The Phenotypic Spectrum of Desanto-Shinawi Syndrome: A Comparative Report of the First Reported Case in Turkey

DeSanto-Shinawi syndrome (DESSH, OMIM #616708) is a rare genetic disorder caused by pathogenic variants in the WAC gene. This syndrome is characterized by a wide range of physical and neurological symptoms including dysmorphic features, developmental delay, intellectual disability, and behavioral abnormalities. DESSH was described by DeSanto in 2015, and since then, only a few dozen cases have been reported worldwide. Recent research has focused on identifying the underlying genetic cause of the syndrome as well as exploring potential treatments. In this report, we describe a female case who had dysmorphic features including long palpebral fissures, depressed nasal root, mild bulbous nasal tip, thin upper lip, hypertrichosis, short fingers, and intellectual disability, speech delay, and motor retardation. In addition, she had behavioral abnormalities such as agitation, anxiety, and attention deficit hyperactivity disorder (ADHD). Clinical exome sequencing showed a pathogenic heterozygous nonsense variant in exon 13 of the WAC gene c.1837C>T, p.(Arg613Ter) with de novo inheritance. To the best of our knowledge, this is the first case of DESSH reported from Turkey. We aimed to report this rare syndrome and compare the clinical findings of our case with previously reported cases in the literature.

A Genetics Study in the Foreskin of Boys with Hypospadias

Introduction

Hypospadias is a malformation of the genitourinary system in males, characterized by the placement of the urethral opening in the ventral surface of the penis. Although controversies continue about etiology, endocrine disrupting chemicals that disrupt normal endocrine signaling at the receptor or signal transduction level are thought to play an essential role in etiology. This study aimed to investigate the receptor gene expressions of the sex hormones and FGFR2, HOXA13, and TGFB1, which are considered to play an essential role in developing hypospadias.

Methods

The samples from the foreskin of 26 patients with hypospadias and 26 healthy children who underwent circumcision operations were collected. ESR1, AR, FGFR2, HOXA13, and TGFB gene expressions were investigated by real-time PCR in samples obtained during surgery.

Results

In the hypospadias group, ESR1 expression was increased (p = 0.013), and AR and FGFR2 expressions were decreased, which were found to be statistically significant (p = 0.027 and p = 0.003, respectively). There was no statistically significant difference between hypospadias and control groups in TGFBand HOXA13expression levels (p > 0.05).

Discussion

The results suggest that sex hormone receptors and FGFR2 may play an essential role in developing male external genital structures at the gene level. The defects in the expression of these genes can contribute to understanding the development of hypospadias.

The Frequency of SMN1, SMN2 Copy Numbers in 246 Turkish Cases Analyzed with MLPA Method

This study aimed to define the copy numbers of SMN1 and SMN2 genes and the diagnosis rate and carrier frequency of spinal muscular atrophy (SMA) in the Thrace region of Turkey. In this study, the frequency of deletions in exons 7 and 8 in the SMN1 gene and SMN2 copy numbers were investigated. A total of 133 cases with the preliminary diagnosis of SMA and 113 cases with the suspicion of being an SMA carrier from independent families were analyzed by multiplex ligation-dependent probe amplification method for SMN1 and SMN2 gene copy numbers. SMN1 homozygous deletions were detected in 34 patients (25.5%) of 133 cases with the suspicion of SMA. Cases diagnosed with SMA type I was 41.17% (14/34), 29.4% (10/34) with type II, 26.4% (9/34) with type III, and 2.94% (1/34) with type IV. The SMA carrier rate was 46.01% in 113 cases. In 34 SMA cases, SMN2 copy numbers were: two copies - 28 cases (82.3%), three copies - 6 cases (17.6%). SMN2 homozygous deletions were detected in 15% (17/113) of carrier analysis cases. The consanguinity rate of the parents was 23.5% in SMA diagnosed cases. In this study, we had a 25.5% of SMA diagnosis rate and 46% SMA carrier frequency. The current study also showed the relatively low consanguinity rate of the Thrace region, with 23.5% according to the east of Turkey.

Contribution of genotypes in Prothrombin and Factor V Leiden to COVID-19 and disease severity in patients at high risk for hereditary thrombophilia

Thrombotic and microangiopathic effects have been reported in COVID-19 patients. This study examined the contribution of the hereditary thrombophilia factors Prothrombin (FII) and Factor V Leiden (FVL) genotypes to the severity of COVID-19 disease and the development of thrombosis. This study investigated FII and FVL alleles in a cohort of 9508 patients (2606 male and 6902 female) with thrombophilia. It was observed that 930 of these patients had been infected by SARS-CoV-2 causing COVID-19. The demographic characteristics of the patients and their COVID-19 medical history were recorded. Detailed clinical manifestations were analyzed in a group of cases (n = 4092). This subgroup was age and gender-matched. FII and FVL frequency data of healthy populations without thrombophilia risk were obtained from Bursa Uludag University Medical Genetic Department's Exome Databank. The ratio of males (31.08%; 27.01%) and the mean age (36.85 ± 15.20; 33.89 ± 14.14) were higher among COVID-19 patients compared to non-COVID-19 patients. The prevalence of FVL and computerized tomography (CT) positivity in COVID-19 patients was statistically significant in the thrombotic subgroup (p < 0.05). FVL prevalence, CT positivity rate, history of thrombosis, and pulmonary thromboembolism complication were found to be higher in deceased COVID-19 patients (p < 0.05). Disease severity was mainly affected by FVL and not related to genotypes at the Prothrombin mutations. Overall, disease severity and development of thrombosis in COVID-19 are mainly affected by the variation within the FVL gene. Possible FVL mutation should be investigated in COVID-19 patients and appropriate treatment should be started earlier in FVL-positive patients.

Investigation of the Genetic Etiology in Idiopathic Generalized Epileptic Disorders by Targeted Next-generation Sequencing Technique

Background

Idiopathic generalized epilepsy is the most common group of epilepsy disorders in children and adolescents. Various types of genetic abnormality were identified among the hereditary factors that explain epilepsy.

Aims

To determine the variations in the etiopathogenesis, treatment protocol planning, and prognosis of idiopathic generalized epilepsy using the next-generation sequencing method.

Study Design

A cross-sectional study.

Methods

This study included 32 patients with idiopathic generalized epilepsy. Genomic DNA was obtained from peripheral venous blood samples taken from the patients. A total of 18 genes encoding ion channel subunits that are involved in monogenic disorders and are associated with idiopathic generalized epilepsy were included. The targeted custom next-generation sequencing panel was designed to cover all coding exons and all exon/intron splice site regions of 18 genes.

Results

We detected 9 (28%) variations, including 1 likely pathogenic (a variant in the SCN1A gene) and 8 of unknown clinical significance (2 in the CLCN2 genes, GABBR2, SCN1B, SLC2A1, SLC4A10 genes, and 2 in the TBC1D24 gene).

Conclusion

Study results should be supported by functional advanced studies, with increased existing knowledge in the relevant variations.

Investigation on the Effects of Modifying Genes on the Spinal Muscular Atrophy Phenotype

Introduction  Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by the degeneration of motor neurons, muscle weakness, and atrophy that leads to infant's death. The duplication of exon 7/8 in the SMN2 gene reduces the clinical severity of disease, and it is defined as modifying effect. In this study, we aim to investigate the expression of modifying genes related to the prognosis of SMA like PLS3 , PFN2 , ZPR1 , CORO1C , GTF2H2 , NRN1 , SERF1A , NCALD , NAIP , and TIA1.

Methods  Seventeen patients, who came to Trakya University, Faculty of Medicine, Medical Genetics Department, with a preliminary diagnosis of SMA disease, and eight healthy controls were included in this study after multiplex ligation-dependent probe amplification analysis. Gene expression levels were determined by real-time reverse transcription polymerase chain reaction and delta–delta CT method by the isolation of RNA from peripheral blood of patients and controls.

Results   SERF1A and NAIP genes compared between A group and B + C + D groups, and A group of healthy controls, showed statistically significant differences ( p  = 0.037, p  = 0.001).

Discussion   PLS3, NAIP , and NRN1 gene expressions related to SMA disease have been reported before in the literature. In our study, the expression levels of SERF1A , GTF2H2 , NCALD , ZPR1 , TIA1 , PFN2 , and CORO1C genes have been studied for the first time in SMA patients.

Investigating the Genetic Etiology of Pediatric Patients with Peripheral Hypotonia Using the Next-Generation Sequencing Method

Background  Hypotonia occurs as a result of neurological dysfunction in the brain, brainstem, spinal cord, motor neurons, anterior horn cells, peripheral nerves, and muscles. Although the genotype–phenotype correlation can be established in 15 to 30% of patients, it is difficult to obtain a correlation in most cases.

Aims  This study was aimed to investigate the genetic etiology in cases of peripheral hypotonia that could not be diagnosed using conventional methods.

Methods  A total of 18 pediatric patients with peripheral hypotonia were included. They were referred to our genetic disorders diagnosis center from the Pediatric Neurology Department with a prediagnosis of hypotonia. A custom designed multigene panel, including ACTA1 , CCDC78 , DYNC1H1 , GARS , RYR1 , COL6A1 , COL6A2 , COL6A3 , FKRP , FKTN , IGHMBP2 , LMNA , LAMA2 , LARGE1 , MTM1 , NEM , POMGnT1 , POMT1 , POMT2 , and SEPN1 , was used for genetic analysis using next-generation sequencing (NGS).

Results  In our study, we found 13 variants including pathogenic (two variants in LAMA2) and likely pathogenic variants (three variants in RYR1 and POMGnT1) and variants of uncertain clinical significance (eight variants in RYR1, COL6A3, COL6A2, POMGnT1 and POMT1) in 11 (61%) out of 18 patients. In one of our patients, a homozygous, likely pathogenic c.1649G > A, p.(Ser550Asn) variant was defined in the POMGnT1 gene which was associated with a muscle–eye–brain disease phenotype.

Conclusion  The contribution of an in-house designed gene panel in the etiology of peripheral hypotonia with a clinical diagnosis was 5.5%. An important contribution with the clinical diagnosis can be made using the targeted multigene panels in larger samples.

Comprehensive Genetic Analysis of RASopathy in the Era of Next-Generation Sequencing and Definition of a Novel Likely Pathogenic Variation

<b><i>Introduction:</i></b> 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. <b><i>Methods:</i></b> 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 <i>PTPN11</i> hotspot regions (10/51 probands), or by a targeted amplicon next-generation sequencing panel (41/51 probands) covering the exonic regions of <i>BRAF</i>, <i>CBL</i>, <i>HRAS</i>, <i>KRAS</i>, <i>LZTR1</i>, <i>MAP2K1</i>, <i>MAP2K2</i>, <i>NF1</i>, <i>NRAS</i>, <i>PTPN11</i>, <i>RAF1</i>, <i>RASA2</i>, <i>RIT1</i>, <i>SHOC2</i>, <i>SOS1</i>, <i>SOS2</i>, <i>SPRED1</i>, and <i>KAT6B</i> genes. <b><i>Results:</i></b> Pathogenic/likely pathogenic variations found in 22 out of 51 probands (43.13%) and their 4 affected family members were located in <i>PTPN11</i>, <i>BRAF</i>, <i>KRAS</i>, <i>NF1</i>, <i>RAF1</i>, <i>SOS1</i>, and <i>SHOC2</i> genes. The c.148A&#x3e;C (p.Thr50Pro) variation in the <i>KRAS</i> gene was a novel variant detected in a sibling in our patient cohort. We found supportive evidence for the pathogenicity of the <i>NF1</i> gene c.5606G&#x3e;T (p.Gly1869Val) variation which we defined in an affected boy who inherited the mutation from his affected father. <b><i>Conclusion:</i></b> Although <i>PTPN11</i> 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.

Comprehensive Genetic Analysis Results of TSC1/TSC2 Genes in Patients with Clinical Suspicion of Tuberous Sclerosis Complex and Definition of 3 Novel Variants

BACKGROUND

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.

Clinical Features of Aberrations Chromosome 22q: A Pilot Study

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 Application of Next Generation Sequencing Maturity Onset Diabetes of the Young Gene Panel in Turkish Patients from Trakya Region

OBJECTIVE

The aim of this study was to investigate the molecular basis of maturity-onset diabetes of the young (MODY) by targeted-gene sequencing of 20 genes related to monogenic diabetes, estimate the frequency and describe the clinical characteristics of monogenic diabetes and MODY in the Trakya Region of Turkey.

METHODS

A panel of 20 monogenic diabetes related genes were screened in 61 cases. Illumina NextSeq550 system was used for sequencing. 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 (VUS) in the GCK, RFX6, CEL, PDX1, KCNJ11, HNF1A, G6PC2, GLIS3 and KLF11 genes were identified. There were six different pathogenic/likely pathogenic variants and six different VUS which were novel.

CONCLUSION

This is the first study including molecular studies of twenty monogenic diabetes genes in Turkish cases in the Trakya Region. The results 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.

Targeted massively parallel sequencing in the management of cytogenetically normal lymphoid malignancies

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.

The Importance of Multiple Gene Analysis for Diagnosis and Differential Diagnosis in Charcot Marie Tooth Disease

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.

Customized Targeted Massively Parallel Sequencing Enables More Precisely Diagnosis of Patients with Epilepsy

BACKGROUND

Advancement in genetic technology has led to the identification of an increasing number of genes in epilepsy. This will provide a huge information in clinical practice and improve diagnosis and treatment of epilepsy.

METHODS

this was a single-center retrospective cohort study of 80 patients who underwent NGS testing with customize epilepsy panel.

RESULTS

In total 54 out of 80 patients (67, 5%), pathogenic / likely pathogenic and variants of uncertain significance variants were identified according to ACMG criteria. Pathogenic or likely pathogenic variants (n=35) were identified in 29 out of 80 individuals (36.25%). Variants of uncertain significance (VOUS) (n=34) have identified in 28 out of 80 patients (35%). Pathogenic, likely pathogenic, and variants of uncertain significance (VOUS) were most frequently identified in TSC2 (n = 11), SCN1A (n = 6) and TSC1 (n = 5) genes. Other common genes were KCNQ2 (n = 3), AMT (n = 3), CACNA1H (n = 3), CLCN2 (n = 3), MECP2 (n = 2), ASAH1 (n = 2) and SLC2A1 (n = 2).

CONCLUSIONS

NGS based testing panels contributes the diagnosis of epilepsy and may change the clinical management by preventing unnecessary and potentially harmful diagnostic procedures and management in patients. Thus, our results highlighted the benefit of genetic testing in children suffered with epilepsy. This article is protected by copyright. All rights reserved.

Relationship between arginase genes polymorphisms and preschool wheezing phenotypes

BACKGROUND

The association between arginase I (ARG1) and arginase II (ARG2) genes and asthma has been reported in previous studies, but associations between polymorphisms in ARG genes and preschool wheezing (PSW) phenotypes are still unknown.

OBJECTIVE

To examine the association between genetic variation in ARG1 and ARG2 genes and PSW phenotypes.

METHODS

We enrolled 83 patients and 86 healthy controls. The patient group included two subgroups: episodic wheezing (EW) (n = 42, median age 41 months) and multiple-trigger wheezing (MW) (n = 41, median age 39 months). We genotyped six single nucleotide polymorphisms (SNPs) in ARG1 and six SNPs in ARG2. Eighteen haplotypes for ARG1 and 31 haplotypes for ARG2 were constituted, and the distributions of SNPs and haplotypes in patients and controls were analyzed.

RESULTS

The frequency of the homozygote cytosine-cytosine (CC) genotype of ARG1 rs2781667T>C SNP and the ARG1 haplotype 4 in the MW group was significantly higher than the EW group (p = .002; odd ratios [OR]: 5.25; confidence interval [CI]: 1.9-14.51 and p < .001; OR: 7.77; CI: 2.54-23.74, respectively). The frequency of the ARG1 haplotype 5 was significantly higher but the frequency of ARG1 haplotype 9 was significantly lower in the all patients than in the healty controls (p = .019; OR: 10.34; CI: 1.28-83.53 and p = .015; OR: 0.093; CI:0.01-0.74, respectively). The frequency of the ARG1 haplotype 2 was significantly higher in the EW group than in the MW group (p = .014; OR: 5.68; CI: 1.48-21.8).

CONCLUSION

Variations in ARG1 may potentially be related to phenotypes and risk of PSW.

Targeted High-Throughput Sequencing Analysis Results of Osteogenesis Imperfecta Patients from Different Regions of Turkey

Objective: Osteogenesis imperfecta (OI) includes a group of disorders characterized by susceptibility to bone fractures with different severities. The increasing number of genes that may underlie the disorder, along with the broad phenotypic spectrum that overlaps with other skeletal diseases, provided a compelling case for the use of high-throughput sequencing (HTS) technology as an aid to OI diagnoses. The aim of this analysis was to present the data from our 5-year targeted HTS results, that includes the reporting of 9 novel and 24 known mutations, found in OI patients, from 5 different regions of Turkey. Materials and Methods: We performed a retrospective cross-sectional study, reporting the HTS results of 43 patients (23 female and 20 male; mean age: 9.5 years), directed to our center with a suspicion of OI between February 2015 and May 2020. Genetic analyses were also performed for 24 asymptomatic parents to aid the segregation analyses. We utilized an HTS panel targeting the coding regions of 57 genes associated with a reduction, increase, or abnormal development of bone mineralization. In addition, we sequenced the entire coding region of the IFITM5 gene through HTS. Results: Thirty-nine patients had at least one pathogenic/likely pathogenic variation (90.69%) in the COL1A1 (56.41%), COL1A2 (20.51%), FKBP10 (7.7%), P3H1 (5.13%), IFITM5 (5.13%), CTRAP (2.56%), or TMEM38B (2.56%) genes. Nine of the determined pathogenic/likely pathogenic variations were novel. The recurrent pathogenic mutations were c.1081C>T (p.Arg361Ter) (3/43), c.1405C>T (p.Arg469Ter) (2/43), and c.3749del (p.Gly1250AlafsTer81) in COL1A1 gene, along with c.-14C>T variation in the 5'UTR of the IFITM5 gene (2/43) and the c.890_897dup variation in the FKBP10 gene (2/43). Three out of 43 patients were carrying at least one additional variant of unknown significance, highlighting the importance of a multigene panel approach and segregation analyses. Conclusion: We suggest that a targeted HTS panel is a feasible tool for genetic diagnosis of OI in patients.

The Importance of Targeted Next-Generation Sequencing Usage in Cytogenetically Normal Myeloid Malignancies

Advanced diagnostic methods give an advantage for the identification of abnormalities in myeloid malignancies. Various researchers have shown the potential importance of genetic tests before the disease's onset and in remission. Large testing panels prevent false-negative results in myeloid malignancies. However, the critical question is how the results of conventional cytogenetic and molecular cytogenetic techniques can be merged with NGS technologies. In this paper, we drew an algorithm for the evaluation of myeloid malignancies. To evaluate genetic abnormalities, we performed cytogenetics, molecular cytogenetics, and NGS testing in myeloid malignancies. In this study, we analyzed 100 patients admitted to the Medical Genetics Laboratory with different 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%). NGS's pathogenic variation detection rate varies in disease groups: they were present in 85% of A.M.L. and 23% of M.D.S. Here, we identified 24 novel variations out of total pathogenic variations in myeloid malignancies. A total of 18 novel variations were identified in A.M.L., and 6 novel variations were identified in M.D.S. Despite long turnaround times, conventional techniques are still a golden standard for myeloid malignancies but sometimes cryptic gene fusions or complex abnormalities cannot be easily identified by conventional techniques. In these conditions, advanced technologies like NGS are highly recommended.

Investigation of the Relationship between Autism Spectrum Disorder and FOXP2, GRIN2B, KATNAL2 and GABRA4 Genes

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.

Targeted next-generation sequencing as a diagnostic tool in gastrointestinal system cancer/polyposis patients

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.

Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders

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.

Genetic screening results of individuals with high risk BRCA-related breast/ovarian cancer in Trakya region of Turkey

PURPOSE

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.

METHODS

Next generation sequencing (NGS) and multiplex ligation-dependent probe amplification methods (MLPA) were used to define germline BRCA1/BRCA2 positivity.

RESULTS

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.

CONCLUSION

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.

Genetic Analyses of the NF1 Gene in Turkish Neurofibromatosis Type I Patients and Definition of three Novel Variants

Neurofibromatosis Type I (NF1) is a multi systemic autosomal dominant neurocutaneous disorder predisposing patients to have benign and/or malignant lesions predominantly of the skin, nervous system and bone. Loss of function mutations or deletions of the NF1 gene is responsible for NF1 disease. Involvement of various pathogenic variants, the size of the gene and presence of pseudogenes makes it difficult to analyze. We aimed to report the results of 2 years of multiplex ligation-dependent probe amplification (MLPA) and next generation sequencing (NGS) for genetic diagnosis of NF1 applied at our genetic diagnosis center. The MLPA, semiconductor sequencing and Sanger sequencing were performed in genomic DNA samples from 24 unrelated patients and their affected family members referred to our center suspected of having NF1. In total, three novel and 12 known pathogenic variants and a whole gene deletion were determined. We suggest that next generation sequencing is a practical tool for genetic analysis of NF1. Deletion/duplication analysis with MLPA may also be helpful for patients clinically diagnosed to carry NF1 but do not have a detectable mutation in NGS.

aChE and BuChE inhibition by rivastigmin have no effect on peripheral insulin resistance in elderly patients with Alzheimer disease

BACKGROUND

Insulin resistance (IR) may play a role in most pathogenic processes that promote the development of Late Onset Alzheimer Disease (LOAD). This study was designed to determine the interaction between inhibition of both butyrylcholinesterase (BuChE) and acetylcholinesterase (AChE) with rivastigmine and peripheral insulin resistance (IR) in LOAD.

METHODS

Seventy-Nine consecutive elderly patients, 31 late onset AD and 48 non-demented patients were evaluated. IR was calculated with HOMA. All of the patients were evaluated through comprehensive geriatric assessments at baseline and in the 6th and 12th months.

RESULTS

End of the study, compared to the baseline values, there was a significant increase in the 6th month in both MMSE and IADL scores (t =2.200, p = 0.036 for MMSE and t =2.724, p= 0.011 for IADL, respectively). Rivastigmine was improved both the scores of MMSE and IADL in elderly patients with LOAD, but there was no significance or correlation between HOMA scores and cognitive status.

CONCLUSION

In conclusion, inhibition of both BuChE and AChE with rivastigmine was improved the cognition without affecting on the peripheral IR in the elderly patients with LOAD by HOMA. Due to the complexity of disease pathogenesis, it is too early to make general comments, and further longitudinal and long-term studies on this issue are needed.

Interaction between apolipoprotein-E and angiotensin-converting enzyme genotype in Alzheimer's disease

Both apolipoprotein-E (apo-E) epsilon 4 allele and angiotensin-converting enzyme (ACE) deletion (D) polymorphism have been associated with a high risk for coronary heart disease. Increased frequency of the epsilon 4 allele has also been reported in patients with late-onset of familial and sporadic Alzheimer's disease (AD). The primary aim of this study is to examine the possible relationship between the ACE gene polymorphism and AD. The second aim of this study is to explore the relation of the ACE and apo-E genotypes with AD. Polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), and agarose gel electrophoresis techniques were used to determine the apo-E and ACE genotypes. The frequencies of ACE D and ACE insertion (I) allele among AD patients and controls were 55.7 percent versus 44.2 percent and 51.7 versus 48.2 percent, respectively. Apo-E allele frequencies in the AD group for epsilon 2, epsilon 3 and epsilon 4 were, 1.7 percent, 96.5 percent, and 1.7 percent, respectively. The apo-E allele frequencies of healthy groups for epsilon 2, epsilon 3 and epsilon 4 were 1 percent, 56 percent, and 1.7 percent, respectively. In conclusion ACE D and apo epsilon 4 allele were found to be more frequent in patients with Alzheimer's disease than in the control group.

Apolipoprotein-E gene polymorphism and lipid profiles in Alzheimer's disease

In this study, the relationship between lipid profiles of sera and apolipoprotein E (apo E) gene polymorphism was investigated in 35 patients with Alzheimer's disease (AD) and 29 healthy people. Apo E genotypes and allele frequencies of the AD patient group were: apo E2/3, 2 (5.7 percent); apo E2/4, 1 (2.9 percent); apo E3/3, 26 (74.3 percent); apo E3/4, 5 (14.3 percent); apo E4/4, 1 (2.9 percent); epsilon 2, 3(4.2 percent); epsilon 3, 59 (84.2 percent); epsilon 4, 8 (11.4 percent). The healthy group's apo E genotypes and allele frequencies were: apo E2/3, 1 (3.4 percent); apo E3/3, 27 (93.1 percent); apo E3/4, 1 (3.4 percent); epsilon 2, 1 (1.7 percent); epsilon 3, 56 (96.5 percent); epsilon 4, 1 (1.7 percent). In Alzheimer's cases, epsilon 4 allele frequencies increased significantly as compared to the healthy group (p < 0.05). When the effects of the apo E isoforms on lipid profiles were evaluated, a relationship between apo E epsilon 4 allele and high total levels of serum cholesterol was found, whereas of apo E epsilon 2 allele was associated with the low total cholesterol of serum, although the difference was not statistically significant (p > 0.05). This study confirms the association of apo E epsilon 4 allele with lipid profiles in AD patients.

Generality of support sources and psychometric properties of a scale of perceived social support in Turkey

PURPOSE

The purpose of the study was to check the generality of the structure of social support sources as measured by the Multidimensional Scale of Perceived Social Support (MSPSS) and to examine the instrument's psychometric properties in Turkey. A previous study in Turkey showed that the definitions of support sources may differ across cultures and an attempt was made in the present study to incorporate definitions to make the scale more meaningful in Turkey.

METHOD

Three samples (psychiatry, surgery, and normal), each consisting of 50 subjects, were selected from a hospital in Turkey. No significant demographic differences were present between the samples. Factor analysis, Cronbach's alpha, correlations with other validated scales, and group comparisons were used for the analyses.

RESULTS

The original three support sources (family, friends, significant other) were found. However, in this version of the MSPSS the Family and the Significant other subscales incorporated definitions more meaningful in our samples. Internal consistency was high and correlations with the other scales showed adequate validity, particularly for the psychiatry and the surgery samples. The psychiatry sample reported the lowest levels of support.

CONCLUSION

The generality of support sources, with some differing definitions, was supported. The psychometric properties of the MSPSS were adequate for it to be used in Turkey. However, social support may be especially relevant for groups with psychological/medical problems, and support from close people (particularly the family) may be especially predictive of health.

Influence of a 3-week psychiatric training programme on attitudes toward mental illness in medical students

The present study was carried out to assess the influence of psychiatric training, including direct patient contact, on attitudes toward mental illness. An experimental group consisting of medical students going through their 3-week training in psychiatry was compared with a control group going through training in ophthalmology. The psychiatric training involved direct patient contact and course work. Attitudes toward three different vignettes were assessed before and after training. Analyses showed that there were no significant changes in the attitudes of the psychiatry group when compared to the ophthalmology group. Inconsistent findings in the literature were pointed out and a more analytical approach, focusing on the specific features of exposure, was suggested.

Perceived social support: psychometric properties of the MSPSS in normal and pathological groups in a developing country

The factorial structure, reliability and construct validity of the Multidimensional Scale of Perceived Social Support (MSPSS) were investigated in Turkey to check the generality of some of the previous findings from Western samples. Using samples consisting of normals and subjects with medical or mental health problems, the original three factors (subscales) were obtained. The internal consistencies of the MSPSS and its subscales were high. In general, the scales correlated significantly in the expected direction with measures of depression and anxiety, thus supporting the construct validity of the MSPSS. Among the samples, subjects with psychiatric/psychological problems perceived, in general, the least social support. This result further contributed to the construct validity of the scale.

Effect of psychiatric labels on attitudes toward mental illness in a Turkish sample

The influence of specific psychiatric labels and types of psychopathology on various attitudes were investigated in a sample (N = 84) of visitors of patients in a Turkish hospital. Vignettes representing two types of psychopathology with and without labels were used as the stimulus material and the attitudes toward those descriptions were assessed with the use of a questionnaire. Statistical analyses showed that labels had significant influence on recognition of mental illness, social distance, expected physical burden, and perception of treatment necessity. Type of psychopathology significantly influenced recognition of mental illness, social distance, expected physical burden, prognosis, and treatment choice. The results were discussed within the context of previous findings and the need for research pointed out.

Influence of having a hospitalized mentally ill member in the family on attitudes toward mental patients in Turkey

The influence of having a mentally ill member in the family on various attitudes was assessed. An exposed group (those having a mentally ill member) was compared with a no-exposure group. The attitudes assessed toward two vignettes included recognition of mental illness, social distance, expected burden, expected influence on one's health, treatment choice, and prognosis. The total sample consisted of 84 subjects selected from the family members of patients from psychiatric (exposed) and other (no-exposure) clinics. Direct experience with a mentally ill family member did not make a significant difference in the attitudes toward the vignettes, but the type of psychopathology did. The results were discussed within the context of findings from Western cultures.

Experienced Turkish nurses' attitudes towards mental illness and the predictor variables of their attitudes

General attitudes towards mental illness, attitudes towards two vignettes, and possible predictor variables of these attitudes were investigated among experienced Turkish nurses. The analyses showed that the nurses accepted both organic and psychological causation and had rather positive views on drug treatment, psychotherapy, and prognosis. However, they were more favourably disposed towards psychological causation and psychotherapy; the paranoid schizophrenia description was more readily perceived as mental illness and more 'negative' ratings were recorded for this than was the case in the description of neurosis. In terms of predictors, university education was related to lower acceptance of psychotherapy and chances of recovery; older respondents showed higher social distance to the neurosis vignette. The findings were discussed within the context of previous findings from Turkey and other countries.

Depression among alcoholics in a Turkish sample

The aim of the present study was to identify the predictor variables of depression among alcoholics in a Turkish mental hospital. A questionnaire and the Beck Depression Inventory (BDI) were utilized to collect data from 71 male alcoholics. A stepwise multiple regression analysis between the BDI scores and demographic and health-related variables resulted in the identification of marital problems and physical problems due to alcohol as the risk factors. The findings are discussed within the context of the findings from Western countries and the similarities are pointed out.

Attitudes toward mental illness: recognition, desired social distance, expected burden and negative influence on mental health among Turkish freshmen

Attitudes toward three types of disorders and a normal subject portrayed in vignettes were assessed among university students. The variables assessed were: perception of mental illness in the vignettes; desired social distance; emotional and physical burden expected; and expected negative influence on one's mental health from association with the type of persons portrayed in the vignettes. Analysis revealed that, in terms of variables assessed, the most "negative" ratings were recorded for the paranoid schizophrenic case and the most "positive" recorded for the normal subject. The simple schizophrenia and the anxiety neurosis/depression cases fell between the other two cases. Finally, with a few exceptions, all the variables assessed were significantly correlated with each other.

Diagnosis of mental disorders among Turkish and American clinicians

Turkish and American clinicians from two centres in each country were compared in terms of diagnosing mental disorders in standard cases and in terms of stereotypes of symptomatology. Statistical comparisons showed that the American clinicians rated higher symptom severity in the cases and in the stereotypes. In the diagnoses assigned the particular orientations of the centres became evident. Confidence in diagnosis was rather high in spite of inadequate information in the short cases. The shortcoming of psychiatric classification due to differences among clinicians and the need for more studies of their inferential strategies were pointed out.

Effect of type of cause on attitudes toward mental illness and relationships between the attitudes

The effects of four types of supposedly causative factors on judgements of mental illness, social distance, and prognosis were assessed among university students. Correlations between the components of attitudes were also examined. A vignette format was utilized. Analysis showed that the etiology of the case and the sex of the respondents had no significant influence except for sex in only one social distance item. However, there were statistically nonsignificant tendencies. Correlations revealed few significant relationships between the components of attitudes. The results are considered to be in line with previous research in the sense that attitudes toward mental illness are not highly structured.

Attitudes of Turkish and American clinicians and Turkish psychology students toward mental patients

A comparative study of Turkish and American clinicians and first and fourth year Turkish psychology undergraduates was carried out. The respondents' attitudes about the "behavior of a mental patient" were assessed through a semantic differential task. Statistical comparisons showed that the four groups were very similar to each other although there were some significant differences. The possibilities of Western influence, similar groups selecting the fields of psychiatry and psychology, and psychology students forming a special well-informed group were discussed. A need for further research to clarify the findings was pointed out.