucesan, Emrah; Ng, Ozden Hatirnaz; Yalniz, Fevzi Firat; Yilmaz, Hulya; Salihoglu, Ayse; Sudutan, Tugce; Eskazan, Ahmet Emre; Ongoren, Seniz; Baslar, Zafer; Soysal, Teoman; Ozbek, Ugur; Sayitoglu, Muge; Ar, M. CemObjectives Immune thrombocytopenia (ITP) is an autoimmune disease with heterogeneous background. FCGR2C mutations were defined in one third of the patients but genetic players have not been fully elucidated yet. Although childhood ITP present as benign, ITP in adulthood is chronic disease with treatment challenges. This study aimed to focus on adult ITP patients using a whole genome genotyping that is valuable approach to identify the responsible genomic regions for the disease. Methods Herein 24 adult primary-refractory for ITP patients were evaluated using HumanCytoSNP12BeadChip,Illumina. Forty-six age and sex matched healthy individuals, and ptients awith nonhematological conditions were analyzed as controls. Identified CNV regions were verified by qRTPCR. T-cell receptor beta and delta (TCRB/TCRG) clonality were assessed by heteroduplex analysis in mosaic cases. Results Several CNV losses and gains were defined (losses:2q,7q,17q,19p, and gains: 1q,2p,3q,4q,7q,10q,12p,13q,14q,15q,17p,20q,21p,22q,Xp). Mosaic changes of different sizes (0.2-17.77Mb) were identified in five patients and three of them showed clonality. CNV regions that were unique to ITP patients were identified for the first time and among these genes, those related to immune regulation, and cellular trafficking were noteworthy. Conclusion: Identified CNV regions harbor several candidate genes, the functions of which might shed light on the pathogenesis of chronic ITP.Item Dealing with the gray zones in the management of gastric cancer: The consensus statement of the Istanbul Group(AVES, 2019-01-01) Aytac, Erman; Aslan, Fatih; Cicek, Bahattin; Erdamar, Sibel; Gurses, Bengi; Guven, Koray; Falay, Okan; Karahasanoglu, Tayfun; Selcukbiricik, Fatih; Selek, Ugur; Atalar, Banu; Balik, Emre; Tozun, Nurdan; Rozanes, Izzet; Arican, Ali; Hamzaoglu, Ismail; Baca, Bilgi; Mandell, Nil Molinas; Saruc, Murat; Goksel, Suha; Demir, Gokhan; Agaoglu, Fulya; Yakicier, Cengiz; Ozbek, Ugur; Ozben, Volkan; Ozyar, Enis; Guner, Ahmet Levent; Er, Ozlem; Kaban, Kerim; Bolukbasi, Yasemin; Bugra, Dursun; Ahishali, Emel; Asian, Fatih; Boz-bas, Aysun; Hamzaoglu, Hulya; Karaman, Ahmet; Kucukmetin, Nurten Turkel; Vardareli, Eser Kutsal; Onder, Fatih Oguz; Sisman, Gurhan; Tiftikci, Arzu; Unal, Hakan Umit; Yapali, Suna; Acar, Sami; Agcaoglu, Orhan; Aghayeva, Afag; Akyuz, Ali; Atasoy, Deniz; Batik, Emre; Bayraktar, Ilknur Erenler; Bayram, Onur; Bilgic, Cagri; Bilgin, Ismail Ahmet; Can, Ugur; Dulgeroglu, Onur; Durukan, Ugur; Gencosmanoglu, Rasim; Gonenc, Murat; Gurbuz, Bulent; Kaya, Mesut; Omarov, Nail; Ozben, Volkan; Ozgur, Ilker; Ozoran, Emre; Sobutay, Erman; Uras, Cihan; Uymaz, Derya; Zenger, Serkan; Ozbek, Ugur; Yakicier, M. Cengiz; Afsar, Cigdem Usul; Bozkurt, Mustafa; Demir, Atakan; Er, Ozlem; Kanitez, Metin; Korkmaz, Taner; Mandel, Nil Molina; Mert, Askhan Guven; Ozer, Leyla; Sonmez, Ozlem; Tunali, Didem; Uluc, Basak Oyan; Yazar, Aziz; Yildiz, Ibrahim; Demirkurek, Cengiz; Guner, Ahmet Levent; Vardareli, Erkan; Armutlu, Aye; Baba, Fisun; Ersozlu, Ilker; Kapran, Yersu; Sahin, Davut; Abacioglu, Mehmet Ufuk; Bese, Nuran; Durankus, Nilufer Kilic; Gural, Zeynep; Ozyar, Enis; Sengoz, Meric; Sezen, Duygu; Caliskan, Can; Guven, Koray; Karaaslan, Ercan; Kizilkaya, Esref; Suleyman, Erdogan; Grp, IstanbulThe geographical location and differences in tumor biology significantly change the management of gastric cancer. The prevalence of gastric cancer ranks fifth and sixth among men and women, respectively, in Turkey. The international guidelines from the Eastern and Western countries fail to manage a considerable amount of inconclusive issues in the management of gastric cancer. The uncertainties lead to significant heterogeneities in clinical practice, lack of homogeneous data collection, and subsequently, diverse outcomes. The physicians who are professionally involved in the management of gastric cancer at two institutions in Istanbul, Turkey, organized a consensus meeting to address current problems and plan feasible, logical, measurable, and collective solutions in their clinical practice for this challenging disease. The evidence-based data and current guidelines were reviewed. The gray zones in the management of gastric cancer were determined in the first session of this consensus meeting. The second session was constructed to discuss, vote, and ratify the ultimate decisions. The identification of the T stage, the esophagogastric area, imaging algorithm for proper staging and follow-up, timing and patient selection for neoadjuvant treatment, and management of advanced and metastatic disease have been accepted as the major issues in the management of gastric cancer. The recommendations are presented with the percentage of supporting votes in the results section with related data.Item Frontline nilotinib treatment in Turkish patients with Philadelphia chromosome-positive chronic Myeloid Leukemia in chronic phase: updated results with 2 years of follow-up(TAYLOR \& FRANCIS LTD, 2018-01-01) Saydam, Guray; Haznedaroglu, Ibrahim Celalettin; Kaynar, Leylagul; Yavuz, Akif S.; Ali, Ridvan; Guvenc, Birol; Akay, Olga M.; Baslar, Zafer; Ozbek, Ugur; Sonmez, Mehmet; Aydin, Demet; Pehlivan, Mustafa; Undar, Bulent; Dagdas, Simten; Ayyildiz, Orhan; Akin, Gulnur; Dag, Ilkiz M.; Ilhan, OsmanObjectives: This report presents final results (24 months of follow-up) from the first prospective, national study of frontline nilotinib in chronic myeloid leukemia (CML) patients in Turkey. Methods: Patients with newly diagnosed Philadelphia chromosome-positive CML in chronic phase (CML-CPItem Gamma-irradiated SARS-CoV-2 vaccine candidate, OZG-38.61.3, confers protection from SARS-CoV-2 challenge in human ACEII-transgenic mice(NATURE PORTFOLIO, 2021-01-01) Turan, Raife Dilek; Tastan, Cihan; Kancagi, Derya Dilek; Yurtsever, Bulut; Karakus, Gozde Sir; Ozer, Samed; Abanuz, Selen; Cakirsoy, Didem; Tumentemur, Gamze; Demir, Sevda; Seyis, Utku; Kuzay, Recai; Elek, Muhammer; Kocaoglu, Miyase Ezgi; Ertop, Gurcan; Arbak, Serap; Elmas, Merve Acikel; Hemsinlioglu, Cansu; Ng, Ozden Hatirnaz; Akyoney, Sezer; Sahin, Ilayda; Kayhan, Cavit Kerem; Tokat, Fatma; Akpinar, Gurler; Kasap, Murat; Kocagoz, Ayse Sesin; Ozbek, Ugur; Telci, Dilek; Sahin, Fikrettin; Yalcin, Koray; Ratip, Siret; Ince, Umit; Ovali, ErcumentThe SARS-CoV-2 virus caused the most severe pandemic around the world, and vaccine development for urgent use became a crucial issue. Inactivated virus formulated vaccines such as Hepatitis A and smallpox proved to be reliable approaches for immunization for prolonged periods. In this study, a gamma-irradiated inactivated virus vaccine does not require an extra purification process, unlike the chemically inactivated vaccines. Hence, the novelty of our vaccine candidate (OZG-38.61.3) is that it is a non-adjuvant added, gamma-irradiated, and intradermally applied inactive viral vaccine. Efficiency and safety dose (either 10(13) or 10(14) viral RNA copy per dose) of OZG-38.61.3 was initially determined in BALB/c mice. This was followed by testing the immunogenicity and protective efficacy of the vaccine. Human ACE2-encoding transgenic mice were immunized and then infected with the SARS-CoV-2 virus for the challenge test. This study shows that vaccinated mice have lowered SARS-CoV-2 viral RNA copy numbers both in oropharyngeal specimens and in the histological analysis of the lung tissues along with humoral and cellular immune responses, including the neutralizing antibodies similar to those shown in BALB/c mice without substantial toxicity. Subsequently, plans are being made for the commencement of Phase 1 clinical trial of the OZG-38.61.3 vaccine for the COVID-19 pandemic.Item Hydrogen Sulphide and Nitric Oxide Cooperate in Cardioprotection Against Ischemia/Reperfusion Injury in Isolated Rat Heart(INT INST ANTICANCER RESEARCH, 2020-01-01) Ustunova, Savas; Takir, Selcuk; Yilmazer, Nadim; Bulut, Huri; Altindirek, Didem; Ng, Ozden Hatirnaz; Tansel, Cihan Demirci; Dogan, B. Sonmez Uydes; Ozbek, Ugur; Armutak, Elif Ilkay; Gurevin, Ebru GurelBackground/Aim: This study was designed to provide further evidence for the interactions between hydrogen sulfide (H2S) and nitric oxide (NO) in ischemia/reperfiision (I/R) injury. Materials and Methods: Rat hearts were studied with the Langendorff technique using the H2S donor sodium hydrosulfide (NaHS, 40 mu M) and the cystathionine gamma-lyase (CTH or CSE) inhibitor DL-propargylglycine (PAG, 1 mM). NO synthase inhibitor L-NG-nitroarginine methyl ester (L-NAME, 30 mg/kg, 7 days) was administered before the isolation. The hearts were homogenized for biochemical and molecular analysis. Results: NaHS reversed I/R-induced cardiac performance impairment, increased tissue nitric oxide production and decreased tissue markers for cardiac injury, while L-NAME inhibited these effects. The expression of CTH was increased with PAG, which was suppressed by L-NAME. Conclusion: H2S and NO increase each other's production suggesting their interaction and cooperation in cardioprotection against I/R injury.Item Identification of epilepsy related pathways using genome-wide DNA methylation measures: A trio-based approach(PUBLIC LIBRARY SCIENCE, 2019-01-01) Ozdemir, Ozkan; Egemen, Ece; Iseri, Sibel Aylin Ugur; Sezerman, Osman Ugur; Bebek, Nerses; Baykan, Betul; Ozbek, UgurGenetic generalized epilepsies (GGE) are genetically determined, as their name implies and they are clinically characterized by generalized seizures involving both sides of the brain in the absence of detectable brain lesions or other known causes. GGEs are yet complex and are influenced by many different genetic and environmental factors. Methylation specific epigenetic marks are one of the players of the complex epileptogenesis scenario leading to GGE. In this study, we have set out to perform genome-wide methylation profiling to analyze GGE trios each consisting of an affected parent-offspring couple along with an unaffected parent. We have developed a novel scoring scheme within trios to categorize each locus analyzed as hypo or hypermethylated. This stringent approach classified differentially methylated genes in each trio and helped us to produce trio specific and pooled gene lists with inherited and aberrant methylation levels. In order to analyze the methylation differences from a boarder perspective, we performed enrichment analysis with these lists using the PANOGA software. This collective effort has led us to detect pathways associated with the GGE phenotype, including the neurotrophin signaling pathway. We have demonstrated a trio based approach to genome-wide DNA methylation analysis that identified individual and possibly minor changes in methylation marks that could be involved in epileptogenesis leading to GGE.Item Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure(PUBLIC LIBRARY SCIENCE, 2021-01-01) Hatirnaz Ng, Ozden; Akyoney, Sezer; Sahin, Ilayda; Soykam, Huseyin Okan; Bayram Akcapinar, Gunseli; Ozdemir, Ozkan; Kancagi, Derya Dilek; Sir Karakus, Gozde; Yurtsever, Bulut; Kocagoz, Ayse Sesin; Ovali, Ercument; Ozbek, UgurThe Coronavirus Disease 2019 (COVID-19) was declared a pandemic in March 2020 by the World Health Organization (WHO). As of May 25th, 2021 there were 2.059.941 SARS-COV2 genome sequences that have been submitted to the GISAID database, with numerous variations. Here, we aim to analyze the SARS-CoV-2 genome data submitted to the GISAID database from Turkey and to determine the variant and clade distributions by the end of May 2021, in accordance with their appearance timeline. We compared these findings to USA, Europe, and Asia data as well. We have also evaluated the effects of spike protein variations, detected in a group of genome sequences of 13 patients who applied to our clinic, by using 3D modeling algorithms. For this purpose, we analyzed 4607 SARS-CoV-2 genome sequences submitted by different lab centers from Turkey to the GISAID database between March 2020 and May 2021. Described mutations were also introduced in silico to the spike protein structure to analyze their isolated impacts on the protein structure. The most abundant clade was GR followed by G, GH, and GRY and we did not detect any V clade. The most common variant was B.1, followed by B.1.1, and the UK variant, B.1.1.7. Our results clearly show a concordance between the variant distributions, the number of cases, and the timelines of different variant accumulations in Turkey. The 3D simulations indicate an increase in the surface hydrophilicity of the reference spike protein and the detected mutations. There was less surface hydrophilicity increase in the Asp614Gly mutation, which exhibits a more compact conformation around the ACE-2 receptor binding domain region, rendering the structure in a ``down{''} conformation. Our genomic findings can help to model vaccination programs and protein modeling may lead to different approaches for COVID-19 treatment strategies.Item No evidence for a BRD2 promoter hypermethylation inblood leukocytes of Europeans with juvenile myoclonic epilepsy(WILEY, 2019-01-01) Schulz, Herbert; Ruppert, Ann-Kathrin; Zara, Federico; Madia, Francesca; Iacomino, Michele; Vari, Maria S.; Balagura, Ganna; Minetti, Carlo; Striano, Pasquale; Blanche, Amedeo; Marini, Carla; Guerrini, Renzo; Weber, Yvonne G.; Becker, Felicitas; Lerche, Holger; Kapser, Claudia; Schankin, Christoph J.; Kunz, Wolfram S.; Moller, Rikke S.; Oliver, Karen L.; Bellows, Susannah T.; Mullen, Saul A.; Berkovic, Samuel F.; Scheffer, Ingrid E.; Caglayan, Hande; Ozbek, Ugur; Hoffmann, Per; Schramm, Sara; Tsortouktzidis, Despina; Becker, Albert J.; Sander, ThomasJuvenile myoclonic epilepsy (JME) is a common syndrome of genetic generalized epilepsies (GGEs). Linkage and association studies suggest that the gene encoding the bromodomain-containing protein 2 (BRD2) may increase risk of JME. The present methylation and association study followed up a recent report highlighting that the BRD2 promoter CpG island (CpG76) is differentially hypermethylated in lymphoblastoid cells from Caucasian patients with JME compared to patients with other GGE subtypes and unaffected relatives. In contrast, we found a uniform low average percentage of methylation (<4.5\%) for 13 CpG76-CpGs in whole blood cells from 782 unrelated European Caucasians, including 116 JME patients, 196 patients with genetic absence epilepsies, and 470 control subjects. We also failed to confirm an allelic association of the BRD2 promoter single nucleotide polymorphism (SNP) rs3918149 with JME (Armitage trend test, P=0.98), and we did not detect a substantial impact of SNP rs3918149 on CpG76 methylation in either 116 JME patients (methylation quantitative trait loci {[}meQTL], P=0.29) or 470 German control subjects (meQTL, P=0.55). Our results do not support the previous observation that a high DNA methylation level of the BRD2 promoter CpG76 island is a prevalent epigenetic motif associated with JME in Caucasians.Item Optimizing the Personalized Care for the Management of Rectal Cancer: A Consensus Statement(AVES, 2022-01-01) Aytac, Erman; Ozer, Leyla; Baca, Bilgi; Balik, Emre; Kapran, Yersu; Taskin, Orhun Cig; Uluc, Basak Oyan; Abacioglu, Mehmet Ufuk; Gonenc, Murat; Bolukbasi, Yasemin; Cil, Barbaros E.; Baran, Bulent; Aygun, Cem; Yildiz, Mehmet Erdem; Unal, Kemal; Erkol, Burcak; Yalti, Tunc; Ozbek, Ugur; Attila, Tan; Tozun, Nurdan; Gurses, Bengi; Erdamar, Sibel; Er, Ozlem; Bese, Nuran; Bilge, Orhan; Ceyhan, Guralp Onur; Mandel, Nil Molinas; Selek, Ugur; Yakicier, Cengiz; Karabey, Hulya Kayserili; Saruc, Murat; Ozben, Volkan; Esen, Eren; Ozoran, Emre; Vardareli, Erkan; Guner, Levent; Hamzaoglu, Ismail; Bugra, Dursun; Karahasanoglu, Tayfun; Grp, IstanbulColorectal cancer is the third most common cancer in Turkey. The current guidelines do not provide sufficient information to cover all aspects of the management of rectal cancer. Although treatment has been standardized in terms of the basic principles of neoadjuvant, surgical, and adjuvant therapy, uncertainties in the management of rectal cancer may lead to significant differences in clinical practice. In order to clarify these uncertainties, a consensus program was constructed with the participation of the physicians from the Acibadem Mehmet Ali Aydinlar and Koc Universities. This program included the physicians from the departments of general surgery, gastroenterology, pathology, radiology, nuclear medicine, medical oncology, radiation oncology, and medical genetics. The gray zones in the management of rectal cancer were determined by reviewing the evidence-based data and current guidelines before the meeting. Topics to be discussed consisted of diagnosis, staging, surgical treatment for the primary disease, use of neoadjuvant and adjuvant treatment, management of recurrent disease, screening, follow-up, and genetic counseling. All those topics were discussed under supervision of a presenter and a chair with active participation of related physicians. The consensus text was structured by centralizing the decisions based on the existing data.Item Preclinical efficacy and safety analysis of gamma-irradiated inactivated SARS-CoV-2 vaccine candidates(NATURE RESEARCH, 2021-01-01) Karakus, Gozde Sir; Tastan, Cihan; Kancagi, Derya Dilek; Yurtsever, Bulut; Tumentemur, Gamze; Demir, Sevda; Turan, Raife Dilek; Abanuz, Selen; Cakirsoy, Didem; Seyis, Utku; Ozer, Samed; Elibol, Omer; Elek, Muhammer; Ertop, Gurcan; Arbale, Serap; Elmas, Merve Acikel; Hermsinlioglu, Canso; Kocagoz, Ayse Sesin; Ng, Ozden Hatirnaz; Akyoney, Sezer; Sahin, Ilayda; Ozbek, Ugur; Telci, Dilek; Sahin, Fikrettin; Yalcin, Koray; Ratip, Siret; Ovali, ErcumentCOVID-19 outbreak caused by SARS-CoV-2 created an unprecedented health crisis since there is no vaccine for this novel virus. Therefore, SARS-CoV-2 vaccines have become crucial for reducing morbidity and mortality. In this study, in vitro and in vivo safety and efficacy analyzes of lyophilized vaccine candidates inactivated by gamma-irradiation were performed. The candidate vaccines in this study were OZG-3861 version 1(V1), an inactivated SARS-CoV-2 virus vaccine, and SK-01 version 1 (V1), a GM-CSF adjuvant added vaccine. The candidate vaccines were applied intradermally to BALB/c mice to assess toxicity and immunogenicity. Preliminary results in vaccinated mice are reported in this study. Especially, the vaccine models containing GM-CSF caused significant antibody production with neutralization capacity in absence of the antibody-dependent enhancement feature, when considered in terms of T and B cell responses. Another important finding was that the presence of adjuvant was more important in T cell in comparison with B cell response. Vaccinated mice showed T cell response upon restimulation with whole inactivated SARS-CoV-2 or peptide pool. This study shows that the vaccines are effective and leads us to start the challenge test to investigate the gamma-irradiated inactivated vaccine candidates for infective SARS-CoV-2 virus in humanized ACE2+ mice.Item Primary antibody deficiencies in Turkey: molecular and clinical aspects (Oct, 10.1007/s12026-021-09242-z, 2021)(HUMANA PRESS INC, 2022-01-01) Firtina, Sinem; Ng, Yuk Yin; Ng, Ozden H.; Kiykim, Ayca; Ozek, Esra Yucel; Kara, Manolya; Aydiner, Elif; Nepesov, Serdar; Camcioglu, Yildiz; Sayar, Esra H.; Gungoren, Ezgi Yalcin; Reisli, Ismail; Torun, Selda H.; Haskologlu, Sule; Cogurlu, Tuba; Kaya, Aysenur; Cekic, Sukru; Baris, Safa; Ozbek, Ugur; Ozen, Ahmet; Sayitoglu, MugeItem PTEN and AKT1 Variations in Childhood T-Cell Acute Lymphoblastic Leukemia(GALENOS YAYINCILIK, 2020-01-01) Kucukcankurt, Fulya; Erbilgin, Yucel; Firtina, Sinem; Ng, Ozden Hatirnaz; Karakas, Zeynep; Celkan, Tiraje; Unuvar, Aysegul; Ozbek, Ugur; Sayitoglu, MugeObjective: PTEN/AKT pathway deregulations have been reported to be associated with treatment response in acute leukemia. This study examined pediatric T-cell acute lymphoblastic leukemia (T-ALL) samples for PTEN and AKT1 gene variations and evaluated the clinical findings. Materials and Methods: Fifty diagnostic bone marrow samples of childhood T-ALL cases were investigated for the hotspot regions of the PTEN and AKT1 genes by targeted next-generation sequencing. Results: A total of five PTEN variations were found in three of the 50 T-ALL cases (6\%). Three of the PTEN variations were first reported in this study. Furthermore, one patient clearly had two different mutant clones for PTEN. Two intronic single-nucleotide variations were found in AKT1 and none of the patients carried pathogenic AKT1 variations. Conclusion: Targeted deep sequencing allowed us to detect both low-level variations and clonal diversity. Low-level PTEN/AKT1 variation frequency makes it harder to investigate the clinical associations of the variants. On the other hand, characterization of the PTEN/AKT signaling members is important for improving case-specific therapeutic strategies.Item Rare coding variants in genes encoding GABA(A) receptors in genetic generalised epilepsies: an exome-based case-control study(ELSEVIER SCIENCE INC, 2018-01-01) May, Patrick; Girard, Simon; Harrer, Merle; Bobbili, Dheeraj R.; Schubert, Julian; Wolking, Stefan; Becker, Felicitas; Lachance-Touchette, Pamela; Meloche, Caroline; Gravel, Micheline; Niturad, Cristina E.; Knaus, Julia; De Kovel, Carolien; Toliat, Mohamad; Polvi, Anne; Iacomino, Michele; Guerrero-Lopez, Rosa; Baulac, Stephanie; Marini, Carla; Thiele, Holger; Altmueller, Janine; Jabbari, Kamel; Ruppert, Ann-Kathrin; Jurkowski, Wiktor; Lal, Dennis; Rusconi, Raffaella; Cestele, Sandrine; Terragni, Benedetta; Coombs, Ian D.; Reid, Christopher A.; Striano, Pasquale; Caglayan, Hande; Siren, Auli; Everett, Kate; Moller, Rikke S.; Hjalgrim, Helle; Muhle, Hiltrud; Helbig, Ingo; Kunz, Wolfram S.; Weber, Yvonne G.; Weckhuysen, Sarah; De Jonghe, Peter; Sisodiya, Sanjay M.; Nabbout, Rima; Franceschetti, Silvana; Coppola, Antonietta; Vari, Maria S.; Trenite, Dorothee Kasteleijn-Nolst; Baykan, Betul; Ozbek, Ugur; Bebek, Nerses; Klein, Karl M.; Rosenow, Felix; Nguyen, Dang K.; Dubeau, Francois; Carmant, Lionel; Lortie, Anne; Desbiens, Richard; Clement, Jean-Francois; Cieuta-Walti, Cecile; Sills, Graeme J.; Auce, Pauls; Francis, Ben; Johnson, Michael R.; Marson, Anthony G.; Berghuis, Bianca; Sander, Josemir W.; Avbersek, Andreja; McCormack, Mark; Cavalleri, Gianpiero L.; Delanty, Norman; Depondt, Chantal; Krenn, Martin; Zimprich, Fritz; Peter, Sarah; Nikanorova, Marina; Kraaij, Robert; van Rooij, Jeroen; Balling, Rudi; Ikram, M. Arfan; Uitterlinden, Andre G.; Avanzini, Giuliano; Schorge, Stephanie; Petrou, Steven; Mantegazza, Massimo; Sander, Thomas; LeGuern, Eric; Serratosa, Jose M.; Koeleman, Bobby P. C.; Palotie, Aarno; Lehesjoki, Anna-Elina; Nothnagel, Michael; Nuernberg, Peter; Maljevic, Snezana; Zara, Federico; Cossette, Patrick; Krause, Roland; Lerche, Holger; Consortium, Epicure; Consortium, EuroEP.I.N.O.M.I.C.S. C. O. G. I. E.; Consortium, EpiPG. X.Background Genetic generalised epilepsy is the most common type of inherited epilepsy. Despite a high concordance rate of 80\% in monozygotic twins, the genetic background is still poorly understood. We aimed to investigate the burden of rare genetic variants in genetic generalised epilepsy. Methods For this exome-based case-control study, we used three different genetic generalised epilepsy case cohorts and three independent control cohorts, all of European descent. Cases included in the study were clinically evaluated for genetic generalised epilepsy. Whole-exome sequencing was done for the discovery case cohort, a validation case cohort, and two independent control cohorts. The replication case cohort underwent targeted next-generation sequencing of the 19 known genes encoding subunits of GABA(A) receptors and was compared to the respective GABA(A) receptor variants of a third independent control cohort. Functional investigations were done with automated two-microelectrode voltage clamping in Xenopus laevis oocytes. Findings Statistical comparison of 152 familial index cases with genetic generalised epilepsy in the discovery cohort to 549 ethnically matched controls suggested an enrichment of rare missense (Nonsyn) variants in the ensemble of 19 genes encoding GABA(A) receptors in cases (odds ratio {[}OR] 2.40 {[}95\% CI 1.41-4.10]Item SCREENING SLC2A1 GENE FOR SEQUENCE AND COPY NUMBER VARIATIONS ASSOCIATED WITH GLUT-1 DEFICIENCY SYNDROME(ISTANBUL UNIV, FAC MEDICINE, PUBL OFF, 2020-01-01) Ornek Erguzeloglu, Cemre; Kara, Bulent; Karacan, Ilker; Ozdemir, Ozkan; Kesim, Yesim; Bebek, Nerses; Ozbek, Ugur; Ugur Iseri, Sibel AylinObjective: Glucose transporter-1 deficiency syndrome (GLUT1- DS) is defined as a metabolic encephalopathy that is associated with heterozygous and usually de novo pathogenic variations in the SLC2A1 (solute carrier family2 member1) gene. Materials and Methods: In this study, all coding exons and neighboring intronic regions of SLC2A1 were Sanger sequenced in 12 patients with clinically suspected GLUT1-DS. For de novo variations revealed after sequencing and segregation analysis, we also performed genome wide Single Nucleotide Polymor- phism (SNP) genotyping to confirm parental relatedness with the proband. In patients without any sequence variations, real-time quantitative real-time polymerase chain reaction (qPCR) was applied to determine the presence of any copy number variations (CNV). Results: Sanger sequencing followed by bioinformatics analysis, segregation in the family and SNP array genotyping revealed two novel and de novo pathogenic variations associated with the GLUT1-DS phenotype in 2 patients. qPCR results were compatible with one copy loss of SLC2A1 gene in another patient. All variations identified herein are likely to have caused null al-leles and resulted in GLUT1-DS through haplo insufficiency. Disscussion : In this study we used a series of molecular genetic approaches in order to identify all possible variations in SLC2A1 that may be associated with GLUT1-DS. This collective effort fa- cilitated diagnosis in 3 patients.