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    A case report: 13q21-qter deletion with digital anomalies, duodenal atresia and anal atresia
    (Springer, 2015) Ozen, Yasemin; Gurkan, Hakan; Ozbek, Ulfet Vatansever; Atli, Emine Ikbal; Eker, Damla; Acunas, Betul
    [Abstract Not Available]
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    Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders
    (Turkish Neuropsychiatry Assoc-Turk Noropsikiyatri Dernegi, 2020) Gurkan, Hakan; Atli, Emine Ikbal; Atli, Engin; Bozatli, Leyla; Altay, Menguhan Araz; Yalcintepe, Sinem; Ozen, Yasemin
    Introduction: Aneuploids, copy number variations (CNVs), and single nucleotide variants in specific genes are the main genetic causes of developmental delay (DD) and intellectual disability disorder (IDD). These genetic changes can be detected using chromosome analysis, chromosomal microarray (CMA), and next-generation DNA sequencing techniques. Therefore; In this study, we aimed to investigate the importance of CMA in determining the genomic etiology of unexplained DD and IDD in 123 patients. Method: For 123 patients, chromosome analysis, DNA fragment analysis and microarray were performed. Conventional G-band karyotype analysis from peripheral blood was performed as part of the initial screening tests. FMR1 gene CGG repeat number and methylation analysis were carried out to exclude fragile X syndrome. Results: CMA analysis was performed in 123 unexplained IDD/DD patients with normal karyotypes and fragile X screening, which were evaluated by conventional cytogenetics. Forty-four CNVs were detected in 39 (39/123=31.7%) patients. Twelve CNV variant of unknown significance (VUS) (9.75%) patients and 7 CNV benign (5.69%) patients were reported. In 6 patients, one or more pathogenic CNVs were determined. Therefore, the diagnostic efficiency of CMA was found to be 31.7% (39/123). Conclusion: Today, genetic analysis is still not part of the routine in the evaluation of IDD patients who present to psychiatry clinics. A genetic diagnosis from CMA can eliminate genetic question marks and thus alter the clinical management of patients. Approximately one-third of the positive CMA findings are clinically intervenable. However, the emergence of CNVs as important risk factors for multiple disorders increases the need for individuals with comorbid neurodevelopmental conditions to be the priority where the CMA test is recommended.
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    Genotype-phenotype correlations of pathogenic copy number variations on X chromosome detected by comparative genomic hybridization
    (Elsevier, 2022) Yalcintepe, Sinem; Atli, Engin; Atli, Emine Ikbal; Demir, Selma; Ozen, Yasemin; Mail, Cisem; Gurkan, Hakan
    The aim of this study was to present genotype-phenotype correlations of pathogenic copy number variations (CNVs) on X chromosome. Clinical and microarray data of the cases were collected. Conventional cytogenetics and CytoSure 4x180K oligonucleotide array (Agilent Technologies, Inc.) (Comparative Genomic Hybridization - CGH) was applicated to all cases. Molecular and clinical characterisation of these CNVs was performed in this study. 18 cases were included in this study for having a pathogenic CNV on X chromosome. The changes were reported pathologically by evaluating break points, anomaly size, number of involved genes and their functions and phenotypic correlations. 16 cases with pathogenic CNVs of X chromosome were examined with the clinical findings of multiple congenital anomalies, mental retardation, eosophageal atresia, duodenal atresia, autism spectrum disorder, hypogonadotropic hypogonadism, dysmorphic features, muscular dystrophy, hydrocephaly, neuromotor growth retardation, trigonocephaly, high risk of prenatal screening test, recurrent pregnancy loss with reciprocal translocation, fetal loss with multiple congenital anomalies. 2 cases were diagnosed as Turner Syndrome with rare karyotypes and array-CGH results. Our study contributes to the genotype/phenotype correlation with the delineation of laboratory criteria which help to classify the different CNVs detected on X chromosome. Atypical microdeletions/duplications allowed us to define minimal critical regions that could be responsible for specific clinical findings of the syndromes and to highlight some genes.
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    Homozygous Paternally Inherited ASPA Variant in a Patient with Canavan Disease
    (Karger, 2024) Yalcintepe, Sinem; Maras, Tuba; Kizilyar, Ilke; Guler, Hazal Sezginer; Zhuri, Drenushe; Atli, Engin; Ozen, Yasemin
    Introduction: Canavan disease is an autosomal recessive disorder that causes accumulation of N-acetyl ASPArtic acid in the brain due to ASPArtoacylase deficiency with homozygous or compound heterozygous pathogenic variants in the ASPA gene located on the short arm of chromosome 17. Clinical findings are hypotonia, progressive macrocephaly, deafness, nystagmus, blindness, and brain atrophy. Case Presentation: A one-year-old female case was evaluated in our medical genetics clinic for hypotonia, nystagmus, and strabismus. Chromosome analysis and array-comparative genomic hybridization showed no pathology. Clinical exome sequencing by next-generation sequencing was performed and a homozygous likely pathogenic variant NM_000049.4(ASPA):c.857C > A p.(Ala286Asp) was identified. Sanger sequencing of the parents showed that the index case had a homozygous genotype, the father was heterozygous and the mother had a wild genotype for the identified variant in ASPA. A single nucleotide polymorphism (SNP) array test was planned for the family to explain this homozygosity and a loss of maternal heterozygosity was determined in the 17p13.3-p13.2 region of the ASPA gene. Conclusion: In this report, we aimed to present the first case of Canavan disease with maternal loss of heterozygosity in the ASPA gene. (c) 2024 S. Karger AG, Basel
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    Investigation of Genetic Alterations in Congenital Heart Diseases in Prenatal Period
    (Thieme Medical Publ Inc, 2022) Atli, Emine Ikbal; Atli, Engin; Yalcintepe, Sinem; Demir, Selma; Kalkan, Rasime; Akurut, Cisem; Ozen, Yasemin
    The prenatal diagnosis of congenital heart disease (CHD) is important because of mortality risk. The onset of CHD varies, and depending on the malformation type, the risk of aneuploidy is changed. To identify possible genetic alterations in CHD, G-banding, chromosomal microarray or if needed DNA mutation analysis and direct sequence analysis should be planned. In present study, to identify genetic alterations, cell culture, karyotype analysis, and single nucleotide polymorphism, array analyses were conducted on a total 950 samples. Interventional prenatal genetic examination was performed on 23 (2, 4%, 23/950) fetal CHD cases. Chromosomal abnormalities were detected in 5 out of 23 cases (21, 7%). Detected chromosomal abnormalities were 10q23.2 deletion, trisomy 18, 8p22.3-p23.2 deletion, 8q21.3-q24.3 duplication, 11q24.2q24.5 (9Mb) deletion, and 8p22p12 (16.8Mb) deletion. Our study highlights the importance of genetic testing in CHD.
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    A Pilot Study about Clinical Features of Aberrations Chromosome 22q
    (Thieme Medical Publ Inc, 2022) Atli, Emine Ikbal; Atli, Engin; Yalcintepe, Sinem; Demir, Selma; Mail, Cisem; Eker, Damla; Ozen, Yasemin
    Objective A significant number of genetic variations have been identified in chromosome 22, using molecular genetic techniques. Various genomic disorders on chromosome 22, including cat's eye syndrome caused by extra copies of the proximal region of the 22q chromosome, are now well-defined. Our aim in the study was to show phenotypic variability associated with rearrangements of the 22q chromosomal region. Methods We focused our study on clinical aspects of these disorders, including genetic testing, genotype-phenotype correlation, and potential treatments. A total of 998 patients were referred for genetic analysis (Karyotyping, MLPA, array-CGH) during January 2015 to February 2020 because of intellectual deficiency, behavior issues, and/or multiple congenital abnormalities in several genetics departments. Informed consent was obtained from all the patients and/or their parents. Results 22q11.21 or 22q13.33 microdeletions and 22q11.22-q11.23 microduplication were identified in 31 patients out of referrals. The 22q aberrations were detected in 31/998 patients, giving a prevalence of 3.1%. In this study, 18 patients with 22q11.2 (LCR22A-H) deletion, three patients with 22q13.31 deletion, 9 patients with 22q11.2 duplication and one patient with 22q13.31 duplication were identified. We report on the clinical and molecular characterization of 31 individuals with distal deletions and duplications of chromosome 22q. Conclusions The current study demonstrated in the largest postnatal case series reporting the whole spectrum of atypical phenotypic and genotypic variations at 22q. We believe that when all the phenotypic differences are taken into account, various anomalies including developmental delay and intellectual disability might be considered as an indication to search for aberrations of 22q along with congenital heart diseases.