Sümeyra Oğuz

Zeynep Kamil Hospital

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Gülen Eda Ütine

Hacettepe University

PÖ

Pelin Özlem Şimşek‐Kiper

Hacettepe University

Mehmet Alikaşifoğlu

Hacettepe University

Koray Boduroğlu

Hacettepe University

GÜ

Gizem Ürel Demir

Hacettepe University

Ekim Z. Taşkıran

Hacettepe University

Gizem Elif Dizdaroğulları

Zeynep Kamil Hospital

ŞY

Şule Yiğit

İstanbul Galata Üniversitesi

Ayfer Alikaşifoğlu

Hacettepe University

Naz Güleray-Lafcı

Hacettepe University

Cooperative Institutions

Hacettepe University

Sağlık Bilimleri Üniversitesi

Pediatrics and Genetics

Hacettepe University Hospital

Zeynep Kamil Hospital

University of Health Science

Boston Children's Hospital

Ankara University

Ministry of Health

Dr Lütfi Kırdar Kartal Eğitim ve Araştırma Hastanesi

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A very rare case of a newborn with tetrasomy 9p and literature review

The Turkish Journal of Pediatrics (2022)

Merve Süleyman Sümeyra Oğuz Gözdem Kaykı Hasan Tolga Çelik Pelin Özlem Şimşek‐Kiper

Tetrasomy 9p is a rare genetic condition which usually results from a supernumerary isochromosome derived from the short arm of chromosome 9. Phenotypic findings include multiple congenital anomalies, facial dysmorphism, growth and developmental delays, and also vary according to the presence and degree of mosaicism.We report on a newborn with tetrasomy 9p who deceased in the newborn period. She had facial features including low-set and anteverted ears, hypertelorism, prominent nasal bridge, and microretrognathia. Bilateral ventriculomegaly, vermian hypoplasia and corpus callosum agenesis were detected on magnetic resonance imaging and double outlet right ventricle (tetralogy of Fallot type), secundum atrial septal defect, and persistent left superior vena cava were displayed by echocardiography. Microarray analysis revealed 38,584 kb tetrasomic region at 9p24.3p13.1. We also present a review of the literature suggesting that there is a recognizable phenotype for this condition and an assessment of cardiac manifestations based on the size and the localization of the breakpoints.We conclude that cardiac manifestations do not differ according to the localization of the breakpoint. Persistent left superior vena cava seems to be consistent with breakpoints distal to q12, but the present case is different from them by breakpoint p13.1.

Tetrasomy

Septum secundum

Breakpoint

Isochromosome

Corpus Callosum Agenesis

Trigonocephaly

Cerebellar hypoplasia (non-human)

Ventriculomegaly

10.24953/turkjped.2021.685

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Citations (2)

Advantages and limitations of QF-PCR analysis in invasive prenatal genetic diagnosis: a tertiary center experience from Turkey

Perinatal Journal (2022)

Münip Akalın Oya Demirci Gizem Elif Dizdaroğulları Erman Çiftçi Sümeyra Oğuz

Objective: The aim of this study was to investigate the success and reliability of QF-PCR analysis in detecting chromosomal abnormalities and to determine its advantages and limitations. Methods: Patients who underwent karyotype and QF-PCR analysis as a prenatal invasive diagnostic test in a tertiary center were retrospectively analyzed. Invasive genetic test indications, ultrasonographic fetal screening reports, karyotype and QF-PCR analysis results of the patients were obtained from the electronic data system. Karyotypes were classified as normal, common aneuploidies (trisomies 21, 18, 13, and sex chromosome aneuploidies) and other aneuploidies. QF-PCR analysis and karyotype results were compared for inconsistency. Results: A total of 426 cases (41 [9.6%] chorionic villus sampling, 339 [79.6%] amniocentesis and 46 [10.8%] cordocentesis) were included in the study. The most common indication for prenatal invasive diagnostic testing was fetal structural anomalies (36.7%). Aneuploidy was detected in 61 (14.3%) of the fetuses. Fifty-nine (96.7%) of 61 fetuses with aneuploidy were common aneuploidies. The sensitivity and specificity of the QF-PCR analysis in detecting common aneuploidies was 100%. QF-PCR analysis was indicative if not diagnostic in all fetuses with mosaic trisomy or sex chromosome aneuploidies. Conclusion: QF-PCR analysis is a rapid, robust, and reliable test for the prenatal detection of common aneuploidies. Although QF-PCR analysis has high sensitivity and specificity in detecting common aneuploidies, it should be used for rapid preliminary information and the result of karyotype analysis should be awaited for important clinical decisions.

Amniocentesis

Chorionic villus sampling

Trisomy

Advanced maternal age

10.2399/prn.22.0303002

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A Revisited Diagnosis of Collagen VI Related Muscular Dystrophy in a Patient with a Novel COL6A2 Variant and 21q22.3 Deletion

Neuropediatrics (2020)

Pelin Özlem Şimşek‐Kiper Sümeyra Oğuz Fatma Bilge Ergen Gülen Eda Ütine Mehmet Alikaşifoğlu

Abstract The genetic etiology of collagen VI related muscular dystrophies is heterogenous. Genomic deletions in one allele involving COL6A2 or both COL6A1 and COL6A2 unmasking a pathogenic variant in the second nondeleted allele have been described in the etiology. We aimed to report the clinical and molecular findings of a 13-year-old boy with ring chromosome 21 who presented to our clinic with easy fatigability, muscle weakness, and waddling gait. Phenotypic delineation along with chromosomal microarray analysis and DNA sequencing were performed. Affymetrix CytoScan Optima array platform and DNA sequencing revealed a 2,202 kb de novo deletion at 21q22.3, including COL6A1 and COL6A2, and a novel heterozygous variant at position c.2875G > A;p.(Glu959Lys) in COL6A2, respectively. Before his admission to our center, the patient was evaluated for hypotonia elsewhere when he was 15 months old. He was diagnosed with ring chromosome 21 on peripheral blood karyotype analysis; however, no further assessment was performed at that time. He had normal growth with mild dysmorphic facial features, distal laxity, gastrocnemius hypertrophy, proximal muscle weakness, increased lordotic posture with mild flexion contractures at the knees, and gait disturbance. Although the phenotype does not fit into classical Ullrich congenital muscular dystrophies, muscle magnetic resonance imaging (MRI) revealed a complementary pattern consistent with collagen VI related myopathies. Genetic testing confirmed the clinical diagnosis as well. This patient yet represents another example of the effect of large genomic deletions leading to recessive disorders through unmasking a pathogenic variant in the second nondeleted allele.

Collagen VI

Congenital muscular dystrophy

Compound heterozygosity

10.1055/s-0040-1714125

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Citations (3)

A case of Woodhouse-Sakati syndrome with pituitary iron deposition, cardiac and intestinal anomalies, with a novel mutation in DCAF17

European Journal of Medical Genetics (2019)

Süleyman Nahit Şendur Sümeyra Oğuz Gülen Eda Ütine Selçuk Dağdelen Kader Karlı Oğuz

Anorexia nervosa

Delayed puberty

10.1016/j.ejmg.2019.103687

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Citations (11)

Genetic IGF1R defects: new cases expand the spectrum of clinical features

Journal of Endocrinological Investigation (2020)

E. Nazlı Gönç Zeynep Alev Özön Sümeyra Oğuz Serkan Kabaçam Ekim Z. Taşkıran

Hypergonadotropic hypogonadism

Microcephaly

10.1007/s40618-020-01264-y

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Citations (6)

Investigation of Genetic Causes in a Developmental Disorder: Oculoauriculovertebral Spectrum

The Cleft Palate-Craniofacial Journal (2021)

Naz Güleray Lafcı Can Koşukçu Sümeyra Oğuz Gizem Ürel Demir Ekim Z. Taşkıran

Objective Oculoauriculovertebral spectrum (OAVS) is a genetically and clinically heterogeneous disorder that occurs due to a developmental field defect of the first and second pharyngeal arches. Even though recent whole exome sequencing studies (WES) have led to identification of several genes associated with this spectrum in a subset of individuals, complete pathogenesis of OAVS remains unsolved. In this study, molecular genetic etiology of OAVS was systematically investigated. Design/Setting/Patients A cohort of 23 Turkish patients with OAVS, referred to Hacettepe University Hospital, Department of Pediatric Genetics from 2008 to 2018, was included in this study. Minimal diagnostic criteria for OAVS were considered as unilateral microtia or hemifacial microsomia with preauricular skin tag. The cohort was clinically reevaluated for craniofacial and extracranial findings. Molecular etiology was investigated using candidate gene sequencing following copy number variant (CNV) analysis. WES was also performed for 2 of the selected patients. Results Patients in the study cohort presented similar demographic and phenotypic characteristics to previously described patients in the literature except for a higher frequency of bilaterality, cardiac findings, and intellectual disability/developmental delay. CNV analysis revealed a possible genetic etiology for 3 patients (13%). Additional WES in 1 of the 2 patients uncovered a novel heterozygous nonsense variant in Elongation factor Tu GTP-binding domain-containing 2 ( EFTUD2) causing mandibulofacial dysostosis with microcephaly (MFDM), which clinically overlaps with OAVS. Conclusion Detailed clinical evaluation for any patient with OAVS is recommended due to a high rate of accompanying systemic findings. We further expand the existing genetic heterogeneity of OAVS by identifying several CNVs and a phenotypically overlapping disorder, MFDM.

Hemifacial microsomia

Microtia

Goldenhar syndrome

Etiology

Microcephaly

10.1177/10556656211038115

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Citations (5)

Further Phenotypic Delineation of Partial Trisomy 17q and Partial Monosomy 20q due to Rare t(17;20)

Molecular Syndromology (2020)

Gizem Ürel Demir Özlem Akgün Doğan Sümeyra Oğuz Naz Güleray-Lafcı Pelin Özlem Şimşek‐Kiper

Copy number variations in subtelomeric regions of chromosomes 17 and 20 are associated with intellectual disability and various systemic manifestations. Microarray analysis allows identification of submicroscopic chromosomal abnormalities and is applicable to elucidate the etiology of cognitive impairment in approximately one-fifth of the cases. In the present study, we report on 3 male children from 2 sisters, who suffered from intellectual disability, facial dysmorphism, and epilepsy. Despite the initial suggestion of an X-linked inheritance, the condition was associated with 17q25.3 duplication and concomitant 20q13.33 deletion, as detected by microarray analysis. Coexistence of a deletion and a duplication suggests unbalanced segregation of a parental balanced translocation. Further investigations revealed maternal balanced translocations, which resulted in copy number aberrations in the children following unbalanced segregations. The work-up underlined the importance of genomic screening using microarrays as the first-tier diagnostic tool in intellectual disability, despite an apparent X-linked segregation in the pedigree.

Subtelomere

Partial Trisomy

Monosomy

Comparative genomic hybridization

Trisomy

Etiology

10.1159/000505141

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Citations (3)

Diagnostic yield of microarrays in individuals with non‐syndromic developmental delay and intellectual disability

Journal of Intellectual Disability Research (2021)

Sümeyra Oğuz Ümit Arslan Pelin Özlem Şimşek‐Kiper Mehmet Alikaşifoğlu Koray Boduroğlu

Intellectual disability (ID), or developmental delay (DD) when the individual is yet under 5 years of age, is evident before 18 years of age and is characterised by significant limitations in both intellectual functioning and adaptive behaviour. ID/DD may be clinically classified as syndromic or non-syndromic. Genomic copy number variations (CNVs) constitute a well-established aetiological subgroup of ID/DD. Overall diagnostic yield of microarrays is estimated at 10-25% for ID/DD, especially higher when particular clinical features that render the condition syndromic accompany.In this study, we aimed to investigate the diagnostic yield of microarrays in the subgroup of individuals with non-syndromic ID/DD (NSID/NSDD). A total of 302 NSID/NSDD individuals who have undergone microarray analysis between October 2013 and April 2020 were included. Accompanying clinical data, including head circumference, delayed developmental areas, seizures and behavioural problems were collected and analysed separately in NSID and NSDD subgroups.The diagnostic yield of microarray analyses in NSID/NSDD was determined as 10.9% in NSID (10.7%) and in NSDD (11.1%). Presence of behavioural and epileptic problems did not contribute to the diagnostic yield. However, in the presence of macrocephaly, the contribution to diagnostic yield was statistically significant particularly in NSDD group. The most common pathogenic CNVs involved chromosomes 16, 15 and X. Lastly, we propose a Xq21.32q22.1 deletion as likely pathogenic in a child with isolated language delay and accompanying seizures.Particularly in neurodevelopmental diseases, microarrays are useful for establishing the diagnosis and detecting novel susceptibility regions. Future studies would accurately classify the herein presented variants of uncertain significance CNVs as pathogenic or benign.

Macrocephaly

Etiology

10.1111/jir.12892

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Citations (8)

An Unexpected Diagnosis of The Rectal Polyp: Perivascular Epithelioid Cell Tumor

Turkish Archives of Pediatrics (2024)

Muhammed Hamidullah Çakmak Nevzat Aykut Bayrak Şermin Çoban Kökten Aslı Yılmaz Sümeyra Oğuz

Perivascular Epithelioid Cell

10.5152/turkarchpediatr.2024.23261

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Citations (0)