Person: ATA, PINAR
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ATA
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PINAR
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Publication Metadata only The use of long-range pcr protocol in the diagnosis of friedreich ataxia(2020-11-22) ALAVANDA, CEREN; POLAT, HAMZA; SÖYLEMEZ, MEHMET ALİ; GEÇKİNLİ, BİLGEN BİLGE; ATA, PINAR; ARMAN, AHMET; ALAVANDA C., POLAT H., DEMİR Ş., ARSLAN ATEŞ E., SÖYLEMEZ M. A., GEÇKİNLİ B. B., ATA P., ARMAN A.Introduction: Friedreich ataxia(FRDA) is multisystemic disorder characterized by trinucleotide expansions in FXN gene. It’s one of the most common causes of autosomal recessive ataxia. Material/Method: Fragment analysis method was used to detect GAA triple nucleotide repeat expansions in the first intron of the FXN gene. Long-range PCR was performed with primers selected from both in intron and exon for confirmation in patients with more than two hundred repeats. Results: Fragment analysis was performed in 20 patients with FRDA pre-diagnosis. Long-range PCR was performed in 5 patients with more than 200 GAA repeats. After long-range PCR, the number of repetitions between 180 and 1450 was found in these patients. One allele of two siblings whose fragment analysis gave negative results was found to have an approximately 950 repeats. FXN gene sequence analysis was planned in order not to miss point mutations in patients with negative results. In order to provide appropriate genetic counseling to patients, segregation studies are continuing. Discussion: Although fragment analysis is reliable method in this disease, its reliability decreases when the number of repeats is high. Although Southern-blot method can be used for confirmation, long-range PCR protocols which are cheaper and easier, can also be applied.Publication Metadata only Does Genotype-Phenotype Correlation Exist in Vitamin D-Dependent Rickets Type IA: Report of 13 New Cases and Review of the Literature(SPRINGER, 2021) BEREKET, ABDULLAH; Kaygusuz, Sare Betul; Alavanda, Ceren; Kirkgoz, Tarik; Eltan, Mehmet; Yavas Abali, Zehra; Helvacioglu, Didem; Guran, Tulay; Ata, Pinar; Bereket, Abdullah; Turan, SerapVitamin D-dependent rickets type IA (VDDR-IA) is caused by biallelic mutations in CYP27B1. Data regarding genotype-phenotype correlation in VDDR-IA are scarce. Here, we aimed to investigate clinical/genotypic features and long-term follow-up of 13 new cases with VDDR-IA and genotype-phenotype correlation of reported cases in the literature. Thirteen patients with VDDR-IA were evaluated. Eight patients had reached their final height at the time of the study and, for whom, long-term outcome data were analyzed. Further, all VDDR-IA patients in the literature (n:183) were analyzed and clinical-genetic features were recorded. The median age of diagnosis was 2.55 +/- 1.13 (1.0-12) years. Initial diagnoses before referral to our clinic were nutritional rickets (n:7), hypophosphatemic rickets (n:2), and pseudohypoparathyroidism (n:1). All had biochemical evidence suggestive of VDDR-IA; except one with elevated 1,25(OH)(2)D3 and another with hyperphosphatemia, in whom pseudohypoparathyroidism was excluded with molecular tests. Combined analyses of our cohort and other series in the literature demonstrated that three most common CYP27B1 mutations are p.F443Pfs*24, c.195 + 2T > G, and p.V88Wfs*71. In Turkish population, p.K192E mutation along with the former two is the most common mutations. Comparison of clinical features demonstrated that c.195 + 2T > G mutation causes the most severe and p.K192E mutation causes the least severe phenotype with respect to age and height at presentation and calcitriol requirement. We found a clear genotype-phenotype correlation in VDDR-IA, notably CYP27B1 intronic c.195 + 2T > G mutation causes a more severe phenotype with lower height SDS at presentation and, higher calcitriol requirement, while less severe phenotype occurs in p.K192E mutation.Publication Metadata only The Spectrum of Low-Density Lipoprotein Receptor Mutations in a Large Turkish Cohort of Patients with Familial Hypercholesterolemia(MARY ANN LIEBERT, INC, 2021) ALAVANDA, CEREN; Turkyilmaz, Ayberk; Kurnaz, Erdal; Alavanda, Ceren; Yarali, Oguzhan; Kartal Baykan, Emine; Yavuz, Dilek; Cayir, Atilla; Ata, PinarBackground: Monogenic hypercholesterolemia with Mendelian inheritance is a heterogeneous group of diseases that are characterized by elevated plasma low-density lipoprotein cholesterol (LDL-C) levels, and the most common form of this disorder is autosomal-dominant familial hypercholesterolemia (FH). Methods: A total of 104 index cases with the clinical diagnosis of FH were included in this study. Low-density lipoprotein receptor (LDLR) was sequenced using the Sanger sequencing method. Results: Pathogenic/likely pathogenic variants were detected in LDLR in 55 of the 104 cases (mutation detection rate = 52.8%). Thirty different variants were detected in LDLR, three of which were novel. The total cholesterol and LDL-C values of the patients in the group of premature termination codon (PTC) mutation carriers were significantly higher than those of the patients in the group of non-PTC mutation carriers. A total of 87 patients (17 pediatric and 70 adult cases) were diagnosed with cascade genetic screening. Statin treatment was recommended to all 87 patients and was accepted and initiated in 70 of these patients. Conclusions: This study is the largest patient cohort that evaluated FH cases in the Turkish population. Herein, we revealed the LDLR mutation spectrum for a Turkish population and compared the cases in the context of genotype-phenotype correlation. Genetic screening of individuals with suspected FH not only helps to establish their diagnosis, but also facilitates early diagnosis and treatment initiation in other family members through cascade screening.Publication Metadata only Clinical spectrum of cubulin mutations(2022-11-01) ALPAY, HARİKA; DEMİRCİ BODUR, ECE; ALAVANDA, CEREN; YILDIZ, NURDAN; ATA, PINAR; GÖKCE, İBRAHİM; Cicek N., ALPAY H., Guven S., Turkkan O. N. , Polat S., DEMİRCİ BODUR E., ALAVANDA C., YILDIZ N., ATA P., GÖKCE İ.Publication Metadata only Secondary findings in 622 Turkish clinical exome sequencing data(SPRINGERNATURE, 2021) ARMAN, AHMET; Ates, Esra Arslan; Turkyilmaz, Ayberk; Yildirim, Ozlem; Alavanda, Ceren; Polat, Hamza; Demir, Senol; Cebi, Alper Han; Geckinli, Bilgen Bilge; Guney, Ahmet Ilter; Ata, Pinar; Arman, AhmetCES (Clinical Exome Sequencing) is a method that we use to diagnose rare diseases with nonspesific clinical features. Besides primary indication for testing genetic information may be detected about diseases which have not yet emerged. ACMG guidelines recommend to report pathogenic variations in medically actionable 59 genes. In this study we evaluated CES data of 622 cases which were tested for various indications. According to ACMG recommendations 59 genes were screened for reportable variations. The detected variations were reviewed using distinct databases and ACMG variation classification guidelines. Among 622 cases 13 (2.1%) had reportable variations including oncogenetic, cardiogenetic disorders, and malignant hyperthermia susceptibility-related genes. In 15 cases (2.4%) heterozygous pathogenic and likely pathogenic variations were detected in genes showing autosomal recessive inheritance. Ten novel variations causing truncated protein or splicing defect were reported. We detected 11 variations having conflicting interpretations in databases and 30 novel variations, predicted as likely pathogenic via insilico analysis tools which further evaluations are needed. As to our knowledge this is the first study investigating secondary findings in Turkish population. To extract the information that may lead to prevent severe morbidities and mortalities from big data is a valuable and lifesaving effort. Results of this study will contrbute to existing knowledge about secondary findings in exome sequencing and will be a pioneer for studies in Turkish population.Publication Metadata only Whole-exome sequencing reveals new potential genes and variants in patients with premature ovarian insufficiency(SPRINGER/PLENUM PUBLISHERS, 2022) ARMAN, AHMET; Turkyilmaz, Ayberk; Alavanda, Ceren; Ates, Esra Arslan; Geckinli, Bilgen Bilge; Polat, Hamza; Gokcu, Mehmet; Karakaya, Taner; Cebi, Alper Han; Soylemez, Mehmet Ali; Guney, Ahmet Ilter; Ata, Pinar; Arman, AhmetPurpose Premature ovarian insufficiency (POI) is a heterogeneous disorder characterized by the cessation of menstrual cycles before the age of 40 years due to the depletion or dysfunction of the ovarian follicles. POI is a highly heterogeneous disease in terms of etiology. The aim of this study is to reveal the genetic etiology in POI patients. Methods A total of 35 patients (mean age: 27.2 years) from 28 different families diagnosed with POI were included in the study. Karyotype, FMR1 premutation analysis, single nucleotide polymorphism (SNP) array, and whole-exome sequencing (WES) were conducted to determine the genetic etiology of patients. Results A total of 35 patients with POI were first evaluated by karyotype analysis, and chromosomal anomaly was detected in three (8.5%) and FMR1 premutation was detected in six patients (17%) from two different families. A total of 29 patients without FMR1 premutation were included in the SNP array analysis, and one patient had a 337-kb deletion in the chromosome 6q26 region including PARK2 gene, which was thought to be associated with POI. Twenty-nine cases included in SNP array analysis were evaluated simultaneously with WES analysis, and genetic variant was detected in 55.1% (16/29). Conclusion In the present study, rare novel variants were identified in genes known to be associated with POI, which contribute to the mutation spectrum. The effects of detected novel genes and variations on different pathways such as gonadal development, meiosis and DNA repair, or metabolism need to be investigated by experimental studies. Molecular etiology allows accurate genetic counseling to the patient and family as well as fertility planning.Publication Metadata only Etiological analysis of hypophosphatemia: A single-center experience(2022-09-01) ELTAN, MEHMET; ALAVANDA, CEREN; ATA, PINAR; GÜRAN, TÜLAY; DEMİRCİOĞLU, SERAP; BEREKET, ABDULLAH; Eltan M., Alavanda C., Abali Z. Y. , Bayramoglu E., Kaygusuz S. B. , Helvacioglu D., Tosun B. G. , Menevse T. S. , Ata P., Guran T., et al.Publication Metadata only Genetıc tests ın non-neurogenıc neurogenıc bladder: two sıblıngs wıth ochoa syndrome(2022-11-01) GÖKCE, İBRAHİM; ALAVANDA, CEREN; ŞEKERCİ, ÇAĞRI AKIN; DEMİRCİ BODUR, ECE; YILDIZ, NURDAN; YÜCEL, SELÇUK; ATA, PINAR; ALPAY, HARİKA; Pul S., GÖKCE İ., ALAVANDA C., ŞEKERCİ Ç. A. , DEMİRCİ BODUR E., Turkkan O. N. , Guven S., Cicek N., YILDIZ N., YÜCEL S., et al.