Objective: A point mutation in the JAK2 gene, resulting in the substitution of valine for phenylalanine (JAK2 V617F), has been associated with myeloproliferative disorders such as polycythemia vera, essential thrombocythemia, idiopathic myelofibrosis, myelodysplastic syndromes, chronic myelomonocytic leukemia, systemic mastocytosis, chronic neutrophilic leukemia, and eosinophilic disorders. Material and Methods: The relation of JAK2 V617F mutation has been studied in myeloproliferative disorder patients by qPCR. The F617 allele was calculated using a standard calibration curve, including less and more than 50% mutational load groups. Results: A significant relation was found among wild type (wt), less and more than 50% groups, Regarding erythrocyte, hematocrit, platelet, and leukocyte levels. A statistically significant relation was found between wt and more than 50% of groups regarding hemoglobin levels. The mutational load increase has been shown to induce erythrocyte, hematocrit, and leukocyte levels, except platelet levels. Conclusion: In patients with myeloproliferative disorders, qPCR screening of JAK2 gene mutation is indicated.

Mulayim, Muhammed Fatih; Demirbas, Mustafa Hakan; Percin, Ferda E.; Arhan, Ebru; Kayhan, Gulsum Author Information

Objective: Human mitochondrial DNA is a circular, double stranded molecule which is inherited through maternal lineage. Point mutations in tRNA, rRNA or protein coding genes and structural rearrangements such as partial deletions or duplications can cause mitochondrial disorders. The prevalence of mitochondrial diseases is estimated to be 1/5000 worldwide. For the analysis of mtDNA mutations, Sanger sequencing, Southern blot, long and quantitative PCR, Resequencing Array and next-generation sequencing methods can be used. In this study, we analysed whole mitochondrial genomes of six children (along with their mothers) who were admitted to Gazi University Hospital with symptoms suggestive of mitochondrial disease. Materials and Methods: After the extraction of genomic DNA from six children and their mothers, mtDNA resequencing with the analysis of obtained data was performed. In order to determine whether one of the mutations found in Patient 4 was homoplasmic or heteroplasmic, PCR and RFLP techniques were also used. Results: Among six patients included in this study group, none of the variants detected could be attributed to any mitochondrial diseases, except the pathogenic mutation detected in Patient 4. The m.3460 G>A mutation detected in Patient 4 was located in the MT-ND1 gene that was known to be responsible for LHON. This mutation detected in Patient 4 was also detected both in his mother and sister with homoplasmic state. The lack of clinical findings in his mother and sister was thought to be due to decreased penetrance of the disease in females and modifying genes in nuclear genome. Conclusion: Screening of mtDNA using resequencing method could provide fast, effective and more reliable results in the diagnosis of mitochondrial diseases. Also, currently, the NGS technology analysis of nuclear DNA along with mtDNA will provide more reliable results in diagnosis of mitochondrial diseases, thus allowing more accurate genotype-phenotype correlation.

Suleiman-El-Hattab syndrome (SULEHS, OMIM #618950) is an autosomal recessive multisystem developmental disorder characterized by distinctive facial appearance, global developmental delay/intellectual disability, poor expressive speech and happy demeanor. SULEHS is an ultra-rare disorder associated with biallelic loss-of -function variants of the TASP1 gene, and up-to-date, seven patients from five families have been reported in the literature. Loss of TASP1 function has been reported to alter H3K4 histone modifications and expression of TFIIA and HOX transcription factors in the SULEHS phenotype. In this report, a new patient molecularly diag-nosed with SULEHS by a novel homozygous c.404-2A > G variant in the TASP1 gene is presented with the long-term follow-up. Although the majority of the patient's clinical characteristics were similar to those of previously reported SULEHS patients, this study was the first to describe some additional anomalies, such as cystic hygroma, increased nuchal thickness, coarctation of the aorta, pulmonary stenosis, pulmonary sequestration anomaly, chronic constipation, encephalomalacia, and aggressive behavior. Because of the remarkable similarities be-tween the clinical features of Baraitser-Winter syndrome (BRWS) and the patient, BRWS was considered the most likely diagnosis before the molecular diagnosis. Network analysis also supported that the interaction of the SULEHS-associated TASP1 gene with the BRWS-associated ACTB and ACTG1 genes through common interme-diate molecules. Overall, despite the existence of differences in clinical features, inheritance patterns, and un-derlying pathophysiology between BRWS and SULEHS, both diseases could be considered in the differential diagnosis due to the high clinical similarities, including the dysmorphic features, growth parameters, neuro-developmental phenotype, neurological problems, and multisystem involvement. Additionally, this report could contribute to a better understanding of the genotypic and clinical features of SULEHS by describing a novel pathogenic variant and new clinical features, such as prenatal manifestations.

Thauvin-Robinet-Faivre syndrome (TROFAS; OMIM #617107) is a rare autosomal recessive overgrowth syndrome characterized by generalized overgrowth, dysmorphic facial features, and delayed psychomotor development caused by biallelic pathogenic variants in the FGF-1 intracellular binding protein (FIBP) gene. To date, only four patients from two families have been reported. In this report, we present a 4-year-old male patient with generalized overgrowth and delayed developmental milestones consistent with this syndrome. In addition, he has unique features that were not reported in previous patients, including drooling, recurrent pulmonary infections, chronic pulmonary disease, hyperextensible elbow joints, hypoplastic nipples, unilateral cryptorchidism, and frequent spontaneous erections. We identified a homozygous, likely pathogenic variant, c.415_416insCAGTTTG (p.Asp139AlafsTer3), which causes a frameshift in the FIBP. Additionally, we identified a homozygous missense variant in the Toll-like receptor 5(TLR5) gene and a hemizygous missense variant in the chloride voltage-gated channel 4 (CLCN4) gene, with uncertain significance in either case. In this article, we set out the new observations and also discuss the frequency of the characteristic findings of the syndrome in the patients so far reported.

Data sharing is not applicable to this article as no new data were created or analyzed in this study.

Hypoxic-ischemic encephalopathy (HIE) is one of the substantial causes of developmental-cognitive disability in neonates. In this early period, it is difficult to diagnose accompanying or predisposing genetic diseases in HIE patients. Herein, we present a patient with HIE who was diagnosed with Pitt-Hopkins syndrome in the newborn period.

Mesomelic dysplasias are a genetically and clinically heterogeneous group of diseases with more than 10 types defined. This article presents an 18-year-old female patient with normal intelligence and a multisystem phenotype including disproportionate short stature, scoliosis, mesomelic limb shortening, radial bowing, short fourth to fifth metacarpals and metatarsals, fusions in the carpal/tarsal bones, operated pes equinovarus, primary amenorrhea, uterine hypoplasia, vesicoureteral reflux, and chronic kidney disease. Whole-exome sequencing revealed a de novo heterozygous c.881T>G (p.Met294Arg) variant in HOXA11 (NM_005523.6) gene. The variant was located in the homeodomain of HOXA11 and predicted to alter DNA-binding ability of the protein. In silico analyses indicated that the variant could promote the alterations in the protein-protein interaction. The possible functional effect of the variant was supposed as dominant-negative. Hoxa11-mutant mice have been reported to exhibit homeotic transformations in the thoracic and sacral vertebrae, zeugopodal phenotype in forelimb and hindlimb, and urogenital abnormalities. Although mice models were reported as mesomelic dysplasia and urogenital abnormalities (MDUGA), this phenotype has not yet been reported in humans. This was the first case with MDUGA putatively related to a de novo variant in HOXA11.

Backround: Intellectual disabilities, developmental delay and accompanying congenital anomalies are rarely seen on general population, but have a large etiologic spectrum. Chromosomal abnormalities are one of the significant reasons of intellectual disabilities, dysmorphic appearance and various congenital anomalies. Conventional cytogenetic techniques can only detect abnormalities greater than 5 Mb. Array based methods can be useful to detect anomalies smaller than 3 Mb to kilobase levels with a ratio of 12-14%. As a result, small interstitial deletions and duplications could be detected and new genes could be discovered with microarray techniques. Methods: In this study, 29 patients with idiopathic intellectual disability, developmental delay and/or congenital anomaly, had been investigated for small deletions or duplications with "Array CGH 8x60K ISCA". Results: Causative/ probably causative pathology was detected in 6 patients and the diagnostic power of these systems was confirmed, and we obtained a yield of 20.6%. Feingold syndrome 1, Williams syndrome with atypical findings, 14q11.2 deletion syndrome and 1p36 deletion syndrome, 13q14.3-q21.1 duplication spanning PCDH17 gene and a duplication in Xp11.4 chromosomal region containing ATP6AP2 gene were detected. We reported second Feingold syndrome with renal agenesis and first case of 14q11.2 deletion syndrome with episodic vomitting attacks. Conclusion: Microarray technology is the first-tier diagnostic method in patients with intellectual disability with multiple congenital anomalies. The genotype-phenotype correlation studies provide explaining the etiology and molecular mechanism of intellectual disability and developmental delay.

Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever, abdominal pain, serositis, articular manifestations, erysipelas-like erythema, and renal complications as its main features. Caused by the mutations in the MEditerranean FeVer (MEFV) gene, it mainly affects people of Mediterranean descent with a higher incidence in the Turkish, Jewish, Arabic, and Armenian populations. As our understanding of FMF improves, it becomes clearer that we are facing with a more complex picture of FMF with respect to its pathogenesis, penetrance, variant type (gain-of-function vs. loss-of-function), and inheritance. In this study, MEFV gene analysis results and clinical findings of 27,504 patients from 35 universities and institutions in Turkey and Northern Cyprus are combined in an effort to provide a better insight into the genotype-phenotype correlation and how a specific variant contributes to certain clinical findings in FMF patients. Our results may help better understand this complex disease and how the genotype may sometimes contribute to phenotype. Unlike many studies in the literature, our study investigated a broader symptomatic spectrum and the relationship between the genotype and phenotype data. In this sense, we aimed to guide all clinicians and academicians who work in this field to better establish a comprehensive data set for the patients. One of the biggest messages of our study is that lack of uniformity in some clinical and demographic data of participants may become an obstacle in approaching FMF patients and understanding this complex disease.

Interstitial lung disease (ILD) is a condition affecting the lung parenchyma by inflammation and fibrosis and can be caused by various exposures, connective tissue diseases (CTD), and genetic disorders. In this report, a family with five patients having progressive respiratory failure that begins with coughing in adolescence, followed by dyspnea and recurrent spontaneous pneumothorax, and death in early adulthood is presented. The patients were diagnosed to have ILD through clinical and radiological evaluations. Molecular genetic analyses of the family provided two homozygous rare variants in the WRN and SFXN5 genes, co-segregating with the phenotype. The network analyses pointed out that the variant in the WRN, rather than that in the SFXN5 gene, could be the main factor in the existence of the ILD phenotype, putatively through the altered DNA repair and telomere maintenance pathways. In silico analyses suggested that the variant could affect the exonuclease activity or the stability of the WRN protein. Moreover, the adolescent-onset pulmonary phenotype described in the case has not been reported in Werner Syndrome, the only disease known to be associated with biallelic WRN pathogenic variants. Thus, the present phenotype could be either a very atypical presentation of Werner syndrome or a new clinical entity associated with the WRN gene.

ABS TRACT Auriculocondylar syndrome is a rare autosomal dominant or recessive disorder characterized by question-mark ears, a small mandibular condyle, and micrognathia.From a molecular perspective, auriculocondylar syndrome arises due to mutations in the PLCB4, GNAI3, and EDN1 genes that play roles in the endothelin signaling pathway.Here, we report a patient with findings of auriculocondylar syndrome and an additional mild intellectual disability.The patient's whole exome sequencing analyses revealed a novel homozygous frameshift mutation in the PLCB4 gene related to auriculocondylar syndrome Type 2. Our molecular studies indicated that this mutation caused a downregulation of PLCB4.This type of PLCB4 mutation has seldom been reported in auriculocondylar syndrome-2 patients and only 2 of them have had neurodevelopmental anomalies, as in our patient.We think that this study supports the possibility of intellectual disability in individuals with a homozygous truncating variant in the PLCB4 gene and contributes to the literature.

Background/aim: Anorectal malformations (ARM) are classified as multifactorial diseases. The etiology of ARM is still not clear because of the complexity of the pathologic changes. Materials and methods: In the present study, the array-CGH results of 10 patients with ARM not associated with a specific syndrome despite having some additional findings were evaluated. Array-CGH analysis was performed using the 8x60K ISCA, Agilent® microarray platform. Pathogenic CNVs were further confirmed using fluorescence in situ hybridization (FISH) or quantitative real-time polymerase chain reaction (qPCR). Results: Chromosome 22q11.2 deletion was detected in two patients. One of these patients had anal stenosis, minor cardiac abnormalities, and a small 0.89-Mb deletion. The second patient had anal atresia, immune deficiency, inguinal hernia, and a 2.7-Mb cryptic deletion. The overlapping genes in the deletion regions of the two patients were DGCR5, DGCR6 and PRODH . Conclusion: DGCR6 , alters the expression of important genes such as TBX1 and affects neural crest migration. Considering that ARMs are caused by abnormalities in neural crest cell migration, it is thought that these genes may play a role in the etiology of ARM. To our knowledge, this region is one of the smallest interstitial deletions in the chromosome 22q11.2 region to be published to date. Further research on the DGCR6 gene, which may be a candidate gene responsible for anal atresia, will clarify this point. This article been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Reco rd. Please this article as: Ozyavuz P, Kayhan G, Perçin EF. Molecular karyotyping in anorectal malformations: Could DGCR6 gene haploinsufficiency cause anal atresia in 22q11 deletion syndrome?. Erciyes

Recent studies suggest that copy number variations (CNVs) play a significant role in the aetiology of ASD. This study aims to investigate CNVs, which are thought to be an important factor in ASD etiology. In addition it was aimed to specify the clinical usefulness of chromosomal microarrays (CMA) in the examination of ASD patients in Turkish population. Of 47 children (60.34±25.60 months; 82.9% boys) with ASD were constructed the sample. The karyotype structure of all participants was found to be normal using conventional cytogenetic methods. DNA obtained from the venous blood samples of the participants was evaluated using SurePrint G3 ISCA V2 CGH 8x60K Array (Agilent Technologies Santa Clara, CA, USA). We have identified 8 CNVs, ranging in size from 55 kb to 6.5 Mb in 7 (5 boys) of 47 children with ASD of the 4 of 8 CNVs were classified as pathogenic, which were 9p24.3p24.2 deletion in 3 Mb size, 15q11-q13 duplication in 6.5 Mb size, 16p11.2 deletion in 598 kb size and 22q13.3 deletion in 55 kb size. According to results has been demonstrated that diagnostic yield of CMA in Turkish children with ASD was 8.5%. Our results indicate that CNVs contribute a part to the genetic aetiology of Turkish children with ASD. In accordance with the literature, these results emphasize the clinical importance of CMA to investigate the aetiology of ASD.

Background/aim: Prenatal diagnosis is vital to obtain healthy generation for risky pregnancies. There have been several approaches, some of which are routinely applied in clinics to evaluate the possible prenatal deficiencies and/or diseases. In the present study, we aimed to isolate the fetal cells from endocervical samples and try to identify possible anomalies which were proved by Amniocentesis (AS) and chorionic villus sampling (CVS) methods. Materials and methods: Endoservical specimens were collected from 100 pregnant women. Cells were separated in parallel by fluorescence-activated cell sorting (FACS) and magnetic-activated cell sorting (MACS) using human leukocyte antigen (HLA) G233 and placental alkaline phosphatase (PLAP) antibodies. CMA (comprehensive meta-analysis) were carried out and male fetuses were confirmed with Sex determining region Y (SRY) amplification. Results: The percent of HLA G233 and placental and placental alkaline phosphatase (PLAP) positive cells were 4.55% and 84.59%, respectively. The percent of cells positive for both markers was 14.75%. CMA analyses were not informative. (SRY) was amplified in 67% of the samples. Conclusion: However, the success rate of the both cell sorting and scanning of DNA anomalies by aCGH and/or RT-PCR was limited, preventing the applicability of this proposal in the clinics. Still, the success of the proposed method depends on the development of the novel fetal cell-specific antibodies and the improvements in the sorting systems.

Abstract The camptomelic dysplasia syndrome is a rare skeletal dysplasia which includes, in addition to typical angulations of long bones, other skeletal abnormalities and visceral lesions, particularly those of the brain and of the respiratory tract. Respiratory disorders often lead to death in early infancy. Its etiology has not yet been determined. In this article, a case with a bowing of the upper extremities has been presented. Özet Kamptomelik displazi sendromu, uzun kemiklerde özellikle tibiada konjenital kavislenme ile birlikte diğer iskelet anomalileri, özellikle sinir sistemi ve solunum sistemim tutan lezyonlarla karakterize nadir bir iskelet displazisidir, solunum sistemi bozuklukları, sıklıkla erken çocukluk döneminde ölüme yol açar. Etyolojisi henüz bilinmemektedir. Bu yazıda üst ekstremitelerinde de kavislenmesi olan bir olgu sunuldu.

Introduction: The restless legs syndrome (RLS) is a common heritable neurologic disorder which is characterized by an irresistible desire to move and unpleasant sensations in the legs. Methods: We aim to identify new variants associated with RLS by performing genome-wide linkage and subsequent association analysis of forty member's family with history of RLS. Results: We found evidence of linkage for three loci 7q21.11 (HLOD = 3.02), 7q21.13-7q21.3 (HLOD = 3.02) and 7q22.3 (HLOD = 3.09). Fine-mapping of those regions in association study using exome sequencing identified SEMA3A (p-value = 8.5.10(-)(4)), PPP1R9A (p-value = 7.2.10(-4)), PUS7 (p-value = 8.7.10(-4)), CDHR3 (p-value = 7.2.10(-4)), HBP1 (p-value = 1.5.10(-4)) and COGS (p-value = 1.5.10(-4)) genes with p-values below significance threshold. Conclusion: Linkage analysis with subsequent association study of exome variants identified six new genes associated with RLS mapped on 7q21 and q22.

Objective: Anorectal malformations (ARM) are classified as a multifactorial disease. The etiology of ARM is still not clear due to the complexity of the pathological anomalies. Materials and Methods: The microarray-based comparative genomic hybridization (array CGH) results of 10 patients with ARM not associated with a specific syndrome were analyzed using the 8x60K ISCA Agilent microarray platform (Human Genome CGH Microarray; Agilent Technologies, Inc., Santa Clara, CA, USA). Pathogenic copy number variants were further confirmed using fluorescence in situ hybridization or quantitative real-time polymerase chain reaction testing. Results: Chromosome 22q11.2 deletion was detected in 2 patients. One of these patients had anal stenosis, minor cardiac abnormalities, and a small 0.89-Mb deletion. The second patient had anal atresia, immune deficiency, inguinal hernia, and a 2.7-Mb cryptic deletion. The overlapping genes in the deletion regions of the 2 patients were the DGCR5, DGCR6, and PRODH genes. Conclusion: DGCR6 alters the expression of important genes such as TBX1 and affects neural crest migration. Given that ARM are caused by abnormalities in neural crest cell migration, it may be that these genes play a role in the etiology. To our knowledge, this is one of the smallest interstitial deletions in the chromosome 22q11.2 region to be published to date. Further research on the DGCR6 gene, which may be a candidate gene responsible for anal atresia, will clarify this point.