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Objectives: Male infertility is a large and unexplored global health problem in terms of prevalence. Chromosomal polymorphisms may be associated with infertility and recurrent spontaneous abortions. Non-protein coding and frequently repetitive satellite DNA sequences are found in these regions. Methods: This study aims to present a genetic laboratory experience in the evaluation of frequency, type and significance of Y chromosome polymorphism of Turkish patients with reproductive system problems. The study included 435 patients aged 18-60 years with a documented clinical diagnosis of infertility. Results: In our study, 435 individuals were analyzed cytogenetically and 75 of them (17.24%) were found to carry chromosomally polymorphic variants in Y chromosome. We detected increased heterochromatin structure in the long arm of chromosome Y (Yqh+) as a common variant in our patient group. The frequency of chromosomal polymorphism Yqh- is % 11.26. The rate of chromosomal polymorphism we detected is close to those reported in the literature (10-15%) and statistically significant (p < 0.001), twice that found in the normal population (2-5%). Conclusions: Findings support that Y chromosome polymorphisms may be associated with infertility risk and may play an important role in the development of infertility. More research combining genome studies and other fields is needed to clarify the relationship of Y chromosome polymorphisms with and to infertility.

Acute promyelocytic leukemia (APL) differs from other forms of acute myeloid leukemia (AML), including coagulopathy, hemorrhage, disseminated intravascular coagulation (DIC), and treatment success with all-trans retinoic acid (ATRA). Despite ATRA, early deaths (ED) are still common in APL. Here, we evaluated factors associated with ED and applicability of scoring systems used to diagnose DIC. Ninety-one APL patients (55 females, 36 males, and median age 40 years) were included. ED was defined as deaths attributable to any cause between day of diagnosis and following 30th day. DIC was assessed based on DIC scoring system released by the International Society of Thrombosis and Hemostasis (ISTH) and Chinese Diagnostic Scoring System (CDSS). Patients' median follow-up time was 49.2 months, and ED developed in 14 (15.4% of) cases. Patients succumbing to ED had higher levels of the Eastern Cooperative Oncology Group Performance Status (ECOG PS), lactate dehydrogenase (LDH), and ISTH DIC, and lower fibrinogen levels (p0.05). In multivariate Cox regression analysis, age55 and ECOG PS ≥2 rates were revealed to be associated with ED. Based on ISTH and CDSS scores, DIC was reported in 47.3 and 58.2% of the patients, respectively. Despite advances in APL, ED is still a major obstacle. Besides the prompt recognition and correction of coagulopathy, those at high ED risk are recommended to be detected rapidly. Implementation of local treatment plans and creating awareness should be achieved in hematological centers. Common utilization of ATRA and arsenic trioxide (ATO) may be beneficial to overcome ED and coagulopathy in APL patients.

Chromosome 16 is one of the gene-rich chromosomes; however, approximately 10% of the chromosome 16 sequence is composed of segmental copies, which renders this chromosome instable and predisposes it to rearrangements via frequent nonallelic homologous recombination. Microarray technologies have enabled the analysis of copy number variations (CNV), which may be associated with the risk of developing complex diseases. Through comparative genomic hybridisation in 1,298 patients, we detected 18 cases with chromosome 16 CNV. We identified 2recurrent CNV regions, including 1 at 16p13.11 in 4 patients and another at 16p11.2 in 7 patients. We also detected atypical chromosome 16 rearrangements in 7 patients. Furthermore, we noted an increased frequency of co-occurring genomic changes, supporting the two-hit hypothesis to explain the phenotypic variability in the clinical presentation of CNV syndromes. Our findings can contribute to the creation of a chromosome 16 disease map based on regions that may be associated with disease development.

Tam Metin / Full Text Q3 WOS:000723003700004 PMID: 34860161 SCI-Expanded Tuberous Sclerosis Complex is an autosomal dominant multi-system disorder with an incidence of about 1 in 6000 live births. Defects in either TSC1 (* 605284) or TSC2 (* 191092) genes encoding the components of the Tuberous Sclerosis Complex are responsible for the disease. Therefore, consideration of TSC1/TSC2 pathogenic variations is recommended in the updated diagnostic criteria of Tuberous Sclerosis Complex. Aims: To present the TSC1/TSC2 screening results of a mixed patient population as well as possible new variants in 23 cases from 20 different families who were referred to our Genetic Diseases Diagnosis Center with the signs and symptoms of Tuberous Sclerosis Complex. Study design: Retrospective, cross-sectional study. Methods: Germline TSC1/TSC2 variants were screened in DNA samples extracted from peripheral blood samples of 23 patients from 20 unrelated families using targeted high-throughput sequencing and multiplex ligation-dependent probe amplification methods. The variants identified were classified according to ACMG 2015 guidelines. Results: In total, 5 different pathogenic/likely pathogenic changes have been defined. All these pathogenic/likely pathogenic variants were located in the TSC2 gene. Three of the pathogenic/likely pathogenic variants were novel. Two patients who are twin sisters were found to have TSC2/PKD1 contiguous deletion syndrome. One of the 3 novel variants was a mosaic in-frame deletion. We did not identify any pathogenic variants of the TSC1 gene. Conclusion: The novelty of most of the variants found, including a mosaic likely pathogenic variant, and the presence of a large genomic rearrangement, supports the importance of a comprehensive approach in analyzing TSC1/TSC2 genes. Genetic diagnosis should be performed with caution, considering the possibility of mosaic variants with low allelic fractions.

Objective The aim of this study was to investigate the molecular basis of maturity-onset diabetes of the young by targeted-gene sequencing of 20 genes related to monogenic diabetes and estimate the frequency and describe the clinical characteristics of monogenic diabetes and MODY in Trakya Region of Turkey. Methods In 61 cases, a panel of 20 monogenic diabetes related genes were screened. Illumina NextSeq550 system was used for sequencing of the genes. Pathogenicity of the variants were assessed by bioinformatics prediction software programs and segregation analyses. Results In 29 (47,5%) cases, 31 pathogenic/likely pathogenic variants in the GCK, ABCC8, KCNJ11, HNF1A, HNF4A genes and in 11 (18%) cases, 14 variants of uncertain significance in the GCK, RFX6, CEL, PDX1, KCNJ11, HNF1A, G6PC2, GLIS3 and KLF11 genes were identified. 6 different pathogenic/likely pathogenic variants and 6 different variants of uncertain significance were detected as novel. Conclusions This is the first study including molecular studies of twenty monogenic diabetes genes in Turkish cases in Trakya Region. The results of this study showed that pathogenic variants in the GCK gene are the leading cause of MODY in our population. A high frequency of novel variants (32.4%-12/37) in the current study, suggests that multiple gene analysis provides accurate genetic diagnosis in MODY.

AMAÇ: Hipotoni, uzuvlarda, gövdede veya kraniyofasiyal iskelet kaslarında azalmış tonusu belirtmek için kullanılan genel bir terimdir. Doğumda veya daha sonra çocukluk döneminde tespit edilebilir. Tanıyı koymak, prognozu öngörebilmek, tedavi stratejileri ve ailenin daha sonra doğacak çocukları için tekrarlama riskini belirlemek açısından önemlidir. Nörolojik muayene ve beyin görüntülemesine ek olarak konvansiyonel sitogenetik, moleküler sitogenetik ve moleküler genetik testler klinik tanıyı desteklemek açısından önemlidir. Hipotoni, minor veya major malformasyonlarla ve bilişsel yetersizlik ile birlikte olduğu zaman otozomal kromozom anormallikleri düşünülmelidir. Aralarında klinik farklılıklar bulunan değişik kromozom anormallikleri ve sendromlarda atipik yüz görünümü, el ve ayakta dismorfik bulgular veya diğer organ malformasyonları bulunabilir. Genetik testlerdeki son gelişmeler, moleküler tanıların daha da genişleyen yelpazesi spinal müsküler atrofi, konjenital miyotonik distrofi, Prader-Willi sendromu ile hastalık altında yatan mutasyonların (konjenital kas distrofileri ve birkaç konjenital miyopati) tanımlanması, bu semptomu olan çocuklara spesifik tanı imkanı sağlar.GEREÇ VE YÖNTEM: Çalışmamıza Trakya Üniversitesi Hastanesi, Tıbbi Genetik Anabilim Dalı, Genetik Hastalıklar Tanı Merkezi polikliniğine 2017-2019 yılları arasında hipotoni klinik ön tanısı ile birlikte müracaat eden 47 çocuk hasta dâhil edildi. Hasta genomik DNA’ları ile array-karşılaştırmalı genomik hibridizasyon (aCGH) çalışması gerçekleştirildi.BULGULAR: 47 hastanın 12’sinde (%25,53) 557kb ila 40 Mb arası büyüklükte kopya sayısı değişimleri (CNV) saptandı. Tespit edilen kopya sayısı varyantları, Genomik Varyantlar Veritabanı (DGV), Ensembl kaynakları Genomik Varyasyon ve Fenotip Veritabanı (DECIPHER), Sitogenomik Diziler için Uluslararası Standartlar (ISCA) ve Klinik olarak ilgili varyant veritabanlarının yorumlarının genel arşivi veritabanları ile literatür taramalarından araştırılarak değerlendirilmiştir.SONUÇ: Yenidoğan ve infantil dönemde hipotoni nedenleri arasında yer alan tablolar, genetik sendromlar, kas hastalıkları, kranial malformasyonlar, metabolik hastalıklar özellikle peroksizomal ve mitokondriyal hastalıklardır. Bu grup hastalıklar arasında ayırıcı tanısı yapabilmek için EMG, Kranial MR ve kas biopsisi gibi invazif testler uygulanır. Sonuç olarak, yenidoğan ve infantil döneminde ciddi hipotoni varlığında hastanın genetik açıdan değerlendirilmesi, sebebi bilinmeyen hipotoninin nedenini oluşturan pek çok hastalığın tanısı için yapılacak gereksiz invasif testlerin yükünden hastayı kurtarabilir. Erken tanı, ayrıca, hastalığa özgü ortaya çıkabilecek problemlerden korunma ve erken tedavisi açısından da bir o kadar önemlidir. Hastalığın erken dönemde tanısını koymak, hastanın rehabilitasyonuna daha erken başlama imkânı sağlayacağından önem arz etmektedir., OBJECTIVE: Hypotonia is a general term used to denote reduced tone in the limbs, trunk, or craniofacial skeletal muscles. It can be detected at birth or later in childhood. It is important to establish the diagnosis, predict the prognosis, determine treatment strategies and the risk of recurrence for later generations of the family. In addition to neurological examination and brain imaging, conventional cytogenetics, molecular cytogenetics and molecular genetic tests are important to support clinical diagnosis. Autosomal chromosome abnormalities should be considered when combined with hypotonia, minor or major malformations and cognitive impairment. A variety of chromosome abnormalities and syndromes, including clinical differences, may include atypical facial appearance, hand and foot dysmorphic findings or other organ malformations. Recent advances in genetic testing, expanding spectrum of molecular diagnostics, spinal muscular atrophy, congenital myotonic dystrophy, identification of underlying mutations (congenital muscular dystrophies and several congenital myopathies) with Prader-Willi syndrome, provide a specific diagnosis for children with this symptom.MATERIAL AND METHODS: 47 children who applied to the Trakya University Hospital, Medical Genetics Department, Genetic Diseases Diagnosis Center clinic with a pre-diagnosis of hypotonia between 2017-2019 were included in our study. Array-comparative genomic hybridization (aCGH) study was performed with patient genomic DNA.RESULTS: Copy number variations (CNV) in the size of 557kb to 40 Mb was detected in 12 of 47 patients (25.53%). The detected CNVs were researched and evaluated from the literature searches after Database of Genomic Variants (DGV), Database of genomic variation and phenotype in humans using Ensembl Resources (DECIPHER), International Standards for Cytogenomic Arrays and Public archive (ISCA) of interpretations of clinically relevant variants databases.CONCLUSIONS: Conditions that are among the causes of hypotonia in newborn and infantile periods are genetic syndromes, muscle diseases, cranial malformations, metabolic diseases, especially peroxisomal and mitochondrial diseases. In order to make a differential diagnosis among this group of diseases, invasive tests such as EMG, Cranial MR and muscle biopsy are applied. As a result, in the presence of severe hypotonia in the neonatal and infantile period, the genetic evaluation of the patient can save the patient from the burden of unnecessary invasive tests for the diagnosis of many diseases that are the cause of the unknown hypotonia. Early diagnosis is also important in terms of prevention and early treatment of problems that may arise specific to the disease. It is important to diagnose the disease in the early period, as it will allow the patient to start rehabilitation earlier.

Objective The objective of this study was to report the first case of prenatal diagnosis of the fetal 20p13 microdeletion syndrome in the literature. Case report The mother was 31 years old and had a first trimester serum screening that indicated the fetus was at low risk. The prenatal ultrasound at 23 weeks of gestation showed mild ventriculomegaly (10.2 mm) and absent septum pellucidum. She underwent amniocentesis because of the abnormal imaging results. Karyotype analysis revealed normal results. Chromosome microarray analysis (CMA) was then performed to provide genetic analysis of the fetus and parents. CMA detected 317.902 kb deletion of 20p13 in fetus. Finally, pregnancy was terminated at 32 weeks of gestation. Conclusion This study is the first to report the prenatal diagnosis of a 20p13 microdeletion syndrome. Our results further confirmed that genes in this region, including SOX12, NRSN2 are essential for normal fetal growth and TBC1D20 for normal brain development.

Wiedemann-Steiner syndrome (WDSTS) is a rare autosomal dominant disorder with a variable clinical phenotype including synophrys, hypertelorism, thick eyebrows, long eyelashes, wide nasal bridge, long philtrum, hypertrichosis, growth retardation, and intellectual disability. Cornelia de Lange syndrome (CdLS) is a rare disease characterized by synophrys, long eyelashes, limb abnormalities, generalized hirsutism, growth retardation, and intellectual disability. In both WDSTS and CdLS, the malformations are due to transcriptome disturbance caused by defects in the genes encoding the components of chromatin regulation and transcription process. The overlapping features in these two syndromes may complicate the original diagnosis of a patient. Here, we report on a Wiedemann-Steiner patient found to have a de novo pathogenic KMT2A variation who had been clinically suspected as CdLS. We suggest that targeted next-generation sequencing is a feasible tool for the precise diagnosis of patients who have phenotypically and clinically overlapping features of CdLS and WDSTS.

Marfan syndrome is an autosomal dominant disease affecting connective tissue involving the ocular, skeletal systems with a prevalence of 1/5,000 to 1/10,000 cases. Especially cardiovascular system disorders (aortic root dilatation and enlargement of the pulmonary artery) may be life-threatening. We report here the genetic analysis results of three unrelated cases clinically diagnosed as Marfan syndrome. Deoxyribonucleic acid (DNA) was isolated from EDTA (ethylenediaminetetraacetic acid)-blood samples of the patients. A next-generation sequencing panel containing 15 genes including FBN1 was used to determine the underlying pathogenic variants of Marfan syndrome. Three different variations, NM_000138.4(FBN1):c.229G > A(p.Gly77Arg), NM_000138.4(FBN1):c.165–2A > G (novel), NM_000138.4(FBN1):c.399delC (p.Cys134ValfsTer8) (novel) were determined in our three cases referred with a prediagnosis of Marfan syndrome. Our study has confirmed the utility of molecular testing in Marfan syndrome to support clinical diagnosis. With an accurate diagnosis and genetic counseling for prognosis of patients and family testing, the prenatal diagnosis will be possible.

Background: Recent advances in next-generation sequencing (NGS) technology have enabled multigene testing and changed the diagnostic approach to hereditary gastrointestinal cancer/polyposis syndromes. The aim of this study was to analyze different cancer predisposition genes in hereditary/sporadic gastrointestinal cancer/polyposis. Methods: Cancer predisposition genes were analyzed with an Illumina MiSeq NGS system in 80 patients with gastrointestinal cancer/polyposis who were examined between the years 2016 and 2019. Deletion/duplication analysis of MLH1, MSH2, and EPCAM genes was performed by using the multiplex ligation-dependent probe amplification method. Results: Germline testing of hereditary cancer-related genes was performed in 80 patients with gastrointestinal cancer/polyposis. A total of 30 variants in 30 cases (37.5%) were assessed as pathogenic/likely pathogenic. A total of 19 heterozygous variants were assessed as variants of uncertain clinical significance in 17 cases (21.25%) and 18 (22.5%) novel variations (9 pathogenic/likely pathogenic, 9 variants of uncertain significance) were determined. In 4 (5%) cases, multiplex ligation-dependent probe amplification detected deletions in MLH1, MSH2, and EPCAM genes. Conclusion: The accumulation of analyses with multigene testing will increase the available data for cancer predisposition genes in hereditary gastrointestinal cancer/polyposis. Educational campaigns for prevention, efficient screening programs, and more personalized care based on the profile of individual patients are necessary.

Aneuploidy is a very common occurrence in humans and occurs in an estimated 20–40% of all pregnancies. It is the most prominent cause of miscarriages and congenital defects in humans and is the main obstacle to infertility treatment. The vast majority of aneuploidies are caused by maternal meiotic non-disjunction errors. High levels of recombination errors were observed in studies on fetal oocytes. This suggests that some oocytes are more prone to not being separated due to events occurring before birth. Cell cycle checkpoints that work in the meiotic phase and metaphase-anaphase transition work more moderately in women than in men. As a result, while there are abnormal cells that have been sorted out in spermatogenesis, in females these cells can escape the actual control and ultimately give rise to aneuploid eggs.

Trisomy 21 (Down Syndrome) is the model human phenotype for all genome gain-dosage imbalance situations, including microduplications. Years after the sequencing of chromosome 21, the discovery of functional genomics and the creation of multiple cellular and mouse models provided an unprecedented opportunity to demonstrate the molecular consequences of genome dosage imbalance. It was stated years ago that Down syndrome, caused by meiotic separation of chromosome 21 in humans, is associated with advanced maternal age, but defining and understanding other risk factors is insufficient. Commonly referred to as Down syndrome (DS) in humans, trisomy 21 is the most cited genetic cause of mental retardation. In about 95% of cases, the extra chromosome occurs as a result of meiotic non- nondisjunction (NDJ) or abnormal separation of chromosomes. In most of these cases the error occurs during maternal oogenesis, especially in meiosis I.

Jacobsen syndrome is a rare congenital disorder that is caused by the deletion of several genes in chromosome 11. A 10-year-old female with congenital heart disease, dextrocardia, and coarse facial appearance was examined in our medical genetics clinic. Chromosome analysis and array-CGH showed a copy number loss of 9 Mb in the 11q24.2q25 region. Herein, we report her clinical findings. This is the first case of Jacobsen syndrome with dextrocardia.

Bu çalışmada, Trakya Üniversitesi Tıp Fakültesi Hastanesi'nde 8 yıllık süreçte anormal ultrasonografi bulguları ile gelen 141 adet amniyosentez, 9 koryon villus ve 5 fetal kan örneği sitogenetik olarak analiz edilmiştir. Amacımız ultrasonografi taramasında anomali riski öngörülen gebeliklerdeki karyotipik anormalliklerin korelasyonunu belirlemekti. Amniyosentez, koryon villus ve kordosentez örnekleri ile yapılan hücre kültürlerinden elde edilen karyotipler değerlendirilmiştir. Ayrıca hızlı tanı için interfaz nukleuslarında X,Y,13, 18,21 kromozomları için floresan insitu hibridizasyon yöntemi ile anöploidi taraması yapılmıştır. Anormal ultrasonagrafi bulgusu ile refere edilen 155 hastadan 23 tanesinde (%14.83) kromozom anomalisi saptanmıştır. NT artışı en sık tespit edilen ultasonografi bulgusuydu. Kromozom anomalilerinden 2 tanesi yapısal kromozom anomalisi olarak değerlendirildi. Geriye kalan 21 hastada saptanan anomaliler sayısal kromozom anomalisiydi. Bu 21 sayısal anomaliden 5 tanesi trizomi 13, 3 tanesi trizomi 18, 13 tanesi trizomi 21’dir. Trizomi 21 vakalarından 1 tanesi kordosentez materyalinden, 1 tanesi ise CVS materyalinden elde edilmiştir. Sonuçlarımız, yüksek riskli bir populasyonda kromozom anomalileriyle, ultrasonografik bulgular arasındaki ilişkinin anlamlı olduğunu ortaya çıkarırken, seçilen ultrasonografik belirteçlerin fetüsteki anöploidiyi saptamadaki geçerliliğini doğrulamaktadır., In this study, 141 amniocentesis, 9 chorionic villus and 5 fetal blood samples, which come with abnormal ultrasonography findings representing 8 years of experience in Trakya University Medical Faculty Hospital, were analyzed cytogenetically. Our aim is to determine the correlation of karyotypic abnormalities detected by ultrasonography for the detection of fetal anomalies in prenatal diagnosis.Karyotypes in metaphases obtained from amniocentesis, chorionic villus and cordocentesis samples were evaluated. For rapid diagnosis, fluorescent in situ hybridization was performed in the interphase nuclei specific to X, Y, 13,18, 21 chromosomes. Chromosome anomalies were found in 23 (14.83%) out of 155 patients referred with abnormal ultrasound findings. NT increase is the most common abnormal fetal ultrasonography finding. Two of the chromosomal anomalies were evaluated as structural chromosome analysis. Anomalies detected in the remaining 21 patients were numerical chromosome anomalies. Of these 21 numerical anomalies, 5 are trisomy 13, 3 are trisomy 18, 13 are trisomy 21. One of the 21 trisomy cases was obtained from cordocentesis material and 1 was obtained from CVS material. Our results present that the relationship between fetal chromosomal anomalies and ultrasonographic findings is significant in a high-risk population, while verifying the validity of selected ultrasonographic markers in detecting aneuploidy in the fetus.

The variations in clinical and biological background of lymphoid malignancies trigger researchers to try to find out novel therapeutic targets. A typical treatment includes multiagent chemotherapy and/or targeted therapy in the light of driver mutations. Next generation sequencing (NGS) plays a pivotal role during the identification of genetic alterations in lymphoid malignancies. A total of 52 patients [30 men (58%) and 22 women (42%)] having normal cytogenetic and FISH results were enrolled in this study. Usage of NGS based targeted sequencing could confirm or support a particularly preferred diagnosis (41/52, 78%) or make a differential diagnosis in cases of interference. Notably, in 11 out of these 52 cases (21%), the initial suspect diagnosis was not supported by the NGS result and thereby had to be reconsidered. In this study, we highlight the importance of targeted NGS panel testing for diagnosis, prognosis and treatment decision in highly selected instances of lymphoid malignancies and lymphoproliferative disorders in which histopathology and more conventional molecular analyses remain inconclusive.

In this study, we present a case with distal 3p duplication and 22q13.3 deletion due to unbalanced meiotic segregation in her father carrying a balanced translocation. The 2-month-old girl was examined for her severe hypotonia, developmental delay, and mild dysmorphic appearance. Clinical features include broad forehead, hypertelorism, laterally extended eyebrows, long eyelashes, a depressed nasal root, bifid nasal tip, long philtrum, thin lips, posteriorly rotated ears, short neck, partial syndactyly of the right hand (fingers 3, 4) , and partial syndactyly of the right foot (toes 2, 3). After examination, the final karyotype was reported as: 46,XX,der(22)del(22)(qter)dup(3)(p22pter), and the array-CGH results showed arr[GRCh37] 3p26.3p22.1(93949_41518607)×3 and arr[GRCh37] 22q13.31q13.33(44554083_51224252)×1. The mother has a 46,XX karyotype, and her father carries a balanced translocation, 46,XY,t(3;22)(p26.3;q13.3). This is the first case with a distal 3p duplication and 22q13.3 deletion with severe hypotonia and developmental delay.

DergiPark: 640239 tmsj Aims: This study aims to establish the data; including demographic features, molecular response status, disease characteristics, and survival rate of chronic myeloid leukemia patients treated with tyrosine kinase inhibitors in Trakya University School of Medicine. Methods: In this study, the data of 102 patients over 18 years old who were diagnosed with chronic myeloid leukemia in Trakya University School of Medicine between January 2003-October 2019 were analyzed retrospectively. Data was analyzed using SPSS 23.0.0.0. Results: The total number of patients in the study was 102. There were 95 (93.1%) patients on chronic phase and 6 (5.9%) patients on accelerated phase. Eighty-three (81.4%) of the patients had at least a major molecular response and 17 (16.7%) patients could not achieve at least a major molecular response. Conclusion: As our study showed, first line treatment with imatinib may not be enough for some of the patients to recover and therefore different TKIs such as dasatinib, nilotinib, bo-sutinib, and ponatinib are being used in the treatment of CML. Inadequate response, drug side effects and incompliances are the causes of switching the drug choice. Further studies are needed to thoroughly reveal the epidemiology and treatment regimens.Keywords: Chronic myeloid leukemia, tyrosine kinase, neoplasms

Duplications of 6q and deletions of 6p have been reported in more than 30 cases of live born infants and given rise to widespread abnormalities recognizable as a specific clinical syndrome. Different phenotypes have been described with variable clinical signs. Most cases involve the coexistence of unbalanced translocations affecting one or the other of the chromosomes. However, duplication of both chromosome 6q and deletion of 6p regions have been reported in only a few cases. Here, we report the first duplication of chromosome band 6q23.3–q27 with deletion of 6p25.3. This is the first case in the literature involving changes to these specific chromosomal regions; a medium size duplication of the distal long arm and smaller deletion of the terminal short arm of chromosome 6. In the literature, there are no other cases where these two specific chromosomal aberrations are observed together. Conventional chromosome analysis was performed to investigate the patient. Chromosome structure was identified using fluorescence in situ hybridization for subtelomeric regions of chromosome 6 and array comparative genomic hybridization analysis (array-CGH).

Dudak damak yarigi en sik gorulen kraniyofasiyal anomalidir. Olgularin %70 inde eslik eden anomali bulunmaz ve non sendromik dudak damak yarigi olarak adlandirilir. Genetik biliminde molekuler ve kantitatif olarak meydana gelen gelismeler bu patolojinin sendromik ve sendromik olmayan her iki tipinde de genetik mekanizmalarinin rol oynuyor olabilecegini dusundurmektedir. Sendromik olmayan yarik dudak/damak, embriyonik donemde gerceklesen yaygin bir gelisimsel anormalliktir. Bu calisma, yarik dudak/damak patogenezinde yer alan kopya sayisi degisimlerine bagli genetik anormallikleri tanimlamak amaci tasimaktadir. Genom capinda kopya sayisi varyasyonlarini saptama hedefli CytoScan 180K dizisi kullanilarak yaptigimiz calisma, 1-15 yaslari arasindaki 17 yarik damak dudak olan hasta ornegi ile gerceklestirilmistir. Yedi onemli kopya sayisi degisimi saptanmistir. Bu degisimler yarik damak dudak hastalarinda, duplikasyonlardan (9p23-p24, 18q12.1, Xp22.12, Xp22.31, Yq11.21/16q24.1) ve delesyonlardan (5q21.3 ve 6p22.3-23) olusuyordu. Genetik faktorlerin sendromik olmayan vakalarda da rol oynadigi calismamiz ile de gosterilmistir. Daha genis olcekli genom tarama calismalari farkli populasyonlarda da devam etmektedir. Ileriye yonelik hasta yonetiminde goz onunde tutulmasi gereken; aile ve akrabalarda yarik dudak ve damak bulunmasi halinde sonraki cocukta yarik damak dudak gorulme riskinin arttigidir. Anne babanin etkilenmedigi sporadik vakalarda dahi, bir sonraki cocukta oral yarik riskinin arttigi goz onunde tutulmali ve aile, sonraki gebelik icin mutlaka bilgilendirilmelidir.

Aim Charcot-Marie-Tooth (CMT) disease or hereditary motor and sensory neuropathy (HMSN) is the definition of a genetically heterogeneous group of diseases characterized by the impaired function of peripheral nerves. The aim of this study was to investigate the genetic etiology of CMT. Material and methods We herein examined 55 non-related patients with a suspicion of CMT phenotype or HMSN using a customized multigene panel based on the next-generation sequencing technique. All cases were previously analyzed for PMP22 duplication with the Multiplex Ligand Probe Amplification (MLPA) method. Results In 13 cases (7.15%), we identified a pathogenic/likely pathogenic variants. The affected genes were MARS1, NDRG1, GJB1, GDAP1, MFN2, PRX, SH3TC2, and FGD4. In six cases (10.9%), novel variants were identified: pathogenic variants in GJB1 and FGD4 genes, variants of unknown significance (VUS) in HSPB3, CHRNA1, ARHGEF10, and KIF5A genes. In 21 cases (11.55%), VUS with the genes HSPB3, KIF1B, SCN11A, CHRNA1, HSPB1, FIG4, ARHGEF10, DHTKD1, SBF1, EGR2, SBF2, IGHMBP2, KIF5A, and DNAJB2 were identified. Conclusion In this study, we had a 7.15% diagnosis rate with the NGS (Next Generation Sequencing) method in the CMT disease. Targeted next-generation sequencing panels are beneficial, time-saving, and cost-effective in the diagnosis of CMT.

Introduction Autism spectrum disorder is a genetically and phenotypically heterogeneous group. Genetic studies carried out to date have suggested that both common and rare genetic variants play a role in the etiology of this disorder. In our study, we aimed to investigate the effect of FOXP2, GRIN2B, KATNAL2 and GABRA4 gene variants in the pathogenesis of autism spectrum disorder. Method In our prospectively planned study, all exons and exon-intron junctions of FOXP2, GRIN2B, KATNAL2 and GABRA4 genes were screened by next generation sequencing analysis in 96 patients who diagnosed with autism spectrum disorder. Results In our study, the average age was 10.1 and the male/female ratio was 75/21. Pathogenic or likely pathogenic variants were not detected in FOXP2, GRIN2B, KATNAL2 and GABRA4 genes, however, 69 intronic variants of unknown clinical significance were detected in 50 cases (52%). Among those, 26 were in the GABRA4 gene, 22 in the FOXP2 gene, 13 in the KATNAL2 gene, and 8 in the GRIN2B gene. Twenty three of these 69 variants were novel that were not previously reported in the literature. Conclusion In our study, we could not identify a relationship between the autism spectrum disorder and FOXP2, GRIN2B, KATNAL2 and GABRA4 genes. Identifying genetic risk factors that play a role in the etiopathogenesis of autism spectrum disorder will contribute significantly to understanding the molecular mechanisms of the disease and the development of new treatment strategies. In this context, comprehensive molecular genetic studies such as whole exome or whole genome sequencing are required with higher number of cases in different populations.

Advanced diagnostic methods give an advantage for the identification of the abnormalities in myeloid malignancies. Various researchers have shown the potential importance of genetic tests both before the onset of the disease and during the remission. Large testing panels prevents false negative results in myeloid malignancies. But the important question is how the results of conventional cytogenetic and molecular cytogenetic techniques can be merged together with NGS technologies. In this paper, we drew an algorithm for evaluation of the myeloid malignancies. In order to evaluate genetic abnormalities, we performed cytogenetics, molecular cytogenetics and NGS testing in hematologic malignancies. In this study, we analyzed 100 patients who admitted to Medical Genetics Laboratory within different type of myeloid malignancies. We highlighted the possible diagnostic algorithm for cytogenetically normal cases. We applied NGS 141 gene panel for cytogenetically normal patients and we detected two or more pathogenic variations in 61 out of 100 patients (61%). The pathogenic variation detection rate of NGS varies in disease groups: AML were 85% and MDS were 23%. Here, we identified 24 novel variation out of total pathogenic variations in myeloid malignancies. A total 18 novel variation were identified in AML and 6 novel variation were identified in MDS. Despite of long turnaround time, conventional techniques are still golden standard for myeloid malignancies but sometimes cryptic gene fusions or complex abnormalities cannot be identified easily by conventional techniques. In these conditions, advanced technologies like NGS are highly recommended.

The early fusion of the cranial sutures was described as a craniosynostosis. The early diagnosis and management of craniosynostosis is very important. Environmental factors and genetic abnormalities plays a key role during the development of craniosynostosis. Syndromic craniosynostosis cases are related with autosomal dominant disorders but nearly half of the affected cases carry a new mutation. In this study, in order to identify the genetic etiology of craniosynostosis the authors analyzed 20 craniosynostosis patients by using conventional karyotype, aCGH, sanger sequencing, next generation sequencing (NGS) and Multiplex ligation-dependent probe amplification (MLPA) techniques. The authors identified mutations on FGFR2 and FGFR3 genes which were associated with Muenke syndrome, Crouzon syndrome and skeletal dysplasia syndromes. NGS applied all of the cases and 7 clinical variations in 5 different gene were detected in %20 of cases. In addition to these abnormalities; del(11)(q14.1q22.2), del(17)(q21.31), dup(22)(q13.31) and t(2;16)(q37;p13) have been identified in our cohort which are not previously detected in craniosynostosis cases. Our study demonstrates the importance of detailed genetic analysis for the diagnosis, progression and management of the craniosynostosis.

Introduction: Advanced diagnostic methods give a huge advantage for identification of the abnormalities in myeloid malignancies. Researchers tried to show the potential importance of genetic tests both before the onset of the disease and during the remission. Large testing panels prevents false negative results in myeloid malignancies. But the important question is how can be merged with conventional cytogenetic and molecular cytogenetic techniques together with NGS technologies. Methods: In this paper, we draw an algorithm for evaluation of the malignancies. In order to evaluation of genetic abnormities we performed cytogenetics, molecular cytogenetics and NGS testing panels in hematologic malignancies. In this study, we analyzed 132 patients which are referred to Medical Genetics Laboratory within different type of hematologic malignancies. We highlighted possible algorithm for cytogenetically normal cases.Results: We analyzed cytogenetically normal patients by using NGS 141 gene panel and we detected two or more pathogenic variations in 20 out of 132 patients.Conclusions: Despite of long turnaround time conventional techniques is still golden standard for myeloid malignancies but sometimes cryptic gene fusions or complex abnormalities cannot easily be identified by conventional techniques that conditions advanced technologies are recommended.

Balanced de novo non-robertsonian translocations (non-RTs), which involve acrocentric chromosomes, are rare findings in clinical cytogenetics and may be associated with an abnormal phenotype. These translocations, detected by conventional karyotyping, are found in approximately 1:1,000 neonates. In most of these cases, one of the parents carries the same translocation. In this study, we report a rare non-RT involving chromosomes 15 and 22 defined as 45,XX,-22,der(15;22)t(15;22)/46,XX,der(15)t(15;22),der(22). To our knowledge, this is the first report of a non-RT t(15;22) with these breakpoints.

Risk assessment in newly diagnosed multiple myeloma patients (NDMM) is the first and the most crucial determinant of treatment. With the utilization of FISH analysis as a part of routine practice, high risk Multiple Myeloma (MM) is defined as having at least one of the mutations related with poor prognosis including; t(4;14) t(14;16), t(14;20), del 17p, p53 mutation, gain 1q and del 1p. M-Smart MM risk stratification guideline by Mayo Clinic has proposed a concept similar to high grade lymphomas. Having two of the high risk genetic abnormalities were defined as double hit MM and having any three as triple hit MM. Based on these definitions which may bring a much more clinically relatable understanding in MM prognosis, we aimed to assess our database regarding these two concepts and their probable significance in terms of outcome and prognosis. We retrospectively evaluated 159 newly diagnosed multiple myeloma patients and their clinical course. Among these patients; twenty-four patients have one high risk determinant and also seven and two patients were classified as double hit MM and triple hit MM respectively. Overall survival (OS) of the patients with double hit MM was 6 months, 32.0 months for patients with single high risk abnormality and 57.0 months for patients with no high risk abnormality. Univariate analysis showed that Double Hit and Triple Hit MM is a predictive of low OS. Hazard Ratio of patients with one high risk abnormality was 1.42, double-hit MM patients was 5.55, and triple-hit MM patients was 7.3. Despite the development of novel drugs and their effects of prolonging survival, the treatment has not been individualized. Understanding the biology of each patient as a unique process will be the success of the treatment. As it is known that some MM patients harbor high risk genetic abnormalities according to FISH analysis, we can continue the argument that some patients bring an even higher risk and that can be defined as double or triple hit MM.

The balanced non-Robertsonian translocation (ROB) associated with acrocentric chromosomes is an unusual phenomenon. We report the case of rare non-ROB involving chromosomes 15 and 22 with cytogenetic and molecular cytogenetic findings of 46,XY,t(15;22)(p11.2;q11.2). To the best of our knowledge, t(15;22) is the first report of this breakpoint that is not the usual non-ROB. The karyotype of the chorionic villus cell was 46,XY,t(15;22)(p11.2; q11.2) from two different initial cultures. This is different from the usual non-ROB of acrocentric chromosomes. Comparative genomic hybridization has been performed to determine the chromosomal origin. Non-Robertsonian translocation associated with acrocentric chromosomes is an unusual event and only a few cases have been reported. In this study, we observed acrocentric chromosomes 15 and 22 as a rarely balanced non-ROB, where satellites of chromosome 15 translocated to chromosome 22 and part of chromosome 22 were translocated to chromosome 15. To the best of our knowledge, our patient is the first case reported in the literature for this translocation in prenatal and postnatal periods.

To identify the prevalence and types of fetal chromosomal polymorphisms in pregnant women and to examine possible associations with screening test parameters.Fetal chromosomal polymorphism rate was investigated in pregnant women who had been implemented for invasive prenatal test in a tertiary reference center in Thrace Region of Turkey. Fetal chromosomal polymorphisms were determined and their effects on screening tests' parameters were investigated. Possible differences in the first and second-trimester screening test parameters between women; with fetal chromosomal polymorphism who had screening test results (Group 1) and those with a normal karyotype (Group 2) were evaluated.Fetal chromosomal polymorphism prevalence was 5.3% (n = 101). The most common polymorphisms were identified on chromosome 9, 1, and 16 [54.5% (n = 55); 8.9% (n = 9), and 6.9% (n = 7), respectively]. The most common polymorphic variant was 9qh+ (n = 23; 22.8%). Among the screening test parameters, significantly lower pregnancy-associated plasma protein-A (PAPP-A) (p = .028) and higher unconjugated estriol (uE3) (p = .019) values were found in Group 1. In patients having fetuses with polymorphic variants on chromosome 9, a significantly lower PAPP-A values were observed compared to women with other fetal polymorphic variants (p = .048) or women having fetuses with normal karyotype (p = .007).Lower PAPP-A and higher uE3 levels were observed in women having fetuses with chromosomal polymorphisms, which might affect screening test results. Lower PAPP-A levels were apparent in women having fetuses with polymorphism on chromosome 9.

Molecular mechanisms governing the development of the mammalian cochlea, the hearing organ, remain largely unknown. Through genome sequencing in 3 subjects from 2 families with nonsyndromic cochlear aplasia, we identified homozygous 221-kb and 338-kb deletions in a noncoding region on chromosome 8 with an approximately 200-kb overlapping section. Genomic location of the overlapping deleted region started from approximately 350 kb downstream of GDF6, which codes for growth and differentiation factor 6. Otic lineage cells differentiated from induced pluripotent stem cells derived from an affected individual showed reduced expression of GDF6 compared with control cells. Knockout of Gdf6 in a mouse model resulted in cochlear aplasia, closely resembling the human phenotype. We conclude that GDF6 plays a necessary role in early cochlear development controlled by cis-regulatory elements located within an approximately 500-kb region of the genome in humans and that its disruption leads to deafness due to cochlear aplasia.

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.

Background: Schizencephaly is a neuronal migration anomaly characterized by presence of a cleft between ependymal layer of the ventricle and pia mater of the cerebral cortex. It may be associated with additional cerebral abnormalities, including polymicrogyria, pachygyria, gray matter heterotopy, ventriculomegaly and corpus callosum agenesis. Case Report: We present a female fetus with schizencephaly accompanied by occipital encephalocele, polymicrogyria, agenesis of the corpus callosum, dysmorphic facies and cardiac muscular ventricular septal defect. Array comparative genomic hybridization (array-cGH) analysis revealed a deletion of chromosome 22q13.32 including FAM19A5 gene that is a member of TAFA family. Conclusions: Schizencephaly may be accompanied by unexpected structural and genetic anomalies as in our case with occipital encephalocele, dysmorphic facies, cardiac ventricular septal defect and chromosome 22q13.32 deletion.

Phelan McDermid Syndrome (PHMDS) (OMIM #606232), is a contiguous gene disorder resulting from deletion of the distal long arm of chromosome 22. The 22q13.3 deletions and mutations that lead to a loss of a functional copy of SHANK3 (OMIM *606230) cause the syndrome, characterized by moderate to profound intellectual disability, severely delayed or absent speech, hypotonia, and autism spectrum disorder (ASD) or ASD traits. In this study, we present the case of a 9-year-old girl who had earlier been diagnosed with an ASD. Our findings were a clinically mild intellectual disability, rounded face, pointed chin but no autistic findings. We learned that her neuromotor development was delayed and she had neonatal hypotonia in her history. A heterozygous deletion of MLC1, SBF1, MAPK8IP2, ARSA, SHANK3 and ACR genes, located on 22q13.33, was defined by multiplex ligation-dependent probe amplification (MLPA). Deletion of 22q13.3 (ARSA) region was confirmed by a fluorescent in situ hybridization (FISH) technique. The 22q13.3 deletion was found to be de novo in our patient, and she was diagnosed with PHMDS. We confirmed the 22q13.3 deletion and also determined a gain of 8p23.3-23.2 by array comparative genomic hybridization (aCGH). Fluorescent in situ hybridization was performed to determine whether the deletion was of parental origin and to identify regions of chromosomes where the extra 8p may have been located. The parents were found to be normal. The extra copy of 8p was observed on 22q in the patient. She is the first case reported in association with the 22q deletion of 8p duplications in the literature.

The genetic characterization of chronic lymphocytic leukemia (CLL) has made significant progress over the past few years. Chromosomal abnormalities are detected in up to 80% of patients. Determination of new chromosomal disorders is important in the pathogenesis and treatment facilities. A patient was diagnosed with CLL Stage 2 on 2012 and followed since then by hematology clinic. She was 63 years old. Mature, small lymphocytes, and smudge cell was found in the patient's peripheral blood smear. Bone marrow (BM) biopsy made and hypercellularity showing infiltration of atypical cells with CD5+, CD20+, and CD23+ were determined. Hypoplasia is detected in myeloid/erythroid series, and Stage 2 reticular fibers proliferation were detected. The patient was followed up without medication. While follow-up of patient's white blood cell: 57300, hemoglobin: 5.36, and PLT: 99700 are determined in May 2014. According to the patient's flow results, CD5+, CD23+, and FMC7+ were detected. Mature, small lymphocytes and smudge cell was found in the patient's peripheral blood smear. In ultrasonography imaging, multiple laps were found in the abdomen and multiple neck lymph nodes were detected. The patient BM aspiration was performed in 2014, and hypercellularity was found to contain 54% of atypical lymphocytes in the BM. Fluorescence in situ hybridization (FISH) analysis made two times in 2014. At first, FISH analysis patient's rate of 18% in RB1/13q14.2/13qter revealed a deletion of the gene regions. Patient's FISH result was reported as normal (for RB1/13q14.2/13qter) after 5 months at second analysis. Cytogenetic analysis is made from the patient's BM at the same time. According to the results of karyotyping and FISH, 47, XX, isochromosome 4q (+i4q) is determined. According to literature, extra isochromosome 4q is reported by our case for the first time in CLL. She was diagnosed with Stage 4 CLL and FISH treatment was initiated. Our patient showed disease progression compared to previous results. Hence, we offer that this evidence can be considered regarding triggering the disease's progression or as a result of disease progression i4q was occurred.

Advanced diagnostic methods give an advantage for the identification of the abnormalities in myeloid malignancies. Various researchers have shown the potential importance of genetic tests both before the onset of the disease and during the remission. Large testing panels prevents false negative results in myeloid malignancies. But the important question is how the results of conventional cytogenetic and molecular cytogenetic techniques can be merged together with NGS technologies. In this paper, we drew an algorithm for evaluation of the myeloid malignancies. In order to evaluate genetic abnormalities, we performed cytogenetics, molecular cytogenetics and NGS testing in hematologic malignancies. In this study, we analyzed 100 patients who admitted to Medical Genetics Laboratory within different type of myeloid malignancies. We highlighted the possible diagnostic algorithm for cytogenetically normal cases. We applied NGS 141 gene panel for cytogenetically normal patients and we detected two or more pathogenic variations in 61 out of 100 patients (61%). The pathogenic variation detection rate of NGS varies in disease groups: AML were 85% and MDS were 23%. Here, we identified 24 novel variation out of total pathogenic variations in myeloid malignancies. A total 18 novel variation were identified in AML and 6 novel variation were identified in MDS. Despite of long turnaround time, conventional techniques are still golden standard for myeloid malignancies but sometimes cryptic gene fusions or complex abnormalities cannot be identified easily by conventional techniques. In these conditions, advanced technologies like NGS are highly recommended.

Posterior encephalocele is a neural tube defect, which is a sac-like protrusion of the neural tissue and cerebrospinal fluid through a defect in the occipital bone. This embryonic anomaly may coexist with cortical dysplasia, agenesis of the corpus callosum, hydrocephalus, microcephaly, craniofacial abnormalities, ventricular and atrial septal defect. We report a case of a large posterior encephalocele in a fetus accompanied by unexpected major abnormalities including transposition of the great arteries, severe ventriculomegaly and cerebellar atrophy. Postnatal surgical corrections of the posterior encephalocele and then of the transposition of the great arteries were performed but the neonate died 2 months after delivery.

Purpose To establish the frequency of IDH1 mutations and MGMT methylation in primary glioblastomas. Experimental design We screened primary glioblastoma multiforme (GBM) in a population-based study for IDH1 mutations and MGMT methylation and correlated them with clinical data. Results IDH1 mutations were detected in 5 of 40 primary glioblastomas (12,5%). Primary GBM patients carrying IDH1 mutations were significantly younger, mean age of 41 ± 5.06 years, than patients with wild-type IDH1, mean age of 57 ± 2,29 years, p = 0.011. The mean survival time of all GBM patients with and without IDH1 mutations was 19 months (5 cases) and 16 months (35 cases), respectively (p > 0,05). MGMT methylation was detected in 13 of the 40 patients (32,5%). MGMT-promoter methylation did not correlate with overall survival (OS; p > 0,05). Conclusion In summary, our study is the first study to investigate the IDH1 mutation status and MGMT methylation in primary GBMs in Turkish population and confirmed IDH1 mutation as a genetic marker for also primary GBMs. Our data are still insufficient for definite ascertainment; and our preliminary results suggest: IDH1 status shows an association with younger age and there is a lack of association between IDH1 mutation and survival time. Furthermore MGMT promoter methylation had no prognostic value and lower frequency in primary glioblastomas.