Person: ALAVANDA, CEREN
Loading...
Email Address
Birth Date
Research Projects
Organizational Units
Job Title
Last Name
ALAVANDA
First Name
CEREN
Name
8 results
Search Results
Now showing 1 - 8 of 8
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 Enostosis in a patient with KBG syndrome caused by a novel missense ANKRD11 variant(2022-07-01) GEÇKİNLİ, BİLGEN BİLGE; ALAVANDA, CEREN; ARMAN, AHMET; GEÇKİNLİ B. B., ALAVANDA C., Ates E. A., Yildirim O., ARMAN A.KBG syndrome (KBGS-OMIM:#148050) is a rare autosomal dominant disease characterized by short stature, intellectual disability, characteristic facies, skeletal anomalies and macrodontia that most commonly affect the permanent upper central incisors. In 2011, Sirmaci et al. (2011) identified heterozygous loss-of-function variants in the ANKRD11 gene on chromosome 16q24.3. So far, more than 150 patients have been reported in the literature. ANKRD11 gene encodes ankyrin repeat domain-containing protein 11 that regulates transcriptional activation (Zhang et al., 2004). Apart from single-nucleotide variations in the ANKRD11 gene, copy number variations on chromosome 16q24.3 can also cause KBG syndrome-like phenotype. In this study, we present a patient with de-novo novel missense variant in ANKRD11 gene. We have also identified skeletal bone enostosis as an additional finding, which is not previously reported.Publication Metadata only Novel splicing mutation in RAB3GAP1 Gene and microduplication of 3q29 in a patient withWarburg Micro syndrome(2020-11-22) GEÇKİNLİ, BİLGEN BİLGE; ALAVANDA, CEREN; ARMAN, AHMET; GEÇKİNLİ B. B., TÜRKYILMAZ A., ALAVANDA C., SAĞER S. G., ARSLAN ATEŞ E., ARMAN A.Publication Metadata only Meckel-Gruber Syndrome: Clinical and Molecular Genetic Profiles in Two Fetuses and Review of the Current Literature(MARY ANN LIEBERT, INC, 2021) ARMAN, AHMET; Turkyilmaz, Ayberk; Geckinli, Bilgen Bilge; Alavanda, Ceren; Ates, Esra Arslan; Buyukbayrak, Esra Esim; Eren, Sirin Funda; Arman, AhmetBackground: Meckel-Gruber syndrome (MKS; OMIM No. 249000) is a rare, in utero lethal disease characterized by occipital encephalocele, polycystic kidneys, and polydactyly. Methodology and Results: In this study, two fetuses diagnosed as having MKS in the prenatal period were evaluated on the basis of ultrasonographic findings, postmortem autopsy findings, and molecular genetic analyses. Using exome sequencing analyses a novel homozygous frameshift variant (NM_015631: c.530delA, p.Lys177Argfs*47) was detected at exon 4 of TCTN3 gene in case 1, and a novel homozygous synonymous variant (NM_025114: c.180G>A, p Lys60Lys) was detected at exon 3 of CEP290 gene in case 2. Case 1 is the first reported case in the literature, which showed the typical MKS clinical feature with a novel frameshift variation in the TCTN3 gene. The variant in case 2 is the first reported synonymous variant of CEP290 gene in the literature, which has been shown to affect splicing in a functional study at the RNA level. Conclusion: TCTN3 gene variants that were rarely associated with the typical MKS phenotype and all cases with these variations have been discussed in the context of genotype-phenotype. The detection of the first synonymous variant of CEP290 gene and the demonstration of its effect on splicing by a functional study are likely to contribute to the molecular etiology of MKS.Publication Metadata only Molecular analysis of MKRN3 gene in Turkish girls with sporadic and familial idiopathic central(2023-03-01) KIRKGÖZ, TARIK; KAYGUSUZ, SARE BETÜL; ALAVANDA, CEREN; GÜRPINAR TOSUN, BUŞRA; ELTAN, MEHMET; SEVEN MENEVŞE, TUBA; GÜRAN, TÜLAY; ARMAN, AHMET; DEMİRCİOĞLU, SERAP; BEREKET, ABDULLAH; KIRKGÖZ T., KAYGUSUZ S. B., ALAVANDA C., Helvacioglu D., Abali Z. Y., GÜRPINAR TOSUN B., ELTAN M., SEVEN MENEVŞE T., GÜRAN T., ARMAN A., et al.Objectives: Central precocious puberty (CPP) develops as a result of early stimulation of the hypothalamic-pituitary-gonadal (HPG) axis. The loss-of-function mutations in the Makorin-ring-finger3 (MKRN3) gene appear to be the most common molecular cause of familial CPP. We aimed to identify MKRN3 gene mutations in our CPP cohort and to investigate the frequency of MKRN3 mutations.Methods: 102 patients with CPP included. 53 of them had family history of CPP in the first and/or second-degree relatives. MKRN3 gene was analyzed by next-generation sequencing.Results: Possible pathogenic variants were found in 2/53 patients with family history of CPP (3.8%) and 1/49 patient without family history (2%). A novel heterozygous c.1A > G (p.Met1Val) mutation, a novel heterozygous c.683_684delCA (p.Ser228*) and a previously reported c.482dupC (Ala162Glyfs*) frameshift variations were detected. The two novel variants are predicted to be pathogenic in silico analyses.Conclusions: In our cohort, possible pathogenic variants in MKRN3 gene were detected in 2.9% of the total cohort, 3.8% of the familial and 2% of the nonfamilial cases, slightly lower than that reported in the literature. Two novel variants detected contribute to the molecular repertoire of MKRN3 defects in CPP. Classical pattern of paternal inheritance has been demonstrated in all three cases. However, the father of the patient 3 did not have history of CPP suggesting that the father inherited this variant from his mother and had phenotype skipping. Therefore, we emphasize that the absence of history of CPP in the father does not exclude the possibility of a MKRN3 mutation.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 FGF3 related phenotypes : A study of lamm syndrome and otodental dysplasia patients with two novel mutations in FGF3 genee(2020-08-01) GEÇKİNLİ, BİLGEN BİLGE; ALAVANDA, CEREN; ARMAN, AHMET; TÜRKYILMAZ A., GEÇKİNLİ B. B., ALAVANDA C., ZENGİN G., ARSLAN ATEŞ E., ARMAN A.The fibroblast growth factor (FGF) signaling pathway regulates the intracellular events which are involved in the proper formation of the internal organs and limbs during the earliest stages of embryonic development. Here, the researchers performed a detailed examination of clinical and radiological findings from syndromic cases with sensorineural hearing loss and determined their molecular genetic etiology. Family history, physical examination, laboratory and radiological examinations for three Turkish families displaying congenital sensorineural hearing loss, microtia, dental anomalies and neuromotor developmental delay were evaluated and molecular analysis of the FGF3 gene was performed. The researchers detected a heterozygous deletion of a 2.4 Megabase (Mb) segment in the region spanning 68,734,891 to 71,538,481 bases in the chromosome 11q13.3-q13.4. Interestingly, this region included the FGF3 gene in case 1, whereas two novel mutations (NM_005247: c.8T>G, p.Leu3Arg, NM_005247: c.324+2T>C) were identified in case 2 and case 3 respectively. From this study, the researchers conclude that in the absence of inner ear structures in cases of syndromic hearing loss, FGF3 gene related phenotypes should be considered and the FGF3 gene should be examined by sequence analysis and array-CGH methods for both point mutations and gross deletions.