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Prader–Willi, Angelman, Beckwith–Wiedemann, and Russell–Silver are imprinting syndromes. In this study, we aimed to compare the efficiency of single nucleotide polymorphism (SNP) microarray analysis with methylation-specific Multiplex ligation-dependent probe amplification (MS-MLPA) in the detection of uniparental disomy in these syndromes. The patient samples with regions of loss of heterozygosity (LOH), covering 15q11.2 and 11p15.5 critical loci, were analyzed with MS-MLPA to demonstrate the efficiency of SNP microarray in the detection of uniparental disomy (UPD). In a total of seven patients, LOH covering 15q11.2 and 11p15.5 critical loci was detected. Two (28.6%) of these seven patients showed aberrant methylation (suggesting UPD) in MS-MLPA. SNP microarray is a useful tool in the detection of LOH; however, it should be used with caution, since false-positive or false-negative LOH results can be obtained. Although methylation analysis is recommended as the first tier test in the diagnosis of most of the imprinting disorders, combining methylation analysis with SNP microarray can enhance our evaluation process.

Objective The aim of this study is to investigate the efficiency of a first-line molecular genetic evaluation approach, in children with deafness. Methods Patients who were found to have sensorineural hearing loss by age-appropriate audiological tests were selected for the molecular genetic evaluation. The molecular genetic evaluation was carried out with GJB2 gene sequence analysis and mtDNA m.1555A>G mutation Restriction Fragment Length Polymorphism (RFLP) analysis. Additionally, in a small group of patients, hearing loss Multiplex Ligation-dependent Probe Amplification (MLPA) analysis was done out to identify the possible role of copy number changes. Results In this Turkish cohort, which included 104 index patients and 78 relatives, 33 (31.7%) had Pathogenic/Likely Pathogenic variants. One or more GJB2 sequence variants were identified in 46 (44.1%) of the 104 index patients. The homozygous c.35delG mutation by itself explained the etiology in 24% of our ARSNHL group. In one (5%) of the 20 patients of MLPA group, a hemizygous deletion in POU3F4 gene was detected. Conclusion In our Turkish cohort, we applied a first-line molecular genetic evaluation approach using GJB2 gene sequence analysis and mtDNA m.1555A>G RFLP analysis. This approach revealed the genetic etiology of 44.1% of our index patients. Additionaly, the results of hearing loss MLPA analysis revealed the limited role of copy number changes in this patient group. Furthermore, with a detailed genotype-phenotype association workup, 2 rare cases of Deafness with Palmoplantar Hyperkeratosis and Keratitis-Ichthyosis-Deafness syndrome were reported.

SUMMARY OBJECTIVE: Bladder cancer under the age of 40 is extremely rare. Bladder cancer development involves complex and multi-stage processes, one of which is the DNA damage repair mechanism. In this retrospective study, we aimed to evaluate the histopathological features of bladder urothelial carcinoma seen in patients under 40 years of age and tumor microsatellite instability status using immunohistochemistry. METHODS: A total of 50 patients under the age of 40 with urothelial bladder carcinoma from two different centers in the same country were included. Expression of the mismatch repair proteins MLH1, MSH2, MSH6, and PMS2 was analyzed by immunohistochemistry. RESULTS: Age at the time of diagnosis ranged from 17 to 40 years old. Most tumors were non-invasive papillary urothelial carcinoma. Two cases had nuclear loss of MSH-6 and PMS-2. We observed that tumor grade, tumor stage, presence of tumor differentiation, and infiltrative growth pattern of the tumor have significant impact on prognosis, but microsatellite instability does not have an effective role in bladder carcinogenesis in young patients. CONCLUSIONS: Our results indicate that the presence of microsatellite instability is not related to the low tumor grade and stage in urothelial neoplasms in young patients, suggesting that urothelial carcinoma of the bladder in young patients may represent a genetically stable form of neoplasia.

ObjectiveTo investigate the possible predictive value of fetal fraction in the cell-free DNA (cfDNA) test in pregnancies with early- and late-onset fetal growth restriction (FGR).MethodsThis retrospective study comprised 247 women who were screened using the cfDNA test for aneuploidies during the first or second trimester and had deliveries at our institution from January 2016 to December 2019. The fetal fractions of women with early- (n = 14) and late-onset (n = 83) FGR and those with uncomplicated pregnancies (n = 150) were compared.ResultsThe median fetal fractions for the early-onset FGR, late-onset FGR, and control groups were 5.7 [interquartile range (IQR) 2.65], 7 (IQR 5), and 7.35 (IQR 3.65), respectively. The fetal fractions were significantly lower in the early-onset FGR group than in the late-onset FGR and control groups (P = 0.047 and P = 0.037, respectively). There was no difference in fetal fractions between the late-onset FGR and control groups (P = 1.00).ConclusionAs a placenta-related disease, early-onset FGR had lower fetal fractions in the cfDNA test than uncomplicated pregnancies. For clinical use, lower fetal fractions can contribute as a biomarker for screening asymptomatic women for possible placenta-related diseases, such as early-onset FGR. However, more studies are needed to define the “lower” limit.

INTRODUCTION Brain metastasis prevalence is higher in patients with positive epidermal growth factor receptor (EGFR) mutation, anaplastic lymphoma kinase (ALK) and C-ROS oncogene 1 (ROS-1) fusion change in lung adenocarcinoma. OBJECTIVES The purpose of our study is to investigate the relation between the genetic change type and the initial distant metastasis in stage IV lung adenocarcinoma patients with genetic changes. METHODS The study was conducted between January 2007 and December 2018 in a retrospective fashion with patients who had lung cancer diagnosed as stage IV adenocarcinoma. The relation between genetic mutation change (EGFR, ALK or ROS-1) and distant metastasis was analysed. RESULTS A total of 845 patients were included in the study. The median age was 62 (28-88). It was determined that lung and pleura metastases were more frequent at a significant level in patients with positive EGFR mutation (P = 0.032, P = 0.004, respectively). In patients with positive ALK fusion change, pleura metastasis was determined to be more frequent (P = 0.001). Multiple metastases were determined to be significantly more in patients with positive ALK fusion change than single metastasis (P = 0.02). CONCLUSION In patients with EGFR mutant lung adenocarcinoma, lung and pleura metastasis is more frequent and pleura metastasis is more frequent in ALK positive adenocarcinoma. Additionally, multiple organ metastases are higher in ALK positive lung adenocarcinoma.

Background. Immunosuppression at the feto-maternal interface is crucial for a successful pregnancy outcome. Human leukocyte antigen-G (HLA-G) seems to be a major contributor to fetal tolerance. The HLA-G expression is seen in cytotrophoblasts and in maternal blood. Fetal HLA-G acts on decidual antigen-presenting cells (APCs), natural killers (NKs) and T cells. Recent findings revealed that defects in placentation and their consequences are associated with maternal HLA-G variants and their expression levels. Objectives. The objective of this article is to investigate the relationship between fetal HLA-G alleles and miscarriage, which has not been investigated to date. Material and methods. The present study includes 204 recurrent miscarriage (RM) cases who were admitted to our clinic between 2012 and 2016. Twenty-eight miscarriage products without maternal cell contamination and any known pathology were analyzed by HLA-G typing. In addition, 3' untranslated region (UTR) 14-base pair (bp) insertion/deletion polymorphism was also investigated by Sanger sequencing. Results. For our population, the most frequent HLA-G type was G*01:01, both in the study group (30.3%) and in the control group (47%). The study revealed that the G*01:04 allele was significantly associated with miscarriage (p = 0.007). The 3' UTR 14bp deletion was more frequent in the miscarriage group, but there was no significant correlation. Conclusions. HLA-G alleles seem to be related with miscarriage and should be considered in RM cases.

Renal–hepatic–pancreatic dysplasia-1 (RHPD1) is an ultra-rare genetic disorder with a high mortality. It is caused by biallelic pathogenic variants in NPHP3, which encode nephrocytin, an important component of the ciliary protein complex. The NPHP3-related disease phenotype is diverse with RHPD1, nephronophthisis-3, and Meckel syndrome-7. In this case report, we present a female infant with hepatomegaly, cholestasis, and elevated transaminases who was found to carry a homozygous c.2975C > T variant of NPHP3. This is the first description of this genotype and RHPD1 phenotype in the literature. The patient is currently being closely monitored for the necessity of combined renal and liver transplantation under supportive treatment.

Background Chromosomal microarray analysis is the first-tier test for the evaluation of developmental disabilities and congenital anomalies. In this report, we present CMA results of 971 patient and 301 parent samples. Materials and Methods Among 971 patient samples, 133 (13.6%) had pathogenic variants. Results While analyzing, an “in-house” variant database was also used besides other databases. Owing to this, we have found chance to report the most frequent benign variants in Turkish population. Conclusion With the additional data we acquired in this study, we also emphasized the high potential of CMA in revealing single gene disorders and novel gene-phenotype associations as well as copy number variations.

OBJECTIVE

Background Next‐generation sequencing (NGS) and discovery of fetal cell‐free DNA (cfDNA) in the maternal circulation render possible prenatal screening for trisomy 21 (Down syndrome), trisomy 18, trisomy 13, and sex chromosome aneuploidies. The approach is called “fetal cfDNA screening” and in contrast to noninvasive conventional serum screening, it provides the identification of 98%–99% of fetuses with Down syndrome. Methods Retrospective analysis of targeted noninvasive prenatal testing (NIPT) (Clarigo Test) pregnancies with moderate risk, which we have reported between 2016 and 2018 years is presented. Two separate laboratory workflows and NGS platforms are used for the same targeted NIPT analysis. Results In total, 4,594 pregnant women were investigated. Initial 3,594 cases are studied by MiSeq platform, the last 1,000 cases by NextSeq. Failure rate for MiSeq platform is 10.9% and for NextSeq is 8.7%. Automatically reported cases constitute 75% of the MiSeq group and 87% of the NextSeq group. Conclusions Targeted NIPT results suggest that MiSeq platform could be used for NIPT which would be an essential option particularly for laboratories with low sample flow. And, the NextSeq platform has easier wet lab process and also increased success rate in automatic reporting which is suitable for centers with high number of NIPT cases.

Amac: Klinefelter sendromu (KS) olgularinda testikuler sperm ekstraksiyonu (TESE) basarisi icin prediktif parametrelerin degerlendirilmesi amaclandi. Gerec ve Yontem: Calismamizda hastanemizde 2009-2014 yillarinda non-obstruktif azospermi (NOA) nedeniyle TESE yapilmis 322 hastanin verileri retrospektif olarak incelendi. Bu hastalardan genetik analizi 47XXY - KS olarak saptanan 29 hasta calismaya alinarak yas, FSH, LH, FSH/LH orani, prolaktin, T ve E2 degerleri retrospektif olarak incelendi. Parametrelerin istatistiksel analizinde, p

EgeUn###, Exhaled breath is a source of volatile and nonvolatile biomarkers in the body that can be accessed non-invasively and used for monitoring. The collection of lung secretions by conventional methods such as bronchoalveolar lavage, induced sputum collection, and core biopsies is limited by the invasive nature of these methods. Non-invasive collection of exhaled breath condensate (EBC) provides fluid samples that are representative of airway lining fluids. Various volatile and nonvolatile biomarkers can be detected in volatile condensates, such as H2O2, nitric oxide, lipid mediators, cytokines, chemokines, DNA, and microRNAs. Studies have examined cell-freeDNA(cfDNA) in plasma samples from non-small-cell lung cancer patients, offering to new insights and fostering development of the liquid biopsy. However, few studies have examined cfDNA in EBC samples. This study examined whether EBC is an appropriate source of cfDNA using housekeeping-gene-specific primer probes and quantitative real-time polymerase chain reaction in healthy subjects. Ambient (room) air is contaminated with DNA, so caution is needed. Preliminary studies indicated that volatile biopsies are becoming an important diagnostic tool in lung cancer., Department of Scientific Research Projects of Dokuz Eylul University [KB.SAG.049]; Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [216S435, 216S591], Informed consent was obtained from all research subjects. The study was approved by the Ethics Committee of Ege University and was supported by grants from the Department of Scientific Research Projects of Dokuz Eylul University (Project no: 2017.KB.SAG.049) and the Scientific and Technological Research Council of Turkey (Project no: 216S435 and 216S591).

Objective: Malignant melanoma of the larynx is an uncommon tumor type that can be seen as a primary tumor or as a metastasis from a cutaneous primary lesion. Morphological appearances of this tumor are readily confused with the other types of laryngeal cancers. A new case of primary laryngeal malignant melanoma has been presented in this case report . Case: The patient was a 54-year-old man without any clinical evidence of other cutaneous malignant melanocytic lesions. Microscopically, polygonal-epithelioid tumor cells containing cytoplasmic and nuclear melanin were located under the mucosal squamous epithelial cells. Atypical mitotic figures were also present. Ulceration and disruption of the epithelium weren’t observed. Immunohistochemical studies were positive for S100, HMB-45, Melan-A and vimentin while it was negative for cytokeratin. Based on findings this diagnosis was established.

Introduction: About 80% of lung cancer cases are classified as “Non-Small Cell Lung Cancer (NSCLC)”. Case spesific, targeted therapies (precision medicine) are developed for advanced NSCLC. The main targets are the mutations of EGFR gene which are found in 10-30% of cases. Tyrosine kinase inhibitors (erlotinib, gefitinib, afatinib, osimertinib) are offered if the tumor has the mutations. At the 9-13th months of targeted tyrosine kinase therapy, drug resistance related EGFR T790M mutation may occur. Aim: Our goal is to identify the effect of liquid biopsy in the management of NSCLC and share the results of our genetic diagnosis center. Methods: We have examined 42 mutations of EGFR gene, in 114 NSCLC cases that referred to our center in 2017-2018. Plasma derived cell-free DNA (cfDNA) samples are used to identify 42 mutations of EGFR gene including exon 19 (Ex19del), exon 20 (T790M), exon 21 (L858R) variants by “Real-Time Quantitative PCR” (RT-PCR) method. Results: The EGFR mutations are found in 23 liquid biopsy cases (20%). Eleven of the cases (9.6%) have single sensitivity related mutation: Five cases have Ex19del, 4 cases have L858R, 2 cases have Ex20ins. In addition, one case has “Ex19del and G719X” together. The remaining 11 (9.6%) have the drug resistance related T790M mutation in addition to a sensitivity mutation: Six cases have “Ex19del ve T790M”, 4 cases have “L858R ve T790M”, 1 case has “L858R, S768I ve T790M”. The 11 cases with normal liquid biopsy result actually have a EGFR mutation in solid tissue biopsy. Conclusion: The liquid biopsy is successfully took its place in the identification of EGFR mutations of advanced NSCLC cases.

Background Maturity-onset diabetes of the young (MODY) is a common form of monogenic diabetes. Fourteen genes have been identified, each leading to cause a different type of MODY. The aims of this study were to reveal both known and novel variants in MODY genes in patients with MODY using targeted next generation sequencing (NGS) and to present the genotype-phenotype correlations. Methods Mutation analysis of MODY genes (GCK, HNF1A, HNF4A, HNF1B, ABCC8, INS and KCNJ11) was performed using targeted NGS in 106 patients with a clinical diagnosis of MODY. The variants were evaluated according to American College of Medical Genetics and Genomics (ACMG) Standards and Guidelines recommendations. Results A total of 18 (17%) variants were revealed among all patients. Seven variants in GCK, six in HNF4A, four in HNF1A and one in ABCC8 genes were found. Eight of them were previously published and 10 of them were assessed as novel pathogenic or likely pathogenic variants. Conclusions While the most frequent mutations are found in the HNF1A gene in the literature, most of the variants were found in the GCK gene in our patient group using the NGS method, which allows simultaneous analysis of multiple genes in a single panel.

Objective: The aim of this study was to evaluate both the frequency of Asn680Ser polymorphism of follicle stimulating hormone receptor (FSHR) and whether this polymorphism is associated with PCOS in a Turkish population. Patients and Methods: 100 patients with PCOS and 100 controls were recruited from Eastern Turkey. Venous blood samples were obtained for genetic study, hormone profile, glucose and insulin assays. Asn680Ser polymorphism of FSHR was analyzed by polymerase chain reaction (PCR) amplification and direct DNA sequencing. Two groups were compared for body mass index (BMI), modified Ferriman-Gallwey (mFG) score, fasting glucose, fasting insulin, insulin resistance, and hormone and lipid status. Then, all patients were divided into subgroups for genotypes of FSHR polymorphism. These subgroups were also compared for these mentioned parameters. Results: The difference between women with PCOS and controls in allelic frequencies for Asn680Ser polymorphism of FSHR were not significant. When this single nucleotide polymorphism (SNP) at codon 680 was separately analyzed, no significant difference was found in the genotype frequency among the Asn680Asn, Asn680Ser, andSer680Ser subgroups. There were no significant differences in BMI, mFG score, levels of fasting glucose and fasting insulin, HOMA-IR, and also levels of FSH, LH, E2, PRL, TSH and TT among the PCOS patients carrying different genotypes of Asn680Ser polymorphism Conclusion: there is no association between Asn680Ser polymorphism of FSHR and PCOS in Turkish women from eastern provinces of Turkey. In addition, this SNP seems not to be associated with BMI, IR and PCOS-associated endocrine hormones.

Background/aim: QF-PCR has been used for more than 20 years. It is based on investigation of polymorphic short tandem repeats (STRs) and is widely used for prenatal rapid aneuploidy detection. Materials and methods: We report retrospectively our prenatal diagnosis results between January 2012 and May 2014 in Tepecik Training and Research Hospital Genetic Diagnostic Center. Prenatal diagnosis was recommended in 6800 high-risk pregnancies and 2883 patients agreed to invasive diagnosis. Chromosome analysis and QF-PCR were performed in all patients. Results: Normal results were reported in 2711 cases by fetal karyotyping and in 2706 cases by QF-PCR. Anomaly detection rates were similar for the two methods (5.09% for karyotyping and 4.02% for QF-PCR). Conclusion: QF-PCR is a fast and reliable prenatal diagnosis method in all indication groups and may be preferred as the sole prenatal investigation in patients without fetal ultrasonographic findings.