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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.

Introduction: Brittle cornea syndrome (BCS) is a rare connective tissue disorder with ocular and systemic features. Extreme corneal thinning and fragility are the main hallmarks of BCS. Case Report: A 4-year-old boy presented with recurrent spontaneous corneal perforation. He had blue sclera, corneal leucoma, irregular iris, shallow anterior chamber, corneal astigmatism, and bilateral corneal thinning. He also had several systemic features including hearing loss, skin hyperelasticity, joint hypermobility, scoliosis, and umbilical hernia. A diagnosis of BCS was confirmed with molecular analysis. A homozygous c.17T>G, p.(Val6Gly) variation was identified in the PRDM5 gene. Discussion: p.(Val6Gly) variation in PRDM5 was previously reported in 2 patients with BCS. We also considered PRDM5 c.17T>G, p.(Val6Gly) variation as pathogenic based on the following features: the absence of the variation in population databases, in silico predictions, segregation analysis, and clinical signs of our patient. Extremely thin and brittle corneas lead to corneal perforation spontaneously or after minor trauma. Nearly all patients have lost their vision because of corneal rupture and scars. The key challenge in the management of BCS is the prevention of ocular rupture which relies on early diagnosis. Early diagnosis allows for taking prompt measures to prevent ocular rupture.

Amaç: Bu çalışma Antalya’da birinci basamak bünyesinde çalışan sağlık personelinin sağlıklı yaşam biçimi davranışlarını ve sağlıklı davranış geliştirme niyetlerini değerlendirmek amacıyla yapılmıştır. Yöntem: Tanımlayıcı türde olan araştırmamız Aralık 2017 ve Haziran 2018 tarihleri arasında Halk Sağlığı Hizmetleri Başkanlığı bünyesinde çalışan 257 sağlık personeli ile yapılmıştır. Veri toplama yöntemi olarak online anket hazırlanmıştır. Verilerin toplanmasında; sağlık personelinin sosyo-demografik özellikleri soru formu, 'Sağlıklı Yaşam Biçimi Davranışları-II Ölçeği (SYBDÖ II)' ve 'Sağlık Davranışı Değişim Aşamaları Değerlendirme Soru Formu' kullanılmıştır. Etik kurul ve kurum izni alınmıştır. Bulgular: Çalışmaya katılan sağlık personelinin yaş ortalaması 40.79±7.72’dir. Sağlık personelinin SYBDÖ II toplam puan ortalaması 140.41±23,53’tür. Sağlık personelinin sigara içmeyi bırakanların sigara içmeyen ve içenlere göre fiziksel aktivite puan ortalamaları daha yüksek bulunmuştur (F=4.433; p=013). Sağlık algısı yaşıtlarına göre iyi olan sağlık personelinin, sağlık algısı yaşıtları ile aynı ve kötü olanlara göre SYBDÖ II alt boyut puan ortalamaları arasında istatistiksel olarak anlamlı bir fark bulunmuştur (p

Introduction: Germline pathogenic variations of the genes encoding the components of the Ras-MAPK pathway are found to be responsible for RASopathies, a clinically and genetically heterogeneous group of diseases. In this study, we aimed to present the results of patients genetically investigated for RASopathy-related mutations in our Genetic Diagnosis Center. Methods: The results of 51 unrelated probands with RASopathy and 4 affected relatives (31 male, 24 female; mean age: 9.327 ± 8.214) were included in this study. Mutation screening was performed on DNA samples from peripheral blood of the patients either by Sanger sequencing of PTPN11 hotspot regions (10/51 probands), or by a targeted amplicon next-generation sequencing panel (41/51 probands) covering the exonic regions of BRAF, CBL, HRAS, KRAS, LZTR1, MAP2K1, MAP2K2, NF1, NRAS, PTPN11, RAF1, RASA2, RIT1, SHOC2, SOS1, SOS2, SPRED1, and KAT6B genes. Results: Pathogenic/likely pathogenic variations found in 22 out of 51 probands (43.13%) and their 4 affected family members were located in PTPN11, BRAF, KRAS, NF1, RAF1, SOS1, and SHOC2 genes. The c.148A>C (p.Thr50Pro) variation in the KRAS gene was a novel variant detected in a sibling in our patient cohort. We found supportive evidence for the pathogenicity of the NF1 gene c.5606G>T (p.Gly1869Val) variation which we defined in an affected boy who inherited the mutation from his affected father. Conclusion: Although PTPN11 is the most frequently mutated gene in our patient cohort, as in most previous reports, different mutation distribution among the other genes studied motivates the use of a next-generation sequencing gene panel including the possible responsible genes.

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 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.

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 (9 Mb) deletion, and 8p22p12 (16.8 Mb) deletion. Our study highlights the importance of genetic testing in CHD.

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.

The aim of this study was to evaluate germline variant frequencies of pheochromocytoma and paraganglioma targeted susceptibility genes with next-generation sequencing method. Germline DNA from 75 cases were evaluated with targeted next-generation sequencing on an Illumina NextSeq550 instrument. KIF1B, RET, SDHB, SDHD, TMEM127, and VHL genes were included in the study, and Sanger sequencing was used for verifying the variants. The pathogenic/likely pathogenic variants were in the VHL, RET, SDHB, and SDHD genes, and the diagnosis rate was 24% in this study. Three different novel pathogenic variants were determined in five cases. This is the first study from Turkey, evaluating germline susceptibility genes of pheochromocytoma and paraganglioma with a detection rate of 24% and three novel variants. All patients with pheochromocytoma and paraganglioma need clinical genetic testing with expanded targeted gene panels for higher diagnosis rates.

Multiple myeloma (MM) is one of the plasma cell-related hematological malignancies exceeding 10.0% of all marrow cells, and they make a paraprotein that is a marker of the disease. Myeloma is one of the most common types of hematological malignancies in humans. Genetic bio-markers have been used for prognostic markers in patients diagnosed with MM. The genetic and genomic changes have been identified using karyotyping, fluorescent in situ hybridization (FISH), next generation sequencing (NGS), specifically whole-genome sequencing or exome sequencing. Circulatory plasma cells, circulating free DNA (cfD-NA) and microRNAs (miRNAs) comprised in liquid biopsy are potentially used in diagnosis/prognosis of MM. In this study, we analyzed and compared results of karyo-typing, FISH and NGS in 35 MM cases. Diagnostic strategies are expanding rapidly and newly developed NGS-based testing may help the understanding of the complexities of genetic alterations in karyotypically normal cases.

Modifying genes play an exclusive role in the genetic regulation of the risk of breast cancer development in women with a pathogenic variation of BRCA1 or BRCA2. Therefore, it has been suggested that TNFRSF11A, which is among those modifying genes present in breast cancer development, may have a significant role in patients with positive BRCA1 or BRCA2 variations. In our study, we investigated the probable effects of single nucleotide polymorphisms (SNPs) in the TNFRSF11A gene, such as rs4485469, rs9646629, rs34739845, rs17069904, rs 884205, rs4941129 on the risk of breast cancer in patients with BRCA1 or BRCA2 variations. A total of 23 breast cancer patients with pathogenic variations in the BRCA1 or BRCA2 genes, 28 patients with no pathogenic variations in the BRCA1 or BRCA2 genes, and 55 healthy women as a control group, were included in this study. The SNPs were determined with allelic discrimination analysis through the real-time polymerase chain reaction (qPCR) method. There was no statistically significant difference between the SNPs of the TNFRSF11A gene rs4485469, rs9646629, rs34739845, rs17069904, rs884205, rs4941129 and metastasis, estrogen receptor, progesterone receptor and CerB2 receptor positivity between patient and control group (p >0.05). However, the rs4485469 SNP was found to be borderline significant between the patient groups with and without BRCA1 or BRCA2 mutations (p = 0.059). In patients with BRCA1 or BRCA2 pathogenic variations living in the Trakya region of Turkey, we could not determine the relationship between TNFRSF11 SNPs with breast cancer risk.

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.

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.

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.

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.

Several studies have reported differences in radiation toxicity between the sexes, but these differences have not been tested with respect to histopathology and genes. This animal study aimed to show an association between histopathological findings of radiation-induced lung toxicity and the genes ATM, SOD2, TGF-β1, XRCC1, XRCC3 and HHR2. In all, 120 animals were randomly divided into 2 control groups (male and female) and experimental groups comprising fifteen rats stratified by sex, radiotherapy (0 Gy vs. 10 Gy), and time to sacrifice (6, 12, and 24 weeks postirradiation). Histopathological evaluations for lung injury, namely, intra-alveolar edema, alveolar neutrophils, intra-alveolar erythrocytes, activated macrophages, intra-alveolar fibrosis, hyaline arteriosclerosis, and collapse were performed under a light microscope using a grid system; the evaluations were semi quantitatively scored. Then, the alveolar wall thickness was measured. Real-time quantitative reverse transcription PCR (RT-qPCR) was used to determine gene expression differences in ATM, TGF-β1, XRCC1, XRCC3, SOD2 and HHR2L among the groups. Histopathological data showed that radiation-induced acute, subacute, and chronic lung toxicity were worse in male rats. The expression levels of the evaluated genes were significantly higher in females than males in the control group, but this difference was lost over time after radiotherapy. Less toxicity in females may be attributable to the fact that the expression of the evaluated genes was higher in normal lung tissue in females than in males and the changes in gene expression patterns in the postradiotherapy period played a protective role in females. Additional data related to pulmonary function, lung weights, imaging, or outcomes are needed to support this data that is based on histopathology alone.

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.

Objective: Alpha thalassemia is a common type of hemoglobinopathy that occurs as a result of deletions or point mutations in the alpha globin gene cluster. The molecular analysis of alpha thalassemia is challenging due to the presence of genes with high sequence similarities in alpha globin gene clusters and pseudogenes. As well as in all genetic diseases, determining the causative mutation types of alpha thalassemia and their frequencies have critical importance for accurate genetic screening and prevention strategies. Material and Method: In our study, alpha globin copy number variations determined by the Multiplex Ligation-dependent Probe Amplifcation (MLPA) method were examined retrospectively with suspicion of alpha thalassemia in 35 female and 43 male patients tested in the Genetic Diseases Diagnosis Center of the Medical Genetics Department at Trakya University Faculty of Medicine. Results: The most common deletion among our patients was the −α3.7 (35.3%), followed by the -α20.5 (10.3%) deletion. The -αSEA deletion was detected in three patients while 4 out of 78 cases were found to have the -αMED deletion. In three patients, a heterozygous large deletion and in one case HS40 regulatory region deletion were detected. In 14 (18%) of the patients, α globin triplications were detected. The -α4.2 deletion was detected in only one of our patients. Conclusion: Our study is the first to report the presence of eight different alpha globin copy number changes and 13 different alpha globin genotypes in the Trakya region., Amaç: Alfa talasemi, alfa globin gen kümesindeki delesyonların veya nokta mutasyonlarının bir sonucu olarak ortaya çıkan yaygın bir hemoglobinopati türüdür. Alfa talaseminin moleküler analizi, alfa globin gen kümesinde yüksek dizi benzerliklerine sahip genlerin ve psödogenlerin varlığı nedeniyle zordur. Tüm genetik hastalıklarda olduğu gibi, alfa talasemide de, altta yatan mutasyon türlerinin ve sıklıklarının belirlenmesi, doğru genetik tarama ve önleme stratejileri için kritik öneme sahiptir. Gereç ve Yöntem: Çalışmamızda, alfa talasemi şüphesiyle Trakya Üniversitesi Tıp Fakültesi Tıbbi Genetik Anabilim Dalı Genetik Hastalıklar Tanı ve Değerlendirme Merkezinde test edilen 35 kadın ve 43 erkek hastada Multipleks Ligasyon-bağımlı Prob Amplifikasyon (MLPA) yöntemiyle belirlenen alfa globin kopya sayısı varyasyonları geriye dönük olarak incelendi. Bulgular: Olgularımız arasında en sık (%35,3) saptanan delesyon −α3.7 ve ardından %10,3 görülme sıklığı ile −α20.5 delesyonu gelmekteydi. Üç olguda tüm probları kapsayan büyük delesyon, bir olguda ise HS40 düzenleyici bölgesinde delesyon saptanırken, 78 olgunun 4’ünde –αMED, üçünde ise –αSEA delesyonu saptandı. Olguların 14’ünde (%18) α globin triplikasyonları belirlendi. −α4.2 delesyonu olgularımızdan yalnızca bir tanesinde saptandı. Sonuç: Çalışmamız, Trakya bölgesinde sekiz farklı alfa globin kopya sayısı değişikliği ve 13 farklı alfa globin genotipinin varlığını bildiren ilk çalışmadır.

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.

INTRODUCTION: Germline pathogenic variations of the genes encoding the components of the Ras-MAPK pathway are found to be responsible for RASopathies, a clinically and genetically heterogeneous group of diseases. In this study, we aimed to present the results of patients genetically investigated for RASopathy-related mutations in our Genetic Diagnosis Center. METHODS: The results of 51 unrelated probands with RASopathy and 4 affected relatives (31 male, 24 female; mean age: 9.327 ± 8.214) were included in this study. Mutation screening was performed on DNA samples from peripheral blood of the patients either by Sanger sequencing of PTPN11 hotspot regions (10/51 probands), or by a targeted amplicon next-generation sequencing panel (41/51 probands) covering the exonic regions of BRAF, CBL, HRAS, KRAS, LZTR1, MAP2K1, MAP2K2, NF1, NRAS, PTPN11, RAF1, RASA2, RIT1, SHOC2, SOS1, SOS2, SPRED1, and KAT6B genes. RESULTS: Pathogenic/likely pathogenic variations found in 22 out of 51 probands (43.13%) and their 4 affected family members were located in PTPN11, BRAF, KRAS, NF1, RAF1, SOS1, and SHOC2 genes. The c.148A>C (p.Thr50Pro) variation in the KRAS gene was a novel variant detected in a sibling in our patient cohort. We found supportive evidence for the pathogenicity of the NF1 gene c.5606G>T (p.Gly1869Val) variation which we defined in an affected boy who inherited the mutation from his affected father. CONCLUSION: Although PTPN11 is the most frequently mutated gene in our patient cohort, as in most previous reports, different mutation distribution among the other genes studied motivates the use of a next-generation sequencing gene panel including the possible responsible genes.

Amaç: Hücre büyüme, farklılaşma, yaşlanma ve siklus düzenlenmesinde önemli rol oynayan RAS-MAPK (Rat-sarcoma-Mitogen-activated-protein-kinase) yolağında bulunan 29 gendeki dominant patojenik varyantların yol açtığı klinik grup “Rasopatiler” olarak adlandırılır. En sık gözleneni Noonan sendromu (NS)’dur. Olguların ~%50’sinde NS ilişkili PTPN11 varyantları saptanır ve bu varyantların %90’ı peptidin N-önündeki ilk SH2 ve C-yönündeki katalitik domainini kodlayan bölgelerde ortaya çıkar. Prenatal evrede artmış nukal kalınlık (NT) ve ayrıca kistik higroma, plevral efüzyon ve asit gibi lenfatik sistem anomalilerinin yanı sıra kardiyak anomaliler, polihidramniyos, ekstremite kısalığı ve makrosefali NS’nin bulguları arasında sayılır. PTPN11 ilişkisi, kromozom anomalisi dışlanmış NT bulgusu olan fetusların %2-3’ünde, ek NS bulgusu olanlarda ise >%10 olarak bildirilmektedir. Gereç ve Yöntem: Çalışmamızda, NS ilişkili Ultrasonografi (USG) bulgusu olan, kromozom anomalisi dışlanmış 246 prenatal olguda, farklı yaklaşımlarla çalışılan PTPN11 gen analiz sonuçları retrospektif olarak değerlendirildi. Olguların 200’ünde genin hedef ekzonları (ekzon 3, 4, 7, 8, 13 ve 14), 46 olguda ise tüm gen Sanger dizileme yöntemi ile incelendi. Bulgular: Genel seride beş olguda (%2) ikisi novel olan (p.P107S ve p.M504T) beş farklı varyant hedeflenmiş ekzonlarda saptandı. Bu beş olgunun ikisinde izole NT ve üçünde çoklu USG bulguları mevcuttu. PTPN11 varyantı saptanmayan altı olguda, Rasopati ilişkili diğer dört genin hedef bölge analizinde, iki olguda SOS1 ve gebelik terminasyonu yapılan üç olgunun birinde hedeflenmiş gen panel testinde RAF1 geninde ilişkili patojenik varyantlar saptandı. NS ilişkili patojenik varyant saptama oranı hem izole NT grubunda hem de çoklu USG bulgulu grupta %2,3 idi. Tartışma: Rasopatilerin %50 sinden sorumlu olan PTPN11 genindeki patojenik varyantların %90’ı hedef ekzonlarda yer almaktadır. Bu nedenle, ilk aşamada PTPN11 hedef ekzon analizi yapılmasının, patogenezin açıklanamadığı olgularda ise genin diğer ekzonlarının ve Rasopati ilişkili diğer genlerin incelenmesinin fayda-maliyet açısından uygun bir yaklaşım olduğu belirlendi., Objective: Dominant pathogenic variants in 29 RAS-MAPK (Rat-sarcoma-Mitogen-activated-protein-kinase) pathway genes, important for the regulation of cell growth, differentiation, aging and cell-cycle, are responsible for RASopathies, Noonan syndrome (NS) is the most common form. PTPN11 variants are detected in 50% of the cases, 90% being identified in the first SH2 and in the catalytic domain at the N- and C-terminals of the peptide, respectively. Increased nuchal translucency (NT), lymphatic system anomalies (cystic hygroma, pleural effusion, ascites), cardiac anomalies, polyhydramnios, short limb and macrocephaly are the NS-associated prenatal findings. PTPN11 association is reported in 2-3% of normal karyotyped fetuses with NT and in >10% when other NS findings are included. Material and Method: PTPN11 analysis with different approaches in 246 normal karyotyped prenatal cases with NS-associated USG findings were retrospectively evaluated. The targeted PTPN11 regions in 200 and the whole gene structure of 46 cases were examined by Sanger sequencing. Results: Pathogenic variants, including two novel variants (p.P107S and p.M504T), were identified in two fetuses with isolated NT and in three fetuses with multiple USG findings, leading to a 2% of detection rate, all found in targeted exons. Two of six cases, further investigated for targets of four Rasopathy genes, had causative genes in SOS1. One of three terminated fetuses, investigated for the targeted-gene panel, had a causative gene in RAF1 genes. Both the isolated NT and multiple USG finding groups revealed an equal detection rate of 2.3%. Discussion: PTPN11 is responsible for 50% of RASopathies and 90% of the pathogenic variants are delineated in the targeted exons. The rational, cost-effective approach for the clarification of the genetic basis of RASopathies is screening the addressed exons of PTPN11 followed by the other exons and other RASopathy related genes.

DergiPark: 962870 tmsj The popularity of genome editing technologies in the scientific community has been on the rise for several years. These technologies are slowly becoming a ray of hope for many patients with genetic diseases, thanks to their immense potential for clinical application. New genome editing tools are being rap- idly developed and introduced, while pre-existing ones are being perfected. In the process beginning with the completion of the Human Genome Project to the first clinical trials focusing on cancer immunotherapy and treating blindness, studies on genome editing have increased exponentially. The clustered regularly interspaced short palindromic repeats system is a Nobel Prize-winning genome editing tool celebrated by many researchers and is often praised due to its ease of use, low cost, and efficiency compared to other acknowledged genome editing tools. This review aims to discuss the historical development, working mechanisms, present and future clinical applications of zinc-finger nucleases, transcription activator-like effector nucleases, clustered regularly inter- spaced short palindromic repeats, and prime editors, while presenting the ethical aspects of using these genome editing tools. Keywords: Zinc-finger nucleases, transcription activator-like effector nucleases, clustered regularly interspaced short palindromic repeats, gene editing

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.

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.

Pathogenic/likely pathogenic (P/LP) germline variations in BRCA1 and BRCA2 genes are responsible for the majority of hereditary breast and ovarian cancers. This study presents the BRCA1/BRCA2 sequencing and deletion duplication analyses results of of 493 participants (485 women, 8 men) selected based on the National Comprehensive Cancer Network (NCCN) guidelines.Next generation sequencing (NGS) and multiplex ligation-dependent probe amplification methods (MLPA) were used to define germline BRCA1/BRCA2 positivity.Overall, the P/LP frequency of the participants was 17.8%. Five of the likely pathogenic variants were novel. The 5266dupC pathogenic variation, which is a founder mutation in the Ashkenazi Jewish population, was the most common variation among the patients, with a frequency of 5.47%. The pathogenic/likely pathogenic variation frequency was significantly higher (p=0.01) among clinically diagnosed familial cancer patisents than those participants without personal history of cancer but enrolled for BRCA1 testing due to familial risk. BRCA1/BRCA mutation positivity was significantly higher (p=0.000) among those who had at least one first- or second-degree relative with breast/ovarian cancer from patients who had no family history. BRCA1/BRCA2 mutation positivity was 69.23% between the patients who had personal history of both breast and ovarian cancer.Based on our findings, we suggest that sequencing all of the coding regions of the BRCA1/BRCA2 genes using NGS is a feasible approach for individuals who are at risk of developing BRCA-related cancer according to NCCN guidelines. The 5266dupC pathogenic variation, as the most common pathogenic variation in the Trakya region of Turkey, should be included if a targeted mutatin screening is planned.

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.