Direct DNA Sequence Analysis Research Articles

Frequency of the 'Asia type' DEL with weak D phenotype in Chinese.

DEL individuals account for 9-30% of serological RhD negative population in east Asia and majority of them carrying the RHD*DEL1 allele are referred to as 'Asia type' DEL individuals. There is a lack of data on the molecular basis for 'Asia type' DELs with weak RhD phenotype. Therefore, the aim of this study is to unveil 'Asia type' DELs by elucidating the genetic background and analyzing the serological results METHODS: With a microplate typing protocol, RhD characterization was performed in samples from one million blood donors collected at Chengdu blood center during the period from 2019 to 2022. RhD confirmatory test was performed by direct antiglobulin test and indirect antiglobulin test with five anti-D reagents to detect RhD variants. Molecular characterization of samples categorized as RhD variants was studied by using direct genomic DNA sequencing and RHD zygosity analysis, followed by adsorption and elution tests conduced for samples carrying RHD*DEL1 allele to confirm the presence of RhD antigens on the red cells RESULTS: We reported here 21 RhD variant samples were detected by micro-column gel agglutination assay with IgG anti-D antibodies. Moreover, the agglutination reaction was stronger with IgG anti-D reagents in micro-column gel card than with IgM/IgG blended anti-D antibodies. Each of the 21 samples carried the RHD*DEL1 allele, which indicated that they were 'Asia type' DEL. Of the 21 'Asia type' DEL samples, 9 samples were detected to be RHD+/ RHD+ homozygotes, whereas the other 12 samples were RHD+/RHD- hemizygotes. Among the samples phenotyped for RhCE, seven were CCee and four were Ccee. In this study, DEL samples carrying RHD*DEL1 showed weak RhD phenotype with some anti-D reagents in RhD confirmatory test, which suggest that a serology strategy using several anti-D reagents may be helpful to detect this 'Asia type' DEL. Further studies are needed to elucidate whether the 'Asia type' DELs with weak RhD phenotype have stronger antigenicity and could cause serious transfusion reaction.

Genetic diversity of Helicobacter pylori type IV secretion system cagI and cagN genes and their association with clinical diseases

A number of cagPAI genes in the Helicobacter pylori genome are considered the most evolved genes under a diversifying selection and evolutionary pressure. Among them, cagI and cagN are described as a part of the two different-operon of cagPAI that are involved in the T4SS machinery, but the definite association of these factors with clinical manifestations is still unclear. A total of 70 H. pylori isolates were obtained from different gastroduodenal patients. All isolates were examined for the presence of primary H. pylori virulence genes by PCR analysis. Direct DNA sequence analysis was performed for the cagI and cagN genes. The results were compared with the reference strain. The cagI, cagN, cagA, cagL, vacA s1m1, vacA s1m2, vacA s2m2, babA2, sabA, and dupA genotypes were detected in 80, 91.4, 84, 91.4, 32.8, 42.8, 24.4, 97.1, 84.3, and 84.3% of the total isolates, respectively. The most variable codon usage in cagI was observed at residues 20–25, 55–60, 94, 181–199, 213–221, 241–268, and 319–320, while the most variable codon usage in CagN hypervariable motif (CagNHM) was observed at residues 53 to 63. Sequencing data analysis of cagN revealed a hypothetical hexapeptide motif (EAKDEN/K) in residues of 278–283 among six H. pylori isolates, which needs further studies to evaluate its putative function. The present study demonstrated a high prevalence of cagI and cagN genes among Iranian H. pylori isolates with gastroduodenal diseases. Furthermore, no significant correlation between cagI and cagN variants and clinical diseases was observed in the present study. However, all patients had a high prevalence of cagPAI genes including cagI, cagN, cagA, and cagL, which indicates more potential role of these genes in disease outcome.

A novel mutation in TANGO2 gene associated with recurrent muscle weakness with rhabdomyolysis , metabolic encephalopathy and cardiac arrhythmia: a case report

Background TANGO2 depletion was found to cause clinically recognizable multi-organ involvement disorder in pediatrics with episodic muscle weakness recurrent rhabdomyolysis, intellectual disability, metabolic encephalomyopathic crises and cardiac arrhythmia. TANGO2 deficiency is also referred to as \"metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration\" (MECRCN) in OMIM. * 616830 Case presentation We report a case of a 4-year-old Saudi boy from a consanguineous Saudi family with two uncles deceased at 3 year of age with recurrent muscle weakness and hyperammonemia of unknown cause .Patient in last attack progressed to severe metabolic encephalomyopathic crisis that required assisted ventilation for 4 months, complicated with life threatening cardiac tachyarrhythmia. Laboratory findings of hypoglycemia, mild hyperammonemia , severely elevated plasma Creatine Kinase, myoglobinuria , lactic acidosis and increased TSH concentration indicating hypothyroidism have been documented. The clinical profile was highly suggestive of TANGO2-realted disorder. Direct DNA sequence analysis of the entire coding regions of TANGO2 gene identified a novel homozygous deletion for three nucleotides in exon 2 (c.11_13delTCT) resulting in amino acid deletion (phenylalanine) at position 5. Conclusion This report illustrates the importance of collating clinical data and keeping a high index of suspicion in order to reach to the diagnosis.

DNAR-04. BOTH P53 CODON 72 ARG/ARG AND PRO/ARG GENOTYPES IN GLIOBLASTOMA MULTIFORME PATIENTS HAVE A BETTER PROGNOSIS IN BEVACIZUMAB TREATMENT

Abstract BACKGROUND In glioblastoma multiforme (GBM), bevacizumab increased progression-free survival but it has failed to improve overall survival (OS) in controlled trials. This study, therefore, aimed to retrospectively analyze the polymorphisms of p53 codon 72 and the clinical characteristics of GBM specimens from Taiwanese patients. METHODS The polymorphisms of p53 codon 72 in 99 patients with GBM treated at Taichung Veterans General Hospital in Taiwan from 2007 to 2017 were analyzed using direct DNA sequencing and PCR-RFLP analysis. RESULTS We found that among these GBM patients, the polymorphisms of p53 codon 72 were not directly associated with the overall survival of GBM, both the Arg/Arg and Arg/Pro genotypes were associated with significant benefits in terms of overall survival in patients treated with CCRT plus bevacizumab compared to patients treated with CCRT alone. CONCLUSIONS This pilot study suggests that both the Arg/Arg and Arg/Pro genotypes of p53 codon 72 polymorphism may have value as independent prognostic or predictive parameters for bevacizumab treatment response and failure. Relatedly, the results of the study further demonstrate the utility of stratifying GBM patientsaccording to bevacizumab sensitivity.

Molecular heterogeneity of factor XI deficiency in Tunisia.

Factor XI (FXI) deficiency is a rare inherited bleeding disorder that is highly prevalent in Ashkenazi Jewish ancestry but sporadically observed in most ethnic groups. It is heterogeneous both in clinical presentation and in genetic causality. Although a large spectrum of mutations associated with this disorder has been reported in several populations, genetic data of FXI deficiency in Tunisia are poorly described. The purpose of this study was to determine the molecular basis of FXI deficiency among Tunisian patients. Fourteen index cases from nine unrelated families with FXI deficiency, referred to Hemophilia Treatment Center of Aziza Othmana Hospital, were included in this study. The patients' F11 genes were amplified by PCR and subjected to direct DNA sequencing analysis. Sequencing analysis of F11 genes identified three distinct mutations; the Jewish type II nonsense mutation E117X, one previously reported missense mutation E602Q and one novel missense mutation V271M, which led to the disruption of the third apple domain structure of FXI. Furthermore, seven polymorphisms previously described, were also detected: C321F, c. 294A>G, -138 A>C, p.D125D, p.T249T, p.G379G, p.D551D. This report represents the first genetic study analyzing the molecular characteristics of factor XI deficiency within Tunisian population. Identification of the Jewish type II mutation in two families, as well as one missense previously reported mutation and one novel mutation confirmed the genetic heterogeneity of this disorder. Screening a large number of Tunisian factor XI deficient would reveal the spectrum mutations causing factor XI deficiency in Tunisia.

CNS tumor with BCOR internal tandem duplication: Clinicopathologic, molecular characteristics and prognosis factors

The central nervous system tumor with BCOR internal tandem duplication (CNS tumor with BCOR ITD) is a recently identified rare tumor entity, the complete morphologic characteristic, genetic alteration, classification, clinical outcomes and optimal treatment for this tumor entity have not been fully clarified. Here, two new cases of CNS tumor with BCOR ITD were reported and the clinicopathologic, molecular characteristics, and prognosis were analyzed through reviewing of the reported literature. The histological features included a clear border with adjacent brain parenchyma, an extensively microcystic background, and the cells with round to oval nuclei containing delicate chromatin, ependymoma-like perivascular pseudorosettes, and palisading necrosis. Immunohistochemical features showed strong and diffuse positive expression for BCOR, scattered positive expression for OLIG2, and negative expression for GFAP, Syn, and EMA. PCR and direct DNA sequencing analysis identified exon 15 ITD of the BCOR gene in both cases. Interestingly, both cases revealed two duplication segments, which had not been reported in the literature. A review of the literature shows that CNS tumor with BCOR ITD has a poor prognosis with a median survival of 1.7 years; surgical gross total resection is a good prognostic factor. A combination of radiation treatment and chemotherapy, while trending towards significance, does not reach statistical significance. On the contrary, the OS is not associated with age, gender, and tumor location. In conclusion, CNS tumor with BCOR ITD is a rare tumor entity with characteristic morphologic and molecular features and a poor prognosis. The optimal treatment strategies need further studies.

Investigation of androgen receptor gene CAG repeat length polymorphism in pubertal gynecomastia.

Androgen receptor gene CAG repeat, AR (CAG)n, polymorphism is thought to have an effect on male reproductive functions and a relationship between long AR (CAG)n and decreased androgenic activity has been shown. Therefore, we hypothesized that in adolescents with long AR CAG repeat the prevalence of pubertal gynecomastia (PG) will be higher and we aimed to investigate the association between AR (CAG)n polymorphism and PG in Turkish adolescents. Adolescents with PG between 11 and 19 years of age were enrolled as the study group and healthy individuals without a history of PG, who were at least 14 years of age and Tanner 4 or 5 were enrolled as the control group. The AR (CAG)n length was detected by direct DNA sequencing analysis and reproductive hormones were measured by standardized analyses. The mean AR (CAG)n was 22.3±2.6 (mean±SD) in the PG group (n=101) and 21.9±3.1 (mean±SD) in the control group (n=88) (p=0.276). The adolescents with short AR (CAG)n had lower body mass index standard deviation scores (BMI SDS) compared to the adolescents with intermediate and long repeat numbers (p=0.029). The results of this study showed a lack of direct association between AR (CAG)n and PG. However, the significant relationship between the AR (CAG)n quartiles and BMI SDS suggests that long AR (CAG)n might cause PG indirectly. Further studies are needed to better clarify this relationship.

RUS6, a DUF647-containing protein, is essential for early embryonic development in Arabidopsis thaliana

BackgroundThe Arabidopsis RUS (ROOT UV-B SENSITIVE) gene family contains six members, each of which encodes a protein containing a DUF647 (domain of unknown function 647) that is commonly found in eukaryotes. Previous studies have demonstrated that RUS1 and RUS2 play critical roles in early seedling development. All six RUS genes are expressed throughout the plant, but little is known about the functional roles of RUS3, RUS4, RUS5 and RUS6.ResultsWe used a reverse-genetic approach to identify knockout mutants for RUS3, RUS4, RUS5 and RUS6. Each mutant was confirmed by direct DNA sequencing and genetic segregation analysis. No visible phenotypic differences were observed in rus3, rus4, or rus5 knockout mutants under standard growth conditions, but rus6 knockout mutants displayed a strong embryo-lethal phenotype. Two independent knockout lines for RUS6 were characterized. The rus6 mutations could only be maintained through a heterozygote, because rus6 homozygous mutants did not survive. Closer examinations of homozygous rus6 embryos from rus6/ + parent plants revealed that RUS6 is required for early embryo development. Loss of RUS6 resulted in embryo lethality, specifically at the mid-globular stage. The embryo-lethality phenotype was complemented by a RUS6::RUS6-GFP transgene, and GFP signal was detected throughout the embryo. Histological analyses with the β-glucuronidase reporter gene driven by the RUS6 promoter showed tissue- and development-specific expression of RUS6, which was highest in floral tissues.ConclusionOur data revealed that RUS6 is essential for early embryo development in Arabidopsis, and that the RUS gene family functions in multiple stages of plant development.

Association of Erythropoietin Gene Polymorphisms With Type 2 Diabetic Retinopathy in Adult Patients From Northern India

ObjectivesOur aim in this study was to determine the association of erythropoietin (EPO) gene polymorphisms with diabetic retinopathy in patients with type 2 diabetes from northern India. MethodsIn this case-control study, we recruited 614 participants, consisting of 302 diabetic retinopathy cases and 312 individuals with confirmed type 2 diabetes without retinopathy as controls. EPO polymorphism analysis was performed in all participants using polymerase chain reaction and direct DNA sequence analysis. ResultsThe genotype distribution and allele frequency of the c.246+265G>A (rs507392) polymorphism differed significantly (p<0.05) between the retinopathy and control groups. For the −1306C>A (rs1617640) polymorphism, genotype distribution among the 2 groups analyzed differed significantly (p=0.047), but the distribution of allele frequency was not found to be statistically significant (p=0.07). For the c.∗772G>T (rs551238) variant, genotype distribution did not differ significantly when comparing the 2 groups (p=0.062), but allele frequency distribution did differ significantly (p=0.045). For the polymorphisms analyzed, namely rs507392 and rs1617640, a statistically significant association with retinopathy was observed (dominant model: adjusted odds ratio [OR], 2.23; 95% confidence interval [CI], 1.36 to 3.35; p<0.01; codominant model: adjusted OR, 1.45; 95% CI, 1.00 to 2.09; p=0.048). However, no significant association between c.∗772G>T (rs551238) polymorphism and diabetic retinopathy was found. ConclusionsOur findings show 2 polymorphisms (c.246+265G>A [rs507392] and −1306C>A [rs1617640]) in EPO to be risk factors for type 2 diabetic retinopathy in a northern Indian cohort. To our knowledge, this is the first report from India to demonstrate an association between EPO gene polymorphisms and retinopathy.

DeepSRE: Identification of sterol responsive elements and nuclear transcription factors Y proximity in human DNA by Convolutional Neural Network analysis.

SREBP1 and 2, are cholesterol sensors able to modulate cholesterol-related gene expression responses. SREBPs binding sites are characterized by the presence of multiple target sequences as SRE, NFY and SP1, that can be arranged differently in different genes, so that it is not easy to identify the binding site on the basis of direct DNA sequence analysis. This paper presents a complete workflow based on a one-dimensional Convolutional Neural Network (CNN) model able to detect putative SREBPs binding sites irrespective of target elements arrangements. The strategy is based on the recognition of SRE linked (less than 250 bp) to NFY sequences according to chromosomal localization derived from TF Immunoprecipitation (TF ChIP) experiments. The CNN is trained with several 100 bp sequences containing both SRE and NF-Y. Once trained, the model is used to predict the presence of SRE-NFY in the first 500 bp of all the known gene promoters. Finally, genes are grouped according to biological process and the processes enriched in genes containing SRE-NFY in their promoters are analyzed in details. This workflow allowed to identify biological processes enriched in SRE containing genes not directly linked to cholesterol metabolism and possible novel DNA patterns able to fill in for missing classical SRE sequences.

A Partial Phenotype of adFNDI Related to the Signal Peptide c.55G&gt;A Variant of the AVP Gene

The autosomal dominant familial form of neurohypophyseal diabetes insipidus (adFNDI) is a rare inherited endocrine disorder characterized by hypotonic polyuria, severe thirst and polydipsia, which results from a deficient neurosecretion of the antidiuretic hormone, also known as arginine vasopressin (AVP). To date, adFNDI has been linked to more than 70 different heterozygous point mutations of the 2.5 kb AVP gene, encoding the composite precursor protein of AVP. A minority of disease-causing mutations, such as the common c.55G&gt;A variant, are predicted to affect amino acid residues close to the signal peptide (SP) cleavage site, and result in abnormal post-translational processing and intracellular trafficking of AVP precursors exerting neurotoxic activity on vasopressinergic magnocellular neurons. Generally, SP variants cause a gradual decline in the neurohypophyseal secretion of AVP in small children, although a wide variability in clinical onset and severity of manifestations has been reported. For the first time, we describe a kindred from Calabria (Southern Italy) with adFNDI and document a partial clinical phenotype in one female young adult member of the family. Methods: A young adult woman was subjected to clinical, neuroradiological and genetic assessments for a mild, adolescent-onset, polyuric state at our Endocrinology Unit. Her family medical history revealed an early-onset (&lt;12 years of age) occurrence of polyuria and polydipsia, which was successfully managed with high doses of oral desmopressin, and a typical adFNDI inheritance pattern that was seen over three generations. Results: In the index patient, the extensive hypertonic dehydration during fluid deprivation test elicited a prompt elevation of urine osmolality and diuresis contraction, indicative of a partial adFNDI phenotype. Diagnosis was confirmed by concordant hormonal tests and magnetic resonance imaging (MRI) evidence of a reduced hyperintense signal of the neurohypophysis, which was regarded as compatible with the depletion of the vasopressinergic magnocellular neurons. Direct DNA sequencing and restriction enzyme cleavage analysis revealed that a heterozygous c.55G&gt;A transition, predicting a p.Ala19Thr replacement in the C-terminal region of SP, was the cause of adFNDI in the investigated kindred. Conclusions: The identification of the genetic cause of aFNDI in this Calabrian kindred provides further information and confirms the wide variability of disease onset and severity of manifestations related to SP variants of the AVP gene, supporting the need for genetic testing in all patients with familial occurrence of polyuria, regardless of their clinical and radiological phenotype. Even though sexual differences in the antidiuretic responses are documented, it is unclear whether female gender would attenuate clinical disease progression in the presence of a pathogenic c.55G&gt;A mutation.

Glutaric aciduria type 1: Genetic and phenotypic spectrum in 53 patients

IntroductionGlutaric aciduria type 1 (GA1) is a rare and inherited autosomal-recessive metabolic disorder that occurs in the deficiency of glutaryl-co-enzyme A dehydrogenase (GCDH) enzyme encoded by GCDH gene. In this study, we aim to retrospectively investigate the clinical, biochemical, and neuroradiological parameters and examine the spectrum of GCDH gene variants in Turkish patients with glutaric aciduria type 1. MethodsThis is a descriptive cross-sectional study. The study was conducted in fifty-three patients from 39 unrelated Turkish families who were diagnosed with GA1 based on their clinical presentation, neuroimaging, and biochemical measurements, at the department of pediatric metabolism of a university hospital between June 1998 and August 2019. Pathogenic variants screening of GCDH gene was performed by direct DNA sequence analysis in forty-six patients with GA1. Pathogenicity of the novel variants was predicted via computational programs. ResultsA total of 53 patients were diagnosed with GA1. Of those, 32 (60.3%) had encephalopathic crisis and 33 (62.3%) had macrocephaly.Twenty different pathogenic variants were detected, 7 of which are novel (p.Glu57Lys, p.Ser145Profs*79, p.Ser246Glyfs*96 p.Ala293Val, p.His348Gln, p.His417Tyr, p.Asp418Val). The p.Arg402Trp, p.Pro248Leu and p.Leu340Phe variants were the most common in Turkish patients, with a frequency of 21.2%, 18.2% and 12.1% respectively. ConclusionThis study is the first comprehensive research from Turkey that provides information about disease-causing variants in the GCDH gene. The identification of common variants and hot spot regions of the GCDH gene is important for genetic counselling and the prenatal diagnosis of Turkish patients with GA1.

Genes encoding equine β-lactoglobulin (LGB1 and LGB2): Polymorphism, expression, and impact on milk composition.

β-lactoglobulin is one of the most abundant milk whey proteins in many mammal species, including the domestic horse. The aim of this study was to screen for polymorphism in the equine LGB1 and LGB2 gene sequences (all exons, introns, and 5’-flanking region) and to assess potential relationship of particular genotypes with gene expression levels (measured in milk somatic cells) and milk composition traits (protein, fat, lactose, and total β-lactoglobulin content). Direct DNA sequencing analysis was performed for twelve horse breeds: Polish Primitive Horse (PPH), Polish Coldblood Horse (PCH), Polish Warmblood Horse (PWH), Silesian, Hucul, Fjording, Haflinger, Shetland Pony, Welsh Pony, Arabian, Thoroughbred, and Percheron—and revealed the presence of 83 polymorphic sites (47 and 36 for LGB1 and LGB2 genes, respectively), including eight that were previously unknown. Association analysis of the selected polymorphisms, gene expression, and milk composition traits (conducted for the PPH, PCH, and PWH breeds) showed several statistically significant relationships; for example, the two linked LGB1 SNPs (rs1143515669 and rs1144647991) were associated with total milk protein content (p < 0.01). Our study also confirmed that horse breed had significant impact on both gene transcript levels (p < 0.01) and on milk LGB content (p < 0.05), whereas an influence of lactation period was seen only for gene relative mRNA abundances (p < 0.01).

Phenotypic and Molecular Detection of the Metallo-Beta-Lactamases in Carbapenem-Resistant Pseudomonas aeruginosa Isolates from Clinical Samples

Background: Pseudomonas aeruginosa is an opportunistic pathogen that causing high morbidity and mortality, and responsible for a high proportion of hospital infections. Recently, P. aeruginosa infections having carbapenem group antibiotic-resistant have been increasing and serious problems are being experienced in treatment. Carbapenem resistance mechanisms are the loss of OprD porin protein, excretion of drug with the efflux system and production of metallo-beta-lactamase (MBL). Objectives: The aim of this study was to investigate the production of MBL in carbapenem resistant P. aeruginosa isolates phenotypically and genotypically. Study design: In this study, 58 P. aeruginosa isolates were included from various clinical samples between May 2014 and March 2015 at the Microbiology Laboratory of Tertiary Care Hospital of Mersin University, Faculty of Medicine. Methods: The strains were identified by automated system (Vitek 2, BioMerieux, France); and antibiotic susceptibilities were performed by using the disc diffusion method and the automated system (Vitek 2). Gradient test was performed for imipenem (IPM) and meropenem (MEM) to confirm the carbapenem resistance. Combined disc test (CDT) and MBL E-test were used for the detection of MLB phenotypically. The most common MBL genes, blaIMP-1, blaIMP-2, blaVIM1, blaVIM-2, blaSPM, blaGIM-1 were investigated with polymerase chain reaction (PCR). Direct DNA sequence analysis was performed to PCR positive isolates. Results: Of the 58 isolates, 57 (99%) were found resistant to IPM, 43 (74%) to MEM, one was intermediate susceptible to IPM and 15 (25%) to MEM by automated system. Of the 58 isolates, 57 were found to be resistant and one was intermediate susceptible to IPM, 34 isolate were found to be resistant, 17 were intermediate susceptible and 7 were susceptible to MEM by gradient test. MBL positivity was detected on 37 (63.7%) isolates by CDT and 16 (27%) by E-test. MBL gene region was detected on 8 isolates (13.7%) by PCR and 6 isolates were found to be VIM-1 gene region positive and 2 isolates were GIM-1 gene region positive. This study is the first study showing the GIM-1 gene in P. aeruginosa in Turkey. DNA sequence analysis data was compared with the reference NCBI sequence data in the PubMed-BLAST program to confirm gene regions. Conclusions: Phenotypic tests can be used as screening test for the detection of MBL activity in carbapenem resistant P. aeruginosa isolates. However, confirmation of the results by molecular tests and determination of the gene regions responsible for resistance are very important epidemiologically.

Correlation between P-selectin rs1800807 and rs1800808 Gene polymorphisms and plasma soluble P-selectin concentrations in patients with atrial fibrillation complicated with thromboembolism in Xinjiang, China.

This study is to investigate the relationship of P-selectin (Ps) gene rs1800807 and rs1800808 polymorphisms with plasma soluble P-selectin (sPs) in Han, Uygur, and Kazakh people with atrial fibrillation (AF) and thromboembolism (TE) in Xinjiang, China.A total of 778 Han patients (including 131 patients with AF and TE, 229 patients with AF and 418 healthy individuals), 660 Uygur patients (including 118 patients with AF and TE, 232 patients with AF and 310 healthy individuals), and 505 Kazakh patients (including 42 patients with AF and TE, 156 patients with AF and 307 healthy individuals) were enrolled in this study. Polymerase chain reaction-restriction fragment length polymorphism and direct DNA sequence analysis were used to analyze the polymorphisms of rs1800807 and rs1800808 of Ps gene. ELISA was used to determine the plasma sPs level. The association between plasma sPs levels and Ps gene polymorphisms was further analyzed.The sPs concentrations of GG genotype at rs1800807 locus in the Han, Uygur and Kazakh ethnic groups in Xinjiang, China were significantly higher than those of the CC genotype and CG genotype (P < .05). In the rs1800808 locus, plasma sPs concentrations of the heterozygous mutant CT genotypes in Han and Uygur populations were significantly higher than those in the CC and TT genotypes, whereas the plasma sPs concentrations in Kazakh TT genotypes were significantly higher than those in the CC and CT genotypes (P < .05). Among different ethnic groups, there were significant differences in sPs levels of rs1800807 and rs1800808 genotypes (P < .05).Plasma sPs concentrations are associated with Ps genotypes and sPs concentration of the same genotype shows racial differences.

Detection and Molecular Characterization of Human Adenoviruses from Acute Conjunctivitis Cases

Human adenoviruses (hAdV) can cause a wide range of clinical diseases in children and adults that mainly affect respiratory, eye and gastrointestinal systems. Ocular hAdV infections have various clinical manifestations such as epidemic keratoconjunctivitis, pharyngoconjunctival fever and non-specific follicular conjunctivitis. The hAdV genotypes which can cause conjunctivitis vary according to geographic distribution. In the study, we aimed to determine the frequency of the presence of hAdV by molecular methods and to determine the types with phylogenetic analysis in conjunctival swab samples taken from patients diagnosed clinically as acute conjunctivitis. Conjunctival swab samples (n= 100) were taken from the patients with acute conjunctivitis who have admitted to Mersin University Faculty of Medicine Hospital Ophthalmology Clinic and 50 conjunctival swab samples taken from healthy individuals as a control, between September 2014-July 2017 were included in the study. Following the DNA isolation from swab samples, polimerase chain reaction (PCR) amplification was performed using specific primer sequences targeting the hexon gene region of the hAdV genome. In order to determine hAdV types, direct DNA sequence analysis of hexon gene products was performed in "ABI PRISM 3130XL Genetic Analyzer" (Applied Biosystems, Foster City, CA, USA). The obtained hAdV DNA sequences were typed by BLAST analysis and the identified genotypes were compared phylogenetically with the reference hAdV sequences of the NCBI In the study, 30 (30%, 30/100) of the swab samples of the patients with acute conjunctivitis were found positive for hAdV hexon gene PCR. The hAdV DNA was not found in the conjunctival swab samples belonging to the healthy individuals included as controls. A total 27 samples found as positive of the hexon gene PCR were genotyped by direct DNA sequence analysis. A total of 5 genotypes were identified and the most common genotypes were hAdV-8 (n= 17, 63%) and followed by hAdV-53 (n= 4, 14.8%), hAdV-4 (n= 4, 14.8%), hAdV-7 (n= 1, 3.7%) and hAdV-37 (n= 1, 3.7%). In this study, the prevalence of adenoviral conjunctivitis determined by hexon gene PCR in patients with clinical diagnosis of acute conjunctivitis was similar to the prevalence rate reported in other regions of the world. In our region, more than one type of hAdV type was associated with acute conjunctivitis. The predominant type was determined as hAdV-8 with a 63% ratio. These results will significantly contribute to the molecular epidemiology of hAdV types in conjunctivitis cases.

Characterization of the IVS-II-821 (A>C) (HBB: c.316-30A>C) Mutation in a β-Thalassemia Phenotype in Iran

β-Thalassemia (β-thal) is the most frequently observed hereditary blood disorder that results from genetic defects causing deficient synthesis of hemoglobin (Hb) polypeptide chains. Detecting thalassemia mutations are necessary for prenatal diagnosis (PND) programs leading a better quality of life for the patients, as well as a reduction in the cost of their medical care. There are more than 900 different genomic mutations of the β-globin gene described in the human hemoglobin variant (HbVar) database. In this study, we identified a mid-intronic mutation at IVS-II-821 (A>C) (HBB: c.316-30A>C) position in the HBB gene of an Iranian proband and two of her siblings that was associated with β-thal clinical features. Direct DNA sequence analysis was performed by mutation scanning of the β-globin gene. Based on the observed β-thal phenotype and bioinformatics analysis results, we concluded that this β-globin gene mutation was associated with a mild phenotype of β-thal through activating potential splice sites by creating exonic splicing enhancers (ESEs), exon-identity element (EIE) and exonic splicing regulatory sequences (ESRs) sites.

Novel HAX1 Gene Mutation in a Vietnamese Boy with Severe Congenital Neutropenia

Severe congenital neutropenia (SCN) is a rare disease that involves a heterogeneous group of hereditary diseases. Mutations in the HAX1 gene can cause an autosomal recessive form of SCN-characterized low blood neutrophil count from birth, increased susceptibility to recurrent and life-threatening infections, and preleukemia predisposition. A 7-year-old boy was admitted due to life-threatening infections, mental retardation, and severe neutropenia. He had early-onset bacterial infections, and his serial complete blood count showed persistent severe neutropenia. One older sister and one older brother of the patient died at the age of 6 months and 5 months, respectively, because of severe infection. Bone marrow analysis revealed a maturation arrest at the promyelocyte/myelocyte stage with few mature neutrophils. In direct DNA sequencing analysis, we found a novel homozygous frameshift mutation (c.423_424insG, p.Gly143fs) in the HAX1 gene, confirming the diagnosis of SCN. The patient was successfully treated with granulocyte colony-stimulating factor (G-CSF) and antibiotics. A child with early-onset recurrent infections and neutropenia should be considered to be affected with SCN. Genetic analysis is useful to confirm diagnosis. Timely diagnosis and suitable treatment with G-CSF and antibiotics are important to prevent further complication.

Genetic diversity and functional analysis of oipA gene in association with other virulence factors among Helicobacter pylori isolates from Iranian patients with different gastric diseases

Helicobacter pylori (H. pylori) is one of the most genetically diverse bacterial pathogens that persistently colonizes the human gastric epithelium. This remarkable genomic plasticity may act as a driving force for successful adaptation and persistence of the bacteria in the harsh gastric environment. Outer inflammatory protein A (OipA) encoded by oipA gene (HP0638/hopH) is a member of the outer membrane proteins (OMPs) of H. pylori involved in induction of IL-8 secretion and is associated with development of peptic ulcer and gastric cancer. Expression of OipA is regulated by phase variation within a CT dinucleotide repeat motif of the oipA gene. In this study we carried out direct DNA sequence analysis of 53 amplified fragments to investigate the oipA “On/Off” status among Iranian H. pylori isolates from patients with various gastric diseases. The prevalence of cagL, cagA, EPIYA motifs, vacA alleles, babA2 and sabA genotypes as well as cagPAI integrity of the isolates were determined by PCR. Our results demonstrated a high prevalence of strains with functional oipA status (79%) and significant associations were found between functional oipA and cagA (P = 0.027) and vacA s1m1 (P = 0.022) genotypes. The vacA s1m2 genotype was also found to be statistically associated with PUD (P = 0.0001). Interestingly, we showed that H. pylori strains with intact cagPAI co-expressed oipA gene in a significant synergistic relationship (P < 0.01). However, no significant association was observed between the functional oipA status and clinical outcomes (P > 0.05). In conclusion, our findings denotes great diversity in the number and pattern of CT dinucleotide repeats of oipA among Iranian H. pylori strains. The synergistic link between functional oipA and other important virulence factors is proposed to be critical in the pathogenesis of H. pylori, which needs further studies with a larger number of samples.

Denys-Drash Syndrome: a case report

Background: Denys-Drash syndrome (DDS) is a very rare genetic disease. Wilms' tumor, genital abnormalities, and congenital glomerulopathy are the main features of DDS which resulted from a heterozygous mutation in the WT1 gene. Case Presentation: First case of DDS has been diagnosed in Saudi Arabia in four months newborn who admitted to nephrology department with ambiguous bilateral undescended testis, and nephropathy. On admission, he had normal vital signs except high blood pressure. His kidney function tests showed abnormal kidney function. Ultrasonography and MRI were done to figure out his nephropathy and undescended testis, respectively. Both Abdominal ultrasonography and kidney histopathology confirmed diffuse mesangial sclerosis (DMS). MRI graph located the un-identical ectopic testis. The autosomal dominant inherited pathogenic missense mutation in exon 9 of WT1 gene (c.1181G>A (p.Arg394GLu)) was confirmed by DNA direct sequencing analysis. At his 4th year of age, his nephropathy developed to End Stage Renal Disease (ESRD). Conclusion: DDS should be considered in new born baby with nephrotic syndrome and ambiguous gonads. DNA direct sequencing analysis for WT1 gene is very helpful for confirmation of DDS.