Validation of next generation sequencing method for tumor spesificmutations and bioinformatics variant analysis.

TEZ12154Tez (Yüksek Lisans) -- Çukurova Üniversitesi, Adana, 2017.Kaynakça (s. 47-52) var.XIII, 56 s. :_res. (bzs. rnk.), tablo ;_29 cm.Yeni nesil dizileme yöntemi, genetik biliminin günümüzde sahip olduğu önemi bir kez daha ortaya koymakta ve değerini arttırmaktadır. Geleneksel genetik çalışmalarına göre daha hassas ve güvenilir bir çalışma yöntemi olmasına karşın, gerek dünyada gerekse ülkemizde bu yeni teknolojinin kullanımına ve prosedürlerin uygulanmasına yönelik, özellikle de Türkçe, yeterli sayıda kaynak bulunmamaktadır. Günümüzde yeni nesil dizileme yöntemi ile çok daha fazla sayıda geni aynı anda çalışmak ve hem hasta hem de hastalık hakkında daha fazla bilgiye ulaşmak mümkün olmaktadır. Böylece kliniklerde hastaların kesin tanı bilgilerinin yanında, tedavide ve hastalığın seyrinde fayda sağlayacak önemli bilgiler sunulabilmektedir. Bu açıdan oldukça önem arz eden bu uygulamanın doğru ve eksiksiz çalışılması hayati önem taşımaktadır. Yeni nesil dizileme yönteminin ve bunun uygulandığı sistemlerin rutin kullanımında optimizasyonların yapılması, özellikle elde edilen sonucun doğru yorumlanabilmesinde ciddi bir tecrübe ve bilgi birikimine ihtiyaç duyulmaktadır. Tüm dünyada gittikçe yaygınlaşan bu metot ile çalışılmak üzere tıbbi genetik ve tıbbi onkoloji alanında önem arz eden tümör spesifik mutasyonlar için, Çukurova Üniversitesi Adana Genetik Hastalıklar Tanı ve Tedavi Merkezi (ÇÜ AGENTEM) laboratuvarlarında tümör paneli oluşturulmuş ve bu tez çalışmasına olanak sağlanmıştır. Bu çalışmada yeni nesil dizileme yönteminin rutin uygulamadaki validasyonu ve optimizasyonu konu alınmıştır. Bu tez çalışması ile özellikle Türkçe literatürde eksikliği hissedilen bu yeni teknolojiye ait değerli bilgilerin paylaşılması ve böylece literatüre katkı sağlanması amaçlanmıştır.Next Generation Sequencing (NGS) empowers the importance and the other aspects of genetics. NGS has the sensitivity of detection at faster pace than that of traditional diagnostics, the utilization and application of this new technology still remains a constant challenge due to the lack of literature especially in Turkish. NGS has allowed us to analyze thousands of genes at the same time, and made it possible to acquire more data about both the patient and the disease. Thus, NGS allows a more complete overview of patients in diagnostic prognosis and therapy prediction. Therefore, boosting the validity and heighten the trust worthiness of the technical performance becomes more essential. NGS test development, optimization and validation with the reliability of data and its interpretation requires highly experienced clinical and laboratory team. Cukurova University AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center) provides an opportunity to do this thesis through the multi-gene solid tumor panel using a new NGS system to identify variants that are important for medical genetics and medical oncology. In this thesis, the validation and optimization of a new NGS system had been evaluated for clinical utility. This study contributes to literature especially the Turkish, by sharing information and recommendations to help clinical laboratory professionals.Bu çalışma Ç.Ü. Bilimsel Araştırma Projeleri Birimi tarafından desteklenmiştir. Proje No: FYL-2017-7434

Spinal anesthesia in a patient with Darier’s disease: A case report

Darier’s Disease (Darier-White Disease, keratosis follicularis) is a rare genodermatosis characterized by keratinisation defects that affects the skin, nails and mucosal membranes; it is autosomal and dominantly inherited. To the best of our knowledge, only one case has been reported regarding spinal anesthesia management in a patient suffering from Darier’s disease—this was during Cesarean section. Here, we describe a case of spinal anesthesia with standard skin preparation for inguinal hernia surgery in a Darier’s patient. Spinal anesthesia is a safe anesthesia choice when administered in lesion-free areas

Validation and implementation of next-generation sequencing in liquid biopsies by a novel NGS platform: Focus on non-small cell lung cancer

Annual Meeting of the American-Association-for-Cancer-Research (AACR) -- APR 14-18, 2018 -- Chicago, ILWOS: 000468819501397…Amer Assoc Canc Re

The Utility of Next-Generation Sequencing for Primary Immunodeficiency Disorders: Experience from a Clinical Diagnostic Laboratory

Introduction. Primary immune deficiency disorders (PIDs) are a group of diseases with profound defects in immune cells. The traditional diagnostics have evolved from clinical evaluation, flow cytometry, western blotting, and Sanger sequencing to focusing on small groups of genes. However, this is not sufficient to confirm the suspicion of certain PIDs. Our innovative approach to diagnostics outlines the algorithm for PIDs and the clinical utility of immunophenotyping with a custom-designed multigene panel. Materials and Methods. We have designed a diagnostic algorithm based on flow cytometry studies to classify the patients; then the selected multigene panel was sequenced. In silico analysis for mutations was carried out using SIFT, Polyphen-2, and MutationTaster. Results and Discussion. The causative mutation was identified in 46% of PIDs. Based on these results, this new algorithm including immune phenotyping and NGS for PIDs was suggested for the clinical use. Conclusions. This study provides a thorough validation of diagnostic algorithm and indicates that still the traditional methods can be used to collect significant information related to design of most current diagnostics. The benefits of such testing are for diagnosis and prevention including the prenatal and preimplantation diagnosis, prognosis, treatment, and research

Effects of GSM-like radiofrequency irradiation during the oogenesis and spermiogenesis of Xenopus laevis

PubMedID: 27017260We aimed to evaluate the effect of GSM-like radiofrequency electromagnetic radiation (RF-EMR) on the oogenesis, and spermiogenesis of Xenopus laevis, and so the development of the embryos obtained from Normal Females+Normal Males (i.e. "N(F)+N(M)"); Normal Females+RF-exposed Males (i.e. "N(F)+RF(M)"); RF-exposed Female+Normal Male (i.e. "RF(F)+N(M)"); and RF-exposed Female+RF-exposed Male (i.e. "RF(F)+RF(M)". Various, assessments were performed to determine potential teratogenic effects and mortality, body growth and behavior on first generation embryos. After exposing adults frogs of both sexes to 900 MHz RF-EMR (at 1.0 W/kg) for 8 h a day over a 5-week period, the embryos' specific energy absorption rate (SAR) was calculated.In our present study (control group; 2.2% abnormal, 0.0% dead); with the N(F)+RF(M) combination, the long-term exposure of adult males to GSM-like radiation at 900 MHz (RF: 2 W) for 5 week/8 h/day resulted in normal, abnormal and dead embryo ratios of 88.3%, 3.3% and 8.3%, respectively (p<0.001). In the RF(F)+N(M) combination, long-term exposure (5 week/8 h/day) of adult females led to normal, abnormal and dead embryo ratios of 76.7%, 11.7%, and 11.7%, respectively (p<0.001). And in the RF(F)+RF(M) combination, long-term exposure (5 week/8 h/day) of both adult males and females led to normal, abnormal and dead embryo ratios of 73.3%, 11.7%, and 15%, respectively (p<0.001).With the exception RF(F)+RF(M) group (p<0.001), no significant changes were observed on body growth (lengths) in comparison to the control group. It was also observed that the offspring of female adult Xenopus exposed to RF-EMR during oogenesis exhibited a more aggressive behavior compared to the control group. Cell phones radiation can thus lead to detrimental effects in humans' male and female reproductive cells. © 2016 Elsevier Inc..This work was supported by the Scientific Research Office of Cukurova University (I.U.BAP) (Project no.: 3817 )

Synthesis of indole-2-carbohydrazides and 2-(indol-2-yl)-1,3,4-oxadiazoles as antioxidants and their acetylcholinesterase inhibition properties

A range of novel 4,6-dimethoxy-1H-indole-2-carbohydrazides was prepared starting from methyl 4,6-dimethoxy-1H-indole-2-carboxylate which underwent cyclodehydration to generate the corresponding 2-(indol-2-yl)-1,3,4-oxadiazole scaffolds in the presence of N,N-diisopropylethylamine and p-toluenesulfonyl chloride in acetonitrile. All novel compounds were fully characterized by H-1 NMR, C-13 NMR, FT-IR, and high-resolution mass spectroscopic data. Biological importance of the designated compounds was identified by employing three different antioxidant property determination assays, namely DPPH free radical scavenging, ABTS cationic radical decolarization, and cupric reducing antioxidant capacity (CUPRAC). The anticholinesterase properties were also evaluated by the acetylcholinesterase and butyrylcholinesterase enzyme inhibition assays. According to the results, the indole compounds possessing carbohydrazide functionality were found to be more promising antioxidant targets than the 2-(indol-2-yl)-1,3,4-oxadiazole systems. N'-Benzoyl-4,6-dimethoxy-1H-indole-2-carbohydrazide, a member of the dimethoxyindole-2-carbohydrazide group, demonstrated a better inhibition performance than the standards. Additionally, extremely important results were obtained in the anticholinesterase enzyme inhibition assays in the case of 2-(indol-2-yl)-1,3,4-oxadiazole derivatives. [GRAPHICS] .Gebze Technical UniversityGebze Teknik University; Dicle UniversityDicle UniversityWe gratefully acknowledge the financial support for this research from Gebze Technical University and Dicle University

Early Transient Neonatal Cyanosis Related to Interatrial Right-to-Left Shunting at an Altitude of 1890 Meters: A Report of Five Cases

Background: We report five term neonates born at an altitude of 1890 meters with transient early neonatal cyanosis due to right-to-left shunting at atrial level through patent foramen ovale. Case Presentation: The five neonates with no clinical sign or symptom other than marked cyanosis were examined in two neonatal units of Erzurum city. Hematologic and radiologic examinations were normal. Partial oxygen pressure (PO2) in the arterial blood samples was lower than 45 mmHg in all of the patients, and did not increase more than 15 mmHg in any of the patients after inhalation of 100% oxygen. Echocardiography revealed normal intracardiac structure. The right-to-left interatrial shunt at diastole was detected through a patent foramen ovale in all of these infants. By only observation with no treatment, diastolic right-to-left shunt disappeared in 40.15±9.52 hours. Oxygen saturation was increased from 69.80±9.55 percent to 90.40±8.80 percent. The patients were discharged from the hospital at 5.6±0.4 days of life. Follow up for 6 months revealed no clinical problem in any of the cases. Conclusion: Transient cyanosis can be seen in the very early neonatal period because of interatrial right-to-left shunting in some healthy term neonates born at an altitude of 1890 meters. Decreased right atrial compliance due to relative hypoxia at that altitude can be speculated to be the causative mechanism

Familial chylomicronemia syndrome related chronic pancreatitis: a single-center study

BACKGROUND: Hypertriglyceridemia induces acute recurrent pancreatitis, but its role in the etiology of chronic pancreatitis (CP) is controversial. This study aimed to evaluate the clinical, laboratory and radiological findings of 7 patients with CP due to type 1 hyperlipidemia compared to CP patients with other or undefined etiological factors

Synthesis, photophysical and antioxidant properties of carbazole-based bis-thiosemicarbazones

Utilizing Schiff base condensation of the 9-ethylcarbazole-3,6-dicarbaldehyde and thiosemicarbazides, four new N-ethylcarbazole-based bis-thiosemicarbazone compounds 4a-d were successfully synthesized in high yields. The photophysical properties of the targeted compounds 4a-d were investigated using UV-vis absorption and fluorescence emission spectroscopy. The antioxidant properties of targeted compounds 4a-d were determined by DPPH radical scavenging, ABTS Cation Radical Decolarization and CUPRAC Cupric Reducing Antioxidant Capacity assay methods. Moreover, the anti-cholinesterase properties of designated compounds were investigated by the Acetylcholinesterase (Ach) and Butyrylcholinesterase (BCh) enzyme inhibition assays. The compound 4a was determined as a valuable candidate to be a potent antioxidant agent for the DPPH and ABTS assays. The compound 4d was found to be a target compound for the kinetic measurements to identify the mechanism of action in the area of anticholinesterase activity assay.Dicle University Scientific Research Project Coordinator (DUBAP Project)Dicle University [ECZ 15.007]I thank the Dicle University Scientific Research Project Coordinator (DUBAP Project Number: ECZ 15.007) for the financial support given to the research project

Synthesis, photophysical and antioxidant properties of pyrrolo[3,2-c]carbazole and dipyrrolo[3,2-c:2,3-g]carbazole compounds

The synthesis of (6-ethyl-1,6-dihydropyrrolo[3,2-c]carbazol-2-yl)methanol 5 and (6-ethyl-6,11-dihydro-1H-dipyrrolo[3,2-c:2,3-g]carbazole-2,10-diyl)dimethanol 6 were achieved via the reduction of methyl pyrrolo carbazole carboxylate 3 and methyl dipyrrolo carbazole carboxylate 4, respectively. The structures of hydroxymethyl-pyrrolocarbazoles 5 and 6 were supported by FT-IR, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, H-1 and C-13 NMR spectroscopy. The photophysical properties of the targeted compounds 3-6 were investigated by employing absorption and fluorescence spectroscopy in different common organic solvents. Also, the fluorescence lifetime ((F)) of the compounds was measured utilizing a time-correlated single-photon counting technique in tetrahydrofuran. Antioxidant activities of compounds 3-6 were determined by employing three different assays, namely DPPH radical scavenging, ABTS cation radical decolarization and cupric reducing antioxidant capacity. The results revealed that the ABTS cationic scavenging activity assay was found to be the most sensitive method for the determination of inhibition values.Research Fund of the Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [113Z159]We thank the Research Fund of the Scientific and Technological Research Council of Turkey (TUBITAK Project Number: 113Z159) for the financial support given to the research project