Araştırma Çıktıları
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Item DNA Fragmentation Simulation Method (FSM) and Fragment Size Matching Improve aCGH Performance of FFPE Tissues(PUBLIC LIBRARY SCIENCE, 2012-01-01) Craig, Justin M.; Vena, Natalie; Ramkissoon, Shakti; Idbaih, Ahmed; Fouse, Shaun D.; Ozek, Memet; Sav, Aydin; Hill, D. Ashley; Margraf, Linda R.; Eberhart, Charles G.; Kieran, Mark W.; Norden, Andrew D.; Wen, Patrick Y.; Loda, Massimo; Santagata, Sandro; Ligon, Keith L.; Ligon, Azra H.Whole-genome copy number analysis platforms, such as array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) arrays, are transformative research discovery tools. In cancer, the identification of genomic aberrations with these approaches has generated important diagnostic and prognostic markers, and critical therapeutic targets. While robust for basic research studies, reliable whole-genome copy number analysis has been unsuccessful in routine clinical practice due to a number of technical limitations. Most important, aCGH results have been suboptimal because of the poor integrity of DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues. Using self-hybridizations of a single DNA sample we observed that aCGH performance is significantly improved by accurate DNA size determination and the matching of test and reference DNA samples so that both possess similar fragment sizes. Based on this observation, we developed a novel DNA fragmentation simulation method (FSM) that allows customized tailoring of the fragment sizes of test and reference samples, thereby lowering array failure rates. To validate our methods, we combined FSM with Universal Linkage System (ULS) labeling to study a cohort of 200 tumor samples using Agilent 1 M feature arrays. Results from FFPE samples were equivalent to results from fresh samples and those available through the glioblastoma Cancer Genome Atlas (TCGA). This study demonstrates that rigorous control of DNA fragment size improves aCGH performance. This methodological advance will permit the routine analysis of FFPE tumor samples for clinical trials and in daily clinical practice.Item Expression profiles of 151 pediatric low-grade gliomas reveal molecular differences associated with location and histological subtype(OXFORD UNIV PRESS INC, 2015-01-01) Bergthold, Guillaume; Bandopadhayay, Pratiti; Hoshida, Yujin; Ramkissoon, Shakti; Ramkissoon, Lori; Rich, Benjamin; Maire, Cecile L.; Paolella, Brenton R.; Schumacher, Steven E.; Tabak, Barbara; Ferrer-Luna, Ruben; Ozek, Memet; Sav, Aydin; Santagata, Sandro; Wen, Patrick Yung; Goumnerova, Liliana C.; Ligon, Azra H.; Stiles, Charles; Segal, Rosalind; Golub, Todd; Grill, Jacques; Ligon, Keith L.; Chan, Jennifer A.; Kieran, Mark W.; Beroukhim, RameenPediatric low-grade gliomas (PLGGs), the most frequent pediatric brain tumor, comprise a heterogeneous group of diseases. Recent genomic analyses suggest that these tumors are mostly driven by mitogene-activated protein kinase (MAPK) pathway alterations. However, little is known about the molecular characteristics inherent to their clinical and histological heterogeneity. We performed gene expression profiling on 151 paraffin-embedded PLGGs from different locations, ages, and histologies. Using unsupervised and supervised analyses, we compared molecular features with age, location, histology, and BRAF genomic status. We compared molecular differences with normal pediatric brain expression profiles to observe whether those patterns were mirrored in normal brain. Unsupervised clustering distinguished 3 molecular groups that correlated with location in the brain and histological subtype. ``Not otherwise specified{''} (NOS) tumors did not constitute a unified class. Supratentorial pilocytic astrocytomas (PAs) were significantly enriched with genes involved in pathways related to inflammatory activity compared with infratentorial tumors. Differences based on tumor location were not mirrored in location-dependent differences in expression within normal brain tissue. We identified significant differences between supratentorial PAs and diffuse astrocytomas as well as between supratentorial PAs and dysembryoplastic neuroepithelial tumors but not between supratentorial PAs and gangliogliomas. Similar expression patterns were observed between childhood and adolescent PAs. We identified differences between BRAF-duplicated and V600E-mutated tumors but not between primary and recurrent PLGGs. Expression profiling of PLGGs reveals significant differences associated with tumor location, histology, and BRAF genomic status. Supratentorial PAs, in particular, are enriched in inflammatory pathways that appear to be tumor-related.Item Detection of KIAA1549-BRAF Fusion Transcripts in Formalin-Fixed Paraffin-Embedded Pediatric Low-Grade Gliomas(ELSEVIER SCIENCE INC, 2011-01-01) Tian, Yongji; Rich, Benjamin E.; Vena, Natalie; Craig, Justin M.; MacConaill, Laura E.; Rajaram, Veena; Goldman, Stewart; Taha, Hala; Mahmoud, Madeha; Ozek, Memet; Sav, Aydin; Longtine, Janina A.; Lindeman, Neal I.; Garraway, Levi A.; Ligon, Azra H.; Stiles, Charles D.; Santagata, Sandra; Chan, Jennifer A.; Kieran, Mark W.; Ligon, Keith L.Alterations of BRAF are the most common known genetic aberrations in pediatric gliomas. They frequently are found in pilocytic astrocytomas, where genomic duplications involving BRAF and the poorly characterized gene KIAA1549 create fusion proteins with constitutive B-Raf kinase activity. BRAF V600E point mutations are less common and generally occur in nonpilocytic tumors. The development of BRAF inhibitors as drugs has created an urgent need for robust clinical assays to identify activating lesions in BRAF. KIAA1549-BRAF fusion transcripts have been detected in frozen tissue, however, methods for FFPE tissue have not been reported. We developed a panel of FFPE-compatible quantitative RT-PCR assays for the most common KIAA1549-BRAF fusion transcripts. Application of these assays to a collection of 51 low-grade pediatric gliomas showed 97\% sensitivity and 91\% specificity compared with fluorescence in situ hybridization or array comparative genomic hybridization. In parallel, we assayed samples for the presence of the BRAF V600E mutation by PCR pyrosequencing. The data further support previous observations that these two alterations of the BRAF, KIAA1549 fusions and V600E point mutations, are associated primarily with pilocytic astrocytomas and nonpilocytic gliomas, respectively. These results show that fusion transcripts and mutations can be detected reliably in standard FFPE specimens and may be useful for incorporation into future studies of pediatric gliomas in basic science or clinical trials. (J Mal Diagn 2011, 13:669-677Item The Acute and Delayed Effects of Vagal Nerve Stimulation on an Absence Epilepsy Model in WAG/Rij(TURKISH NEUROSURGICAL SOC, 2016-01-01) Uyar, Ramazan; Turk, Cezmi Cagri; Isik, Nejat; Kalelioglu, Mufit; Onat, Filiz; Ozek, MemetAIM: Vagal nerve stimulation (VNS) is an effective method of treatment for epilepsy patients either unresponsive to medical therapy or not suitable for resective surgeries. We designed an experimental study on Wistar Albino Glaxo rats from Rijswijk (WAG\textbackslash{}Rij) to investigate the effects of VNS on a non-convulsive epilepsy model. MATERIAL and METHODS: The experiment was performed on six WAG/Rij rats, a validated strain for genetic absence seizures. The animals were underwent VNS and the effects were investigated on electroencephalography (EEG) recordings at 22, 24, 26 hours of stimulation and 15 days after the cessation, for duration of spike and wave complexes (SWC), the numbers, mean duration of SWC and frequencies in an hour. RESULTS: EEG recordings demonstrated that the mean duration of SWC was 353.1 seconds and the number of activity per hour was 62 at the baseline. There were statistically significant decreases in the total duration of SWC and the number of activities (61.8\% and 78\% decrease, respectively). There were no significant decreases in the mean duration of SWC and the frequencies. CONCLUSION: The acute stimulation of the vagal nerve caused a statistically significant decrease both in overall duration of SWC and the number of complexes in an hour. Moreover, the positive effects seemed to last even 15 days after the cessation of the stimulation. Further studies focusing on different stimulation parameters and delayed effects of the VNS on human absence seizures are warranted.Item Urodynamic Findings in Children with Cerebral Palsy Before Dorsal Rhizotomy Surgery(GALENOS YAYINCILIK, 2021-01-01) Tanidir, Yiloren; Ozgen, Mahir Bulent; Ozek, Memet; Tarcan, TufanObjective: This study aims to investigate the neurourological and urodynamic findings of children with cerebral palsy (CP) that referred for dorsal rhizotomy surgery (DRS). Materials and Methods: All children with CP who were scheduled for selective DRS were assessed with a detailed medical history, physical exam, urinalysis and urodynamic studies to assess bladder function and urinary problems. Urodynamic studies included filling and voiding cystometry, detrusor leak point pressure, external anal sphincter electromyography, flow rate and residual urine volume. All investigations and definitions relied on the standardisation of the International Continence Society. Results: Overall, 24 boys and 10 girls were evaluated. The mean age of boys, and girls and the study group was 6.6 (1.7-9.8), 6.5 (3.5-11.4) and 6.6 (1.7-11.4) years, respectively. The most common complaints of the study group were urinary incontinence (58.8\%), encopresis (32.4\%) and constipation (17.6\%) and 41.2\% of patients needed diapers due to these problems. Twenty-five per cent (n=5) of male patients had an undescended testis. The most common clinical conditions at urodynamics, were low bladder compliance (85.3\%), detrusor overactivity (67.6\%), hyposensitive bladder (52.6\%) and low bladder capacity (41.2\%). Conclusion: Upper motor neuron lesions, like CP, may present with various urodynamic findings. However, patients with CP are not routinely seen by urologists. Our findings revealed serious neurological problems in children referred for DRS. Therefore, every child with CP who has a DRS plan should undergo a detailed urological examination at least once before the procedure.