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Background and Objectives Chickpea, cultivated in rainfed and irrigated fields across many countries. In terms of chickpea cultivation area, Iran ranks fourth, after India, Australia and Pakistan, and in terms of chickpea production, Iran ranks eighth in the world, but it does not have a good position in terms of average yield. Iran ranks 17th in terms of average yield in irrigated agriculture and 50th in rainfed agriculture in the world. Various factors such as water stress in rainfed cultivation, lack of modern inputs and technologies have been mentioned as reasons for the low yield of chickpeas in Iran. Chickpea also faces biological stresses such as Ascochyta blight caused by the pathogenic fungus Ascochyta rabiei. This disease poses a severe threat to chickpea fields, resulting in substantial annual damage in various countries. Identifying resistance sources through molecular methods, specifically genomic tracking of the resistance trait, holds the potential to expedite and enhance control measures effectively. The use of the Amplification Refractory Mutation System (ARMS) method, involving functional point mutations and resistance-related alleles, proves highly efficient in advancing selection programs targeted at combating Ascochyta blight. Materials and methods Pots containing two chickpea genotypes, sensitive (ILC263) and resistant (MCC133) to Ascochyta blight were cultivated and kept for 45 days under greenhouse conditions. The fragment harboring the SNP18-Pos57723 point mutation within the GSh118 gene sequence underwent amplification and sequencing using PSh118-F/R specific primers. This process utilized DNA extracted from both resistant (MCC113) and susceptible (ILC263) chickpea genotypes. The identification of alleles associated with resistance and sensitivity was established. Distinct differentiating primers were formulated for resistant (PSh118-Fc and PSh118-R) and sensitive (PSh18-Fg and PSh18-R) genotypes. The specific annealing temperature for each reaction was determined through a temperature gradient analysis. The efficacy of the designed primers in distinguishing between resistant and sensitive genotypes was assessed by conducting PCR and comparing their electrophoresis patterns. Results The first symptoms of Ascochyta blight disease was observed on seedlings of resistant and sensitive chickpea genotypes seven days after fungal inoculation under greenhouse conditions. The fragment containing the functional point mutation related to GSh118 gene was tracked using PSh118.2-F/R specific primers in the genomic DNA of susceptible (ILC263) and resistant (MCC133) chickpea genotypes so that after PCR amplification resulted a specific fragment with the expected size of 630 bp. The presence of alleles linked to GSh18-2773C resistance and GSh18-2773g sensitivity was confirmed in resistant and sensitive chickpea genotypes, respectively. The specific primers PSh18-Fc and PSh18-R, designed for detecting the resistance allele, successfully amplified the expected 330 bp fragment in the resistant chickpea genotype MCC133. The study results affirmed the accurate amplification of alleles using these designated primers. Discussion In the present study, the ARMS method, known for its high sensitivity, specificity, rapidity, costeffectiveness, multiplexing capabilities, compatibility with high throughput methods, and nondestructive nature, was employed to differentiate chickpea genotypes resistant to Ascochyta blight. The ARMS method's effectiveness in selecting resistance sources among various plant lines and cultivars has been demonstrated through allele tracking related to the resistance gene in prior studies. The results of this study indicated that the ARMS method accurately distinguishes chickpea genotypes resistant and sensitive to Ascochyta blight based on alleles associated with the GSh18-2773 position's point mutation. Thus, employing specific primers for the resistance allele is recommended in molecular selection studies of chickpea sources resistant to Ascochyta blight. [ABSTRACT FROM AUTHOR]

Background: Citrullinemia type 1 is an autosomal recessive disease resulting in ammonia accumulation in the blood, and if uncontrolled may progress to coma or death in the early months after birth. Cases presentation: 7 families from Southwest Iran having one or more children in their families or relatives, who died in the early months after birth due to citrullinemia type 1 visited for genetic counseling and prenatal diagnosis. Whole-exome sequencing was performed on peripheral blood specimens and chorionic villus samples. Sanger sequencing confirmed the genetic results. Both parents were identified as carriers for the exon 15 c.1168G>A mutation in each family. The fetus in 6 out of 7 families was homozygote for A substitution on the argininosuccinate synthetase 1 gene. Conclusion: The presence of a common mutation in the argininosuccinate synthetase 1 gene in all affected families of Southwest Iran shows a possible population cluster in this area. [ABSTRACT FROM AUTHOR]

Background: Hemophilia A (HA) is an X-linked recessive bleeding disorder with a high rate of genetic heterogeneity. The present study was conducted on a large cohort of Iranian HA patients and data obtained from databases. Methods: A total of 622 Iranian HA patients from 329 unrelated families who had been referred to a medical genetics laboratory in Tehran from 2005 to 2019, were enrolled in this retrospective, observational study. Genetic screening of pathogenic variants of the F8 gene was performed using inverse shifting PCR, direct sequencing, and multiplex ligation-dependent amplification (MLPA). Point mutation frequencies in different exons were analyzed for our samples as well as 6031 HA patients whose data were recorded in a database. Results: A total of 144 different pathogenic or likely pathogenic variants including 29 novel variants were identified. A strategy to decrease costs of genetic testing of HA was suggested based on this finding. Conclusion: This study provides comprehensive information on F8 pathogenic/likely pathogenic variants in Iranian HA patients which improves the spectrum of causative mutations and can be helpful to clinicians and medical geneticists in counseling and molecular diagnosis of HA. [ABSTRACT FROM AUTHOR]

Neurofibromatosis type 1 (NF1) is a genetic disorder caused by mutations in the NF1 gene. This disorder shows nearly complete penetrance and high phenotypic variability. We used the whole-exome sequencing technique to identify mutations in 32 NF1 cases from 22 Iranian families. A total of 31 variants, including 30 point mutations and one large deletion, were detected. In eight cases, variants were inherited, while they were sporadic in the remaining. Seven novel variants, including c.5576 T > G, c.6658_6659insC, c.2322dupT, c.92_93insAA, c.4360C > T, c.3814C > T, and c.4565_4566delinsC, were identified. The current study is the largest in terms of the sample size of Iranian NF1 cases with identified mutations. The results can broaden the spectrum of NF1 mutations and facilitate the process of genetic counseling in the affected families., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background and Objective: Alpha thalassemia is one of the most common hemoglobin disorders. Some combination of alpha globin gene mutations may cause HbH disease with severe anemia or intermediate thalassemia. genotype common deletions are routinely tested for suspicious alpha thalassemia couples but because of lack of information about the nature and frequency of point mutations and higher expenosor of sequencing, less attention was paid to them. This study was done to determine the prevalence of common point mutations of alpha globin gene in Babol, Iran. Materials and Methods: This descriptive study was carried out on DNA of 153 adult suspected to α-thalasemia with deleted α- golobolin gene referred to genetic laboratory in Babol, Iran during 2005-09. a1 and a2 genes were amplified by using specific biotinilated primers by PCR method. PCR products were assayed using 11 specific probs corresponding to common point mutations in alpha gene (C19, IVSI (-5nt), C59, Hb constant spring, Hb Icaria, Hb seal Rock, IVSI (148), C14, poly A (-2bp), poly A2, Poly A1) and fixed on byodine C membrabe. Hybridization between the probes and PCR products was visualized after a colorimetric reaction using of conjugated streptavidin peroxidase and TMB (tetra methyle Benzidine) and H2O2. Results: The prevalence of point mutations in poly A2, 5nt, Hb constant spring and poly A1 were 28.75%, 14.38%, 7.84% and 2.61%, respectively. Conclusion: Point mutation in alpha globin genes was detected in %53.60 out of 153 adults suspected with alpha thalassemia without common deletion mutations. [ABSTRACT FROM AUTHOR]

Introduction: HBx is a multifunctional modulator viral protein with key roles in various biological processes such as signal transduction, transcription, proliferation, and cell apoptosis. Also, HBx has an important role in the progression of cirrhosis and hepatocellular carcinoma (HCC). This study aimed to determine mutations in X gene, enhancer II (EnhII), and basal core promoter (BCP) of genotype D of Hepatitis B Virus (HBV) in cirrhotic and chronic HBV patients., Material and Methods: This cross-sectional study was performed on 68 cases with chronic HBV (cHBV) and 50 cases with HBV related cirrhosis. Serum samples were obtained for genomic DNA extraction. Semi-nested PCR was used to amplify the HBx region. Point mutations in the HBx region were detected by sequencing., Result: Novel mutations were detected, including C1491G, C1500T, G1613T, and G1658T in the N-terminal of the X gene. The frequency of C1481T/G1479A, T1498C, C1500T, G1512A, A1635T, C1678T, A1727T, and A1762T/ G1764A/ C1773T was significantly higher in cirrhotic patients compared to chronically HBV infected ones. A higher rate of A1635T, C1678T, A1727T, A1762T, G1764A, and C1773T was observed in cirrhotic patients., Conclusion: Our findings showed that the frequency of mutations in the basal-core promoter, enhancer II, and regulatory region of the HBx gene was more seen in cirrhotic patients than in chronic HBV cases. Novel mutations were detected in the HBx gene, causing amino acid substitutions; however, the clinical impact of these novel mutations is yet to be cleared., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Mutations in the dystrophin gene could cause Duchenne muscular dystrophy (DMD), which is the most common muscular disorder in pediatrics. Considering the growing evidence on appropriateness of gene therapies for DMD, precise genetic diagnosis seems essential. Hence, we conducted a study to determine mutational patterns in Iranian children with DMD. To detect all probable large mutations in the dystrophin gene, 314 DMD patients were evaluated using the multiplex ligation-dependent probe amplification (MLPA). Subjects who were MLPA-negative underwent the next generation sequencing (NGS) to identify potential point mutations. MLPA detected deletions (79.93%) and duplications (5.41%) along the dystrophin gene of 268 patients. Distribution of large mutations was heterogeneous and followed hotspot pattern throughout the gene. From 46 patients who were MLPA-negative, 43 exhibited point mutations including nonsense in 7.64%, frameshifts in 4.77%, splicing in 0.96%, and missense variations in 0.32% of participants. Most of the point mutations were located between exons 19 and 40. In three patients (1%), no mutation was found using either MLPA or NGS. Two subjects had novel nonsense mutations (L1675X and E1199X) in their dystrophin gene, which were considered as the possible reason for elimination of major domains of the gene. The results of this study provided invaluable information regarding the distribution of various large and small mutations in Iranian individuals with DMD. Besides, the novel nonsense mutations L1675X and E1199X were identified within the highly conserved residues, leading to elimination of significant domains of the dystrophin gene.

A wide range of genetic and environmental interactions are involved in the development of coronary artery disease (CAD). Considerable evidence suggests that mitochondrial DNA mutations are associated with heart failure. In this work, we examined the possible mutations in hotspot mitochondrial genes and their association with Iranian patients with coronary artery disease. In this case-control study, nucleotide variations were investigated in 109 patients with coronary atherosclerosis and 105 control subjects with no family history of cardiovascular disease. The molecular analysis of related mitochondrial genes was performed by polymerase chain reaction sequencing. Our results showed 25 nucleotide variations (10 missense mutations, 9 synonymous polymorphisms, and 6 variants in tRNA genes) that for the first time were presented in coronary artery disease. Our results suggest that novel heteroplasmic m.8231 C>A mutation is involved in CAD (p = 0.007). These nucleotide variations suggest the role of mitochondrial mutations as a predisposing factor which in combination with environmental risk factors may affect the pathogenesis of coronary atherosclerosis. So, further investigation is needed for a better understanding of the pathogenesis and predisposing effects of these variations on the disease.

Background and Aims: Helicobacter pylori is a common infectious bacterium mostly found in gastroduodenal diseases. The increased prevalence of clarithromycin-resistant H. pylori strains is a major challenge in the successful treatment of infections caused by this organism. The present study is aimed at detecting the clarithromycin resistance pattern of H. pylori strains isolated from gastric biopsies and evaluating point mutations of the 23S rRNA gene. Patients and methods . In the present descriptive cross-sectional study, 165 patients with gastrointestinal disorders, who were referred to the Endoscopy Center of Dr. Shariati Hospital of Isfahan, Iran, were enrolled from April to July 2018. H. pylori infection was diagnosed by culture, and susceptibility of the isolates to clarithromycin was assessed by the E-test. Minimum inhibitory concentration (MIC) values were obtained based on EUCAST recommendations. Also, fluorescence in situ hybridization (FISH) was used to determine point mutations associated with clarithromycin resistance., Results: By using culturing, H. pylori was isolated from 50.3% (83/165) gastric biopsy specimens. The overall frequency of resistance to clarithromycin was 25.3% (21/83) by the E-test. In the resistance genotypic analysis, 19 isolates had mutations. The prevalence of A2143G and A2144G mutations was 68.4% (13/19) and 31.5% (6/19), respectively. A2143C mutation was not tracked in any isolate. Two isolates with MIC > 0.5  μ g/mL had no mutations that could be related to other mechanisms of resistance., Conclusion: As presented in the study, the high prevalence of clarithromycin-resistant H. pylori due to point mutations of the 23S rRNA gene indicates the necessity of revising the standard treatment regimen based on antibiotic susceptibility pattern of each region., Competing Interests: The authors have no conflict of interests to declare., (Copyright © 2020 Jina Vazirzadeh et al.)

Aims: Wolfram syndrome (WS) is a rare recessive neurodegenerative disorder characterized by diabetes mellitus and optic atrophy. Mortality and morbidity rate of the disease is high in adulthood due to neurological and respiratory defects. So far, two WS genes, WFS1 (more than 90% of cases) and CISD2, have been identified. In the present study, we aimed to determine the role of WFS2 in a group of Iranian WS families., Methods: We recruited 27 families with the clinical diagnosis of WS. Homozygosity mapping was implemented using short tandem repeat polymorphic markers and bi-directional sequencing of the CISD2 gene in families negative for WFS1 mutations. The candidate variant was checked among family members. In silico analysis and protein modeling were applied to assess the pathogenic effect of the variant. Tetra-primers ARMS PCR was set up for checking the variant in 50 ethnic-matched controls., Results: One family showed homozygosity by descent at WFS2. A novel missense variant, c.310T > C (p.S104P), was found in exon 2 of the CISD2 gene. Computational predictions revealed its pathogenic effect on protein structure, function, and stability. Parents and his healthy brother were heterozygous for the variant. The variant was not observed in the control group., Conclusions: This is the first study that elucidates the role of the CISD2 gene among Iranian WS families with a novel disease-causing missense variant. Next-generation sequencing could unravel disease-causing genes in remained families to expand genetic heterogeneity of WS.

Introduction: Mutations in the HFE gene have been shown to be associated with hemochromatosis which is observed in beta-thalassemia major. In this study, we determined the HFE gene mutations (C282Y and H63D) among b-thalassemia major patients to investigate the effect of these mutations on serum Ferritin levels., Material and Methods: In this cross-sectional study, a total of 105 b-thalassemia subjects with a history of regular blood transfusion were selected. They divided into two distinct groups according cut off 1000ng/ml of serum Ferritin levels. The HFE gene mutant allele detected by RFLP-PCR., Results: Of 105 thalassemia patients, 29 patients (14 male and 15 female) were heterozygote for H63D mutation, and just one male was homozygote, but for C282Y mutation just one heterozygote and one homozygote was detected, and overall 31% had coexistence of b-thal and HFE gene mutations. As expected, Ferritin levels significantly differed between groups (P=0.001)., Conclusion: The impact of detection of HFE mutations could prognosis the likelihood of iron overload in multi-transfused patients, and allowing early diagnosis and proper management to overcome complications of iron overload in beta-thalassemia patients., (Copyright © 2019. Published by Elsevier Masson SAS.)

Background: Inflammatory bowel disease (IBD) is one of the most important immune-mediated disorders of the gastrointestinal tract. Besides, IBD is associated with numerous extraintestinal complications such as venous thromboembolism (VTE), an important risk factor for vascular complications, which results in the increased morbidity and mortality. The JAK2 (Janus kinase 2) V617F mutation is a well-known point mutation which is involved in the pathogenesis of IBD, and VTE. Therefore, the aims of this study were to evaluate expression of JAK2 and association of V617F mutation in JAK2 of Iranian patients with IBD., Methods: Two hundred and forty-six patients with IBD (209 UC and 37 CD) and 206 healthy controls were enrolled in this study. The genomic DNA and total RNA were extracted from peripheral blood mononuclear cells (PBMCs). Then, the JAK2 V617F mutation detection was performed using the restriction fragment length polymorphism (RFLP) method. In addition, the JAK2 mRNA expression was evaluated using a quantitative polymerase chain reaction (q-PCR) using the SYBR Green assay., Results: There was no association of V61F mutation in patients with IBD with or without thrombosis compared with healthy control. However, the relative mRNA expression of JAK2 was significantly upregulated in patients with IBD in comparison with healthy control (P < 0.0001). In addition, the JAK2 mRNA expression was significantly decreased in patients with IBD having thrombosis compared with those without thrombosis ( P < 0.0001)., Conclusions: Taken together our findings suggested that JAK2 V61F-independent upregulation of JAK2 mRNA expression in patients with IBD. Moreover, despite the absence of JAK2 V617F mutation in patients with IBD, the increased gene expression of JAK2 can be explained by another molecular mechanism such as regulation of gene expression at the transcriptional level which may play crucial roles in the pathogenesis of IBD., (© 2019 Wiley Periodicals, Inc.)

Dioxins (eg, 2,3,7,8-tetrachlorodibenzo-p-dioxin/TCDD), as environmental endocrine disruptors and toxic carcinogens, can affect male reproductive health. The influence of dioxins is mediated via the aryl hydrocarbon receptor (AhR) pathway and its repressor (AhRR). In this study, we investigated the association of AhRR-c.565C>G transversion polymorphism with male infertility. In a hospital-based case-control study, 221 semen samples (111 infertile and 110 healthy controls) based on World Health Organization guidelines were collected from in vitro fertilization centers of Babol, Iran. The AhRR-c.565C>G (rs2292596) polymorphism was genotyped using a polymerase chain reaction-restriction fragment length polymorphism analysis. The difference in the allele frequency of AhRR-c.565C>G transversion polymorphism did not reach a significant level. The genotype frequency was statistically significantly different between fertile and infertile men. We found that polymorphism rs2292596 (Pro185Ala) was statistically significantly associated with the risk of male infertility. In addition, the statistical difference became more significant when the frequency was compared between the Pro/Pro genotype and the Pro/Ala plus Ala/Ala genotype. The 185 Pro wild-type alleles of AhRR may be associated with the risk of male infertility. The proallele also may diminish inhibition of AhR-mediated signaling of exposure to environmental pollutants., (© 2018 Wiley Periodicals, Inc.)

Genetic contributing factors to non-syndromic hearing loss (NSHL) are remarkably diverse spanning over autosomal to X-linked to mitochondrial inheritance patterns. Facing a quite unconventional pedigree, here we report implementation of whole exome sequencing (WES) to uncover mitochondrial pathogenic variant in a six-generation Iranian family with four cases affected with hereditary NSHL of variable severity. As a result, heteroplasmic transition of A to G at position 1555 of MT-RNR1 gene was identified in all affected individuals co-existing with nuclear c.28G > T (p.A10S) variant in the TRMU gene, only in some patients. The reliability of WES to infer nuclear as well as mitochondrial variants in hearing loss were discussed., (Copyright © 2018 Elsevier B.V. and Mitochondria Research Society. All rights reserved.)

Molecular analysis of antifolate resistance-associated genes-dihydrofolate reductase (dhfr) and dihydropteroate synthetase (dhps) of Plasmodium vivax is important in predicting the emergence of drug resistance to sulphadoxine-pyrimethamine (SP). The present study aimed to determine the polymorphism of dhfr and dhps genes in P. vivax field isolates. Samples from 80 microscopically diagnosed vivax malaria cases were collected from endemic areas of malaria in Hormozgan Province of Iran, from June 2010 to November 2015. The two sets of codons at position 33, 57, 58, 117, 173 of dhfr and 382, 383, and 553 of dhps genes were analysed by direct sequencing of PCR products. The majority of the isolates (70%) harboured a wild-type allele for P. vivax dhfr (Pvdhfr) and P. vivax dhps (Pvdhps). Mutations were detected in three codons of Pvdhfr (P33L, S58R and S117N) and single codon in Pvdhps (A383G). Novel mutations that have not been identified previously at codon 459 (D459A) of Pvdhps were also observed. The high prevalence of point mutation as well as the rising triple mutation of Pvdhfr and Pvdhps genotypes necessitate change in programmes and guidelines to eliminate P. vivax in future., Competing Interests: None

With regard to increasing number of antifungal-resistant dermatophytes, antifungal susceptibility testing of dermatophytes serves as a useful tool in managing clinical dermatophytosis. This study aimed to determine antifungal susceptibility profile of clinically important dermatophytes and determination of point mutations in terbinafine-resistant isolates. Based on our results, dermatophytosis was confirmed in 97 cases by direct microscopic examination, culture, and sequencing of ITS region. Antifungal susceptibility of 97 dermatophyte isolates distributed in four species including Trichophyton interdigitale (26 isolates), T. rubrum (19 isolates), T. tonsurans (29 isolates), and Epidermophyton floccosum (21 isolates) was assessed to nine antifungal agents using CLSI M38-A2 guidelines. Minimum inhibitory concentration range (MIC range) for luliconazole and terbinafine was 0.001-0.008 μg/ml and 0.003-> 32 μg/ml, compared to 0.03-64 μg/ml for griseofulvin, 0.01-16 μg/ml for itraconazole and voriconazole, 0.03-8 μg/ml for ketoconazole, 0.03-32 μg/ml for econazole, 0.03-1 μg/ml for lanoconazole, and 0.01-4 μg/ml for butenafine. Trichophyton tonsurans was the most susceptible (MIC = 0.006 μg/ml) and E. floccosum was the most resistant (MIC = 0.02 μg/ml) species to terbinafine. Terbinafine resistance was reported for two species, i.e., T. rubrum and T. tonsurans at the total rate of 2% which was due to Leu393Phe substitution in both species. Taken together, our results assist clinicians and prompt the current knowledge about the necessity of antifungal susceptibility testing to select effective strategies for management of clinical cases of dermatophytosis.

Disruptions of mitochondrial DNA (mtDNA) may affect male reproductive function. The aim of this study was to investigate the association of three deletions (4977, 7345 and 7599 bp) and two-point mutations (A73G and A3243G) of mitochondrial DNA with male infertility in an Iranian population. In a case-control study, we collected semen samples of 60 infertile men and 60 healthy controls. Detection of the mtDNA deletions and point mutations were performed by long range PCR and PCR-RFLP method, respectively. Our data revealed that 4977 and 7599 bp deletions are associated with male infertility. But, there was no association between mentioned point mutations and male infertility. Our findings suggested that 4977 and 7599 bp deletions of mtDNA may be genetic risk factors for male infertility. However, it is a preliminary study and is presenting data for future comprehensive study for making a clinical conclusion that these deletions are biomarkers for susceptibility to male infertility.

Objective: Increasing antibiotic resistance in Helicobacter pylori is a global concern and is associated with treatment failure. The aim of this study was to evaluate antibiotic resistance of H. pylori to different antibiotics including amoxicillin, erythromycin, ciprofloxacin, furazolidone, tetracycline, metronidazole and clarithromycin. In addition, ​detection of A2143G mutation in clarithromycin resistant isolates was performed using real-time PCR technique., Methods: Ninety patients with upper gastrointestinal symptoms were enrolled in this study. H. pylori were isolated from 32 specimens and the resistance rate of these strains to amoxicillin, erythromycin, ciprofloxacin, furazolidone, and tetracycline was tested by disc agar diffusion method. The resistance level to metronidazole and clarithromycin was determined by agar dilution method. The presence of A2143G point mutation in clarithromycin resistant isolates was determined using real-time PCR technique., Results: The resistance rates to amoxicillin, erythromycin, ciprofloxacin, furazolidone, tetracycline, metronidazole and clarithromycin were 53%, 50%, 37.5%, 62.5%, 25%, 62.5% and 22%, respectively. The A2143G point mutation was detected in 71% of clarithromycin resistant strains (5 out of 7)., Conclusions: The prevalence of H. pylori resistance to metronidazole, ciprofloxacin, erythromycin, amoxicillin and furazolidone in Iran is high. Determination of antibiotic susceptibility plays an important role in selecting of the appropriate anti H. pylori regimen., (Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Background: The high prevalence of clarithromycin-resistant strains of Helicobacter pylori is a main challenge for the successful treatment of gastrointestinal infections. Point mutations in the 23S rRNA gene are one of the main mechanisms leading to the resistance to clarithromycin in Iran. The purpose of the present review was to evaluate the prevalence of clarithromycin-resistant H. pylori strains in Iran and to identify the major molecular mechanisms of resistance in the resistant isolates., Methods: Using related keywords and computer search in English and Persian databases (up to November 21, 2016), available data about prevalence of clarithromycin-resistant H. pylori strains and molecular mechanisms of resistance in Iran were retrieved. Relevant articles were selected using pre-defined inclusion and exclusion criteria., Results: The results of the meta-analysis showed that the overall prevalence of clarithromycin-resistant H. pylori strains in Iran is 14.7%. The highest and the lowest resistance to clarithromycin were reported from Kashan (33.7%) and Rasht (5.5%), respectively. The most prevalent point mutations in Iran were A2143G (59.1%), A2142G (17.8%), A2142C (8.8%), and A2144G (6.2%), respectively., Conclusion: The prevalence of clarithromycin-resistant H. pylori strains was in an acceptable level in our region. Therefore, clarithromycin can be used for the eradication of H. pylori infection in Iran. However, it seems that investigation about the role of other mechanisms involved in the induction of resistance to clarithromycin is needed., (Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

This study aimed to investigate the clarithromycin resistance and its associated molecular mechanisms among Helicobacter pylori isolates from dyspeptic patients in Shiraz, Iran. From January to May 2014, 100 H. pylori strains were isolated from patients with gastroduodenal disorders. The resistance to clarithromycin was quantitatively evaluated, using Epsilometer (E-test) method. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed on all the isolates to detect A2143G and A2142G mutations in 23S rRNA gene. The H. pylori isolation rate was found to be 31.4%. E-test showed that 20% of isolates were resistant to clarithromycin (MIC ≥ 1 mg/L). MIC of clarithromycin ranged between 0.016 and 24 mg/L. Findings of PCR-RFLP showed that the A2142G was the most (90%) frequently point mutation, followed by the A2143G (10%). No statistically significant difference was found between H. pylori clarithromycin resistance point mutations and patients' gender or age. To the best of our knowledge, this is the first report of high frequency of A2142G point mutation in Iran and probably in other regions of the world. Considering the increasing trend of H. pylori resistance to clarithromycin due to these mutations, it is crucial to investigate the new therapeutic approaches against H. pylori infection., (© 2016 APMIS. Published by John Wiley & Sons Ltd.)

Maple syrup urine disease (MSUD) is a rare inborn error of branched-chain amino acid metabolism. The disease prevalence is higher in populations with elevated rate of consanguineous marriages such as Iran. Different types of disease causing mutations have been previously reported in BCKDHA, BCKDHB, DBT and DLD genes known to be responsible for MSUD phenotype. In this study, two sets of multiplex polymorphic STR (Short Tandem Repeat) markers linked to the above genes were used to aid in homozygosity mapping in order to find probable pathogenic change(s) in the studied families. The families who showed homozygote haplotype for the BCKDHA gene were subsequently sequenced. Our findings showed that exons 2, 4 and 6 contain most of the mutations which are novel. The changes include two single nucleotide deletion (i.e. c. 143delT and c.702delT), one gross deletion covering the whole exon four c.(375+1&#95;376-1)&#95;(8849+1&#95;885-1), two splice site changes (c.1167+1G>T, c. 288+1G>A), and one point mutation (c.731G>A). Computational approaches were used to analyze these two novel mutations in terms of their impact on protein structure. Computational structural modeling indicated that these mutations might affect structural stability and multimeric assembly of branched-chain α-keto acid dehydrogenase complex (BCKDC)., (Copyright © 2016. Published by Elsevier B.V.)

Introduction: Mutations of the anion exchanger 1 (AE1) gene encoding the kidney anion exchanger 1 can result in autosomal dominant or autosomal recessive form of distal renal tubular acidosis (DRTA). This study aimed to report deletion mutations of the AE1 and its impact on Iranian children with DRTA., Materials and Methods: Twelve children with DRTA referred to Ali Asghar Children Hospital were investigated for all AE1 gene exons through polymerase chain reaction amplification, DNA sequencing, and bioinformatics analysis., Results: Eleven of 12 patients (91.7%) showed an alteration in AE1 gene with a real hot spot in its exons 11 or 15. Homozygote and heterozygote deletions were confirmed in exon 15 in 5 (41.7%) and 3 (25.0%), respectively. Two patients (16.7%) showed homozygote deletions in exon 11 of AE1 gene, and 1 patient (8.3%) showed point mutation in exon 11. The 3-dimensional structures of the native and these mutant kidney AE1 proteins were determined by the multitemplate method using the Phyre and Hidden Markov Model algorithms., Conclusions: Parents' consanguinity of these patients reveals that cousins are at a high risk for DRTA. This study is considered as a pilot study showing the importance of AE1 mutations in Iranian children with DRTA and further studies is recommended in this geographic region of the world. These models suggest that alteration in the structures leads to alteration in function and change in the current role of AE1.

Background: Clarithromycin is the most commonly suggested antibiotic in Helicobacter pylori eradication regimens. Increasing antibiotic resistance rate to clarithromycin is the main reason for therapeutic failure. The resistance is associated with mutations in the 23S rRNA gene., Aim: The purpose of this study was to determine the clarithromycin resistance rate of isolated H. pylori strains from referral patients in Kashan, Iran., Methods: In total 95 H. pylori strains isolated from gastric mucosa of 246 patients with different clinical signs underwent gastroscopy in Kashan, Iran in 2013. The Epsilometer test was used to determine the minimum inhibitory concentrations (MICs) of clarithromycin (CLR) in isolated H. pylori strains. Occurrence of mutation in 23S rRNA gene of clarithromycin-resistant strains was investigated with polymerase chain reaction-sequencing method., Results: Antibiotic susceptibility pattern showed that 32 strains (33.7%) were resistant to clarithromycin (MICs ≥1 μg/ml), 33.7% were intermediate resistant, while 31 of H. pylori strains (32.6%) were susceptible. The 23S rRNA gene mutations at positions A2143G and A2142G were detected in H. pylori clarithromycin-resistant strains., Conclusion: The resistance rate to clarithromycin in Iran is high. H. pylori clarithromycin-resistant strains were not associated with sex, age, and disease. The A2143G mutation in clarithromycin-resistant H. pylori strains was the predominant finding.

Background: Hearing defects are the most common sensory disorders, affecting 1 out of every 500 newborns. ATP6V1B mutations are associated with early sensorineural hearing loss, whereas ATP6V0A4 mutations are classically associated with either late-onset sensorineural hearing loss or normal hearing. ATP6V1B1 and ATP6V0A4 genetic mutations cause recessive forms of distal renal tubular acidosis., Method: Ten unrelated deaf Iranian families with distal renal tubular acidosis were referred to the Genetics Research Centre, University of Social Welfare and Rehabilitation Sciences, Tehran. All exons of the ATP6V1B1 and ATP6V0A4 genes were sequenced in affected family members., Results: We identified a previously reported ATP6V1B1 frameshift mutation (P385fsX441) in two families and a nucleotide substitution in exon 10 (P346R) in three families. In addition, one patient was homozygous for a novel nucleotide substitution in exon 3., Conclusion: ATP6V1B1 genetic mutations were detected in more than half of the families studied. Mutations in this gene therefore seem to be the most common causative factors in hearing loss associated with distal renal tubular acidosis in these families.

Purpose: To find a relationship between absence of annulus and asthenozoospermia in Iranian men., Methods: In the present study, semen samples from 100 asthenozoospermic and 20 normozospermic patients were analyzed for sperm concentration and motility. Spermatozoa were immunostained for the two septin subunits Sept4 and Sept7. The absence of the annulus structure was confirmed by transmission electron microscopy and western blot analysis for septin 4. DNA sequencing for all coding exons of SEPT12 was performed for a patient using peripheral blood sample., Results: Specific antibodies for SEPT4 and SEPT7 consistently labeled the annuli in spermatozoa from all of the 20 normozospermic men, while in one of 100 patients with asthenozoospermia, 75% of sperms lacking septin 4 or septin 7 proteins at the annulus. It was shown that the structural defect in annulus formation is not caused by point mutation of SEPT12 gene., Conclusions: In conclusion, the results of this study demonstrated that the frequency of the absence of annulus in asthenozoospermic sample of Iranian population has a low frequency and could not be assume as a diagnostic marker for classifying asthenozoospermic patients.

The single nucleotide polymorphism of BMPR-IB gene (bone morphogenetic protein receptor type IB) was analyzed using PCR-RFLP in Iranian native Kalehkoohi sheep. BMPR-IB which affects the fecundity of Booroola Merino sheep was studied as a candidate gene associated with the prolificacy of Kalehkoohi sheep. Improving the reproductive traits in sheep could be one of the key factors in increasing farm profitability. Major genes for litter size trait provide opportunities for large and rapid increases in the efficiency of sheep production. The same FecB (Booroola) mutation occurred in the BMPR-IB gene in Kalehkoohi sheep as found in Booroola Merino. Allele frequency for B and + was 0.35 and 0.65 respectively. The BB, B+ and ++ genotypes have been identified with the 0.13, 0.446 and 0.424, respectively. The Kalehkoohi sheep with genotypes BB and B+ had 0.52 and 0.35 lambs, more than the homozygous wild-type, respectively (P<0.01). No significant difference was observed between B+ and BB in litter size. Also the effect of parity and flock weren't significant in this study. Results of the present study support the concept that BMPR-IB significantly affected litter size and was associated with litter size in Kalehkoohi sheep and thus it could be used for Marker-assisted selection programmers for the genetic improvement of reproductive characteristics in this breed., (Copyright © 2014 Elsevier B.V. All rights reserved.)

GNE myopathy is a rare neuromuscular autosomal recessive disease, resulting from mutations in the gene UDP N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE). The most frequent mutation is the single homozygous missense mutation, M712T-the Middle Eastern mutation-located ten amino acids before the end of the protein. We have used an adeno-associated virus (AAV)-based trans-splicing (TS) vector as a gene therapy tool to overcome this mutation by replacing the mutated last exon of GNE by the wild-type exon while preserving the natural endogenous regulatory machinery. We have designed relevant plasmids directed either to mouse or to human GNE. Following transfection of C2C12 murine muscle cells with the mouse TS vectors, we have been able to detect by nested RT-PCR trans-spliced molecules carrying the wild-type exon 12 of GNE. Similarly, transfection of HEK293 human cells with the human-directed TS vectors resulted in the generation of trans-spliced human GNE RNA molecules. Furthermore, infection of primary muscle cells from a GNE myopathy patient carrying the homozygous M712T mutation, with an AAV8-based viral vector carrying a human-directed TS construct, resulted in the generation of wild-type GNE transcripts in addition to the mutated ones. These studies provide a proof of concept that the TS approach could be used to partially correct the Middle Eastern mutation in GNE myopathy patients. These results provide the basis for in vivo research in animal models using the AAV platform with TS plasmids as a potential genetic therapy for GNE myopathy.

Introduction: FLT3 ITD and D835 mutations occur in high frequency in AML and to a lower rate in ALL patients with poor prognosis., Methods: ITD and D835 mutations were studied in 100 diagnosed acute leukemia patients including 27 AML and 73 ALL with various FAB classifications by PCR and PCR-RFLP, respectively. Subsequently, PCR products of positive samples were confirmed by sequencing analyses., Results: ITD mutations occurred in 10% of all pediatric acute leukemia, including AML and ALL. 25.9% of AML patients harbor a mutation in the ITD in various subtypes. The frequency of ITD mutations was 4% in ALL. Various insertions of nucleotides in ITD were observed, similar to those described in the literature previously., Conclusion: These preliminary data suggest that flt3-ITD mutations may play an important role in leukemogenesis in a proportion of children, particularly in the case of AML.

The genetic diversity of the HBV S gene has a significant impact on the prophylaxis and treatment of hepatitis B infection. The effect of selective pressure on this genetic alteration has not yet been studied in Iranian blood donors. To explore HBV evolution and to analyze the effects and patterns of hepatitis B surface antigen (HBsAg) mutations on blood screening assays, 358 Iranian blood donors diagnosed as asymptomatic HBV carriers were enrolled in this nationwide study. Large S and partial S genes were amplified and sequenced. HBV (sub) genotypes and synonymous and nonsynonymous mutations were investigated. The impact of naturally occurring mutations on HBsAg ELISA results was explored. Phylogenetic analyses revealed that isolated strains were of genotype D. The dominant subgenotype/subtype was D1/ayw2. Deletions and naturally occurring stop codons in the pre-S1 and major hydrophilic region (MHR) were identified. In total, 32.8% of the studied strains harbored 195 single or multiple mutations in the MHR, the majority of which were located at the first loop of the "a determinant" domain. The ayw2 subtype showed a significant effect on the ELISA signal/cut-off value and carried fewer mutations in the MHR. Nonsynonymous/synonymous substitution value indicated that negative selection was the dominant evolutionary force in the HBV S gene. This nationwide study revealed that mutation frequency of HBsAg among Iranian blood donors was much higher than previous reports from the different local regions. These findings regarding the significant differences in reactivity of ELISA among different subtypes of HBV and its correlation with the number of mutations at the MHR will be valuable to public health authorities., (© 2013 Wiley Periodicals, Inc.)

Familial Mediterranean fever (FMF) is an autosomal recessive disorder characterized by periodic provocative attacks of fever with peritonitis, pleuritis, arthritis, or eriseplemya. Tumor necrosis factor-α (TNF-α) plays an important role in the regulation of the immune response as a part of the cytokine network, including activation of macrophages and apoptosis. We investigated the possible association of TNF-α promoter -1031T/C and -308G/A polymorphisms in 86 FMF patients carrying M694 V homozygous mutation and 100 matched healthy controls both from Iranian Azeri Turks. Our data showed that patients with TNF-α -308 GG are more susceptible to the development of amyloidosis and arthritis (P value <.05). These data also showed that the frequency of TNF-α -308 A allele is considerably low among patients with amyloidosis, and it may have protective role among them (odds ratio [OR] = 0.083, χ(2) = 5.46, P value = .003). Further evaluation of this polymorphism may be important and need further studies.

Background: This study was carried out to identify molecular and hematological features of α- globin chain variants and to evaluate their effects on the clinical and hematological characteristics in Iranian individuals suspected of having thalassemia trait., Methods: Analysis of red blood cell indices, hemoglobin (Hb) analysis and  genomic DNA isolation were carried out according to standard methods. For identifying the α-thalassemia (α-thal) genotype, investigation of common Mediterranean α-globin gene deletions (-α3.7, -α4.2 -α20.5 and --MED) was performed by Gap-PCR. To characterize chain variants the entire α1 and α2 genes that spanned from the promoter region to the poly A tail were amplified and directly sequenced., Results: In this study, 19 members of 17 unrelated families showed α-chain variants. Among these cases ten α-chain variantsthat included Hb Setif, Hb Constant Spring (Hb CS), Hb Handsworth, Hb Icaria, Hb Evanston, Hb Val de Marne, Hb Utrecht, Hb Savaria, Hb Adana, and Hb Dartmouth were identified. The hematological profile and molecular basis of these ten α-chain variants and the phenotypic consequences of their interactions were discussed., Conclusions: The knowledge of the spectrum of α-globin variants present in the Iranian population is essential for the molecular diagnosis and prevention of hemoglobinopathies.

The present study compared the genetic variation among 19 different isolates of Fasciola hepatica from cattle and sheep in different areas of Iran using sequence data for mitochondrial DNA gene, the subunit 1 of cytochrome C oxidase gene (CO1). Four different CO1 genotypes were detected among F. hepatica isolates that showed five variable nucleotide positions (accession nos.; GQ398051, GQ398052, GQ398053, GQ398054). Nucleotide sequence variation among 19 isolates for CO1 analyzed in this study ranged from 0% to 0.98% in Iran. Among the five polymorphism sites identified in this study, only one (T to G at position 51 in 5'end of GQ175362) resulted in putative amino acid alteration of phenylalanine (TTT) to leucine (TTG) in CO1. A phylogenetic analysis of the sequence data revealed that host associations and geographic location are likely not useful markers for Fasciola genotype classification. In addition, morphological analysis showed that the ratios of body length and body width of some (n = 5) of the 19 examined F. hepatica isolates were intermediate between F. hepatica and Fasciola gigantica, representing the substantial polymorphism of the F. hepatica species and the difficulty in the accurate recognition based on morphological features. In conclusion, Iranian F. hepatica exhibited the presence of considerable genetic diversity at CO1.

Mutations of HBsAg especially within the "a" determinant could alter the antigenicity of the protein causing failure of HBsAg neutralization and escaping from the host's immune system, resulting in active viral replication and liver disease. This project aimed to investigate mutation in the S gene region of HBV infected patients in Golestan Province-Iran. HBV-DNA extractions from plasma and PCR of 100 patients were performed. Direct sequencing and alignment of S gene were applied using reference sequence from Gene Bank database. All isolates were belonged to genotype D, subgenotype D1, subtype ayw2. Overall 92 point mutations occurred. Of them, 40 (43.47%) were missense and 52 (56.52%) were silent. Mutations were detected in 95 cases (95%). Five of 40 mutations (12.5%) occurred in "a" determinant and 13 (32.5%), 17 (42.5%), and 2 (5%) were seen in antigenic epitope regions of B cell, CD(4)(+) and CTL, respectively. Frame shift mutations were seen in 22 cases (22%). 14% of mutations occurred at Major Hydrophilic Region(MHR) area which P120T/S and R122K/T substitutions were the most frequent ones (4%). Mutation in G145R of the S gene was observed in one case. A large number of MHR mutants are in association with failure of HBsAg detection, vaccine, and immunotherapy escape. This study showed "a" determinant S gene mutations in HBV infected people with HBsAg positivity in Golestan Province-Iran. The rate of mutation in our study was 95%. Collectively, the results of this project exhibited that most of mutations were clustered in CD(4)(+) antigenic epitopes.

Hb Constant Spring (Hb CS, codon 142, TAA>CAA, α2) (HBA2:c.427T>C) and α2 IVS-I donor site (GAGGTGAGG>GAGG - - - - -) (HBA2:c.95+2&#95;95+6delTGAGG) are nondeletional α-thalassemia (α-thal) mutations found all over the world. Identification of α-thal genotypes in at-risk couples for severe anemia or in highly heterogeneous populations requires rapid, accurate and cost-effective genotyping methods. In this study, a pair of primers were used to specifically amplify an 883 bp fragment from the α2-globin gene in order to simultaneously identify these two mutations by a PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) method. We determined the genotypic frequencies of Hb CS and the α2 IVS-I donor site mutations after amplification and enzymatic digestion with Tru9I in 238 northern Iranian samples referred for α-thal testing. Hb CS and the α2 IVS-I donor site mutations accounted for 21 (8.8%) and 29 (12.2%) of the nondeletional cases. This genotyping assay has proven to be a rapid, reliable and useful diagnostic tool for simultaneous detection of these two anomalies for genetic counseling or further prenatal diagnosis.

Duchenne's muscular dystrophy and Becker muscular dystrophy (BMD) are X-linked recessive disorders caused by mutations in the dystrophin gene. In this project, 100 unrelated male patients were initially screened for deletions in the dystrophin gene by multiplex polymerase chain reaction, of whom 52 were positive. We performed the multiplex ligation-dependent probe amplification (MLPA) method on 43 of the remaining 48 patients, as well as 12 females suspected to be carriers, to detect deletions and duplications of their dystrophin gene. The MLPA method found deletions and duplications in 8 unidentified male patients. Sequencing revealed that in one case the deletion detected was a point mutation. One of 12 females was heterozygous for deletion of exons 49 and 50. In conclusion, the MLPA method proved to be reliable for studying affected males as well as female carriers.

Purpose: The roles of several hereditary predispositions for venous thromboembolism have been evaluated in women with habitual abortion. We studied the prevalence of FV Leiden G1691A and FII G20210A mutations in women with habitual abortion and healthy controls., Methods: 60 unrelated fertile females, as controls, and 70 unrelated women with at least three consecutive pregnancy losses entered at the present study. MAS-PCR was carried out for detection of FV Leiden G1691A and FII G20210A mutations., Results: FV Leiden G1691A mutation was not found in the studied cases and controls, that is, all of the cases and the controls had normal FV Leiden 1691GG genotype. FII 20210AA genotype was not found in any of patients or controls. 2.5% of alleles (3 out of 120 chromosomes) in controls and 15.714% of alleles (22 out of 140 chromosomes) in cases had FII 20210A mutation. The FII G20210A allele frequency was 0.157 in cases and 0.025 in controls. Regarding FII G20210A mutation, the distribution of GG, GA and AA genotypes were 48 (68.57%), 22 (31.43%) and 0 (0%) in the cases and 95 (95%), 5 (5%) and 0 (0%) in the controls, respectively. Significant differences in both FII G20210A alleles and FII G20210A genotypes frequencies were observed in the cases versus the controls., Conclusion: FII G20210A mutation is significantly associated with habitual abortion.

Background and Aims: Allgrove (OMIM#231550) or Triple-A syndrome is a rare, autosomal recessive disorder characterized by the triad of familial adrenal insufficiency, achalasia, and alacrima. Approximately one-half of all patients with Triple-A syndrome have been shown to have mutations in the AAAS gene on chromosome 12q13, which results in loss or non-function of the encoded protein., Methods: Five unrelated families clinically diagnosed with Allgrove Syndrome were evaluated for sequence variations in the AAAS gene. Blood samples were collected after informed and written consent was obtained. Isolated DNA derived from subjects was amplified using intronic primers. The entire sequence of the AAAS gene including regulatory region, coding regions and exon-intron boundaries were analyzed for any alteration by PCR and direct sequencing., Results: In six probands of five families, four previously reported and two novel mutations were identified. Two heterozygote and homozygote mutations in exon 9 and the regulatory region, respectively, were detected in one of the probands., Conclusions: This is the first report of Triple-A syndrome from an Iranian population. Collectively, our study findings indicate that mutations scattered across the AAAS gene and upstream regulation elements. Various ethnic groups should develop a mutation database for their own rare genetic disorders. However, mutation databases should initially screen common mutated alleles. Our families present the typical triad of symptoms and the mutation spectrum is similar to the other population studied. Further study is required for phenotype-genotype correlation in the Iranian population., (Copyright © 2011. Published by Elsevier Inc.)

Here we report the result of three cases referred to our lab that had a combination of β-thalassemia and hemoglobin D (Hb D) traits. These individuals had no symptoms of profound anemia and hematological indices were similar to that of a β-thalassemia heterozygote. In all three cases, the Hb D level was elevated and no HbA was detected electrophoretically. The electrophoresis pattern suggested that all cases were homozygotes for Hb D. PCR followed by digestion with EcoRI and sequencing of the β-globin gene confirmed the presence of Cd 121 GAA>CAA in the heterozygous form with another β-globin mutation. In all cases, the mutations in the β-globin gene were detected by ARMS PCR technique and they were either IVSII-I or IVSI-5. Hematological studies of the family members showed that thalassemia which caused the mutations and Hb D were in the trans position.

Hb Setif is a rare type of hemoglobinopathy resulting from an aspartic acid to tyrosine substitution at codon 94 (GAC>TAC) of the α2-globin gene. In manual and automated hemoglobin (Hb) electrophoresis examination of the case, an unusual band was detected and the result of subsequent capillary electrophoresis suggested that to be Hb Setif. Carrying out polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing, a typical Hb Setif mutation (GAC>TAC) was identified. The haplotype of the α cluster was + + - M PZ + - - - -. This is the first report of such a hemoglobinopathy in North Iran. Various reports of such Hb variants in Iran and countries in the Mediterranean region and North Africa, suggest that the mutation may have occurred around 6,000 years ago, prior to colonization of Aryans on the Iranian plateau.

We report the spectrum of β-thalassemia (β-thal) mutations observed in a cohort of at-risk couples, who presented for prenatal diagnosis at the Thalassemia, Hemophilia and Prenatal Diagnosis Genetic Research Center, Shiraz Medical University, Fars, Iran, from March 2001 to April 2002. Using polymerase chain reaction-amplification refractory mutation system (PCR-ARMS), restriction fragment length polymorphism (RFLP) and direct sequencing technologies, in different combinations, we were able to provide preventive medical abortions to 55 couples at-risk of having an affected fetus. Fetal samples of chorionic villus (63.6%) or amniocentesis (37.6%) were collected according to the gestational age. The average presentation age was 11.6 ± 2.6 weeks. The expected prevalent mutations were IVS-II-1 (G>A, 23.6%) and IVS-I-110 (G>A, 10.0%) followed by IVS-I-5 (G>C, 6.4%) and IVS-I, 25 bp deletion (8.2%).

Background: Co-inheritance of β- and δ-globin mutations in Iran is not uncommon. This situation may interfere with correct diagnosis and genetic counseling of α- and β-thalassemia in screening programs. Here we report the co-inheritance of β- and δ-globin gene mutations in an individual with microcytosis, hypochromia and a normal hemoglobin A₂ (HbA₂) level., Methods: Genomic DNA extraction, amplification refractory mutation system (ARMS) polymerase chain reaction and direct DNA sequencing of δ- and β-globin genes were exploited for detection of the mutations in these two genes in an individual with low hematological indices and normal HbA₂., Results: ARMS-PCR technique revealed the β(+) IVSI-5 (G to C) mutation and direct DNA sequencing of the δ-globin gene detected a previously reported delta codon 12 (AAT-->AAA) HbA2-NYU. This study reports HbA2-NYU in association with the β IVSI-5 (G to C) mutation in Iran., Discussion: This report emphasizes that normal HbA₂ expression in a β-goblin carrier is due to mutation in the δ-globin gene and may cause misdiagnosis of thalassemia.

Purpose: Israeli investigators have identified several relatively frequent disorders due to founder point mutations in Persian (Iranian) Jews, who, for nearly three centuries up to the Islamic Revolution of 1979, were completely isolated reproductively., Methods: Using a community-based model previously employed with Tay-Sachs disease prevention, we developed a pilot program for the Persian Jewish community of greater Los Angeles. We screened for mutations responsible for four relatively frequent autosomal recessive conditions in Persian Jews in which effective interventions are available for each: Pseudocholinesterase deficiency (butyryl cholinesterase deficiency); Congenital hypoaldosteronism (corticosterone methyl oxidase II); Autoimmune polyendocrinopathy (autoimmune regulatory element); and Hereditary Inclusion Body myopathy., Results: One thousand individuals volunteered. Mutations were assessed in saliva-derived DNA and were positive for 121/1000 butyryl cholinesterase deficiency; 92/1000 Hereditary Inclusion Body myopathy; 38/1000 corticosterone methyl oxidase II; and 37/1000 autoimmune regulatory element. Ten homozygous individuals (9 butyryl cholinesterase deficiency and 1 Hereditary Inclusion Body myopathy) and 10 "at-risk" couples (seven for butyryl cholinesterase deficiency and one each for the other three disorders) were identified. These frequencies are comparable with those in Israel and indicate an extraordinary level of inbreeding, as anticipated., Conclusions: A carefully planned effort can be delivered to an "increased risk" community if detailed attention is given to planning and organization. However, availability of an effective intervention for those found to be "at-risk" or possibly affected, is essential before embarking.

Background and Aim: One candidate gene for colorectal cancer (CRC) susceptibility is exonuclease 1 (EXO1). It is a member of RAD2 nuclease family, which plays a major role in mismatch repair, DNA replication, and recombination. Single-nucleotide polymorphisms are shown to be related with cancer incidence. The aim of the present study was to examine the association between the L757P polymorphism at exon 13 of the EXO1 gene and the risk of CRC in Iranian patients., Methods: In this case-control study, 90 cases and 98 healthy control samples were analyzed genetically. The EXO1 polymorphism, P757L, was analyzed by polymerase chain reaction-restriction fragment length polymorphism. The obtained polymorphisms were examined for the relationship with CRC risk and also clinicopathological characteristics., Results: Our findings showed that patients with the Leu/Leu genotype have a reduced risk of CRC (adjusted odds ratio [OR] = 0.192, 95% confidence interval [CI]: 0.040-0.921) when the Pro/Leu and Pro/Pro genotypes were blended and they were considered as the reference. The Leu/Leu genotype also showed a reduced risk (adjusted OR = 0.168, 95% CI: 0.034-0.816) when the Pro/Pro genotype was a reference; nevertheless, the Pro/Leu genotype did not reveal a significant association with CRC at the same status (adjusted OR = 0.686, 95% CI: 0.367-1.284)., Conclusions: Our results provide evidence diagnosing that the Leu/Leu genotype of EXO1 showed an inverse association with CRC. In addition, despite other investigations, we could define a significant association between the Leu allele and CRC (p = 0.001).

The genetic base of fertility and ovulation rate in Moghani and Ghezel sheep in northwestern Iran and northeastern Turkey is important because of their fat-tailed meat and carpet quality wool. The genes encoding bone morphogenetic (BM) protein 15 and growth differentiation (GD) factor 9, respectively BMP15 and GDF9 have been shown to affect female productivity in domesticated sheep. Recently, numerous investigations have been performed on a variety of breeds to determine the association between mutations in these genes and fertility. Thus, in this study, we assessed such mutations in the Moghani and Ghezel breeds using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) with appropriate enzymes. Our data were similar to those of the previous studies showing that the genotypes were heterozygous for GD (G -->A) and BM (C -->T) mutations. These heterozygous genotypes resulted in higher ovulation rates, illustrating that one copy of each of the BMP15 and GDF9 mutations had equivalent effects on the ovulation rate. We demonstrate for the first time that the BM variant may not be sufficient on its own for infertility. In addition, although the previous studies have shown no notable relationship between the GD variant, known as the non-effecting mutation and sterility, we report that this mutation has an important role in the Moghani and Ghezel breeds.

Beta-thalassemia (beta-thal) is one of the most common autosomal recessive disorders in Iran, with more than 15,000 registered cases of thalassemia major in the country. Iran has a multiethnic society and knowledge of the mutation spectrum and regional distribution is an essential requirement for health planning and a prenatal diagnosis program. We have determined the spectrum of mutations in patients from the Isfahan region of Iran. A study of 190 chromosomes revealed 24 different mutations, including three novel ones: -41 (A>C), IVS-I-109 (-T) and codon 24 (-G). The most common mutation was IVS-II-1 (G>A) (20.5%), followed by IVS-I-5 (G>C) (11%). The findings for the Isfahan region confirm the extremely heterogeneous nature of the molecular basis of beta-thal in Iran. The results show that a strategy of using the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) for 14 of the most common mutations and DNA sequencing for the rare mutations can be used for prenatal diagnosis of beta-thal in this region.

Background/aims: The rtQ215S mutation in the hepatitis B virus (HBV) polymerase has been described as a secondary mutation associated with resistance to lamivudine (LAM) and adefovir (ADV). We aimed at assessing the prevalence of substitutions at rtQ215 of the HBV polymerase and determining the molecular and functional consequences using phenotypic analyses in vitro., Methods: The polymerase region was directly sequenced in HBV isolates from a cohort of 249 HBV genotype D-infected patients from Iran (174 males/75 females, 194 treatment-nai ve/ 55 LAM-treated). Replication-competent HBV constructs containing the naturally occurring rtQ215H, rtQ215P and rtQ215S mutations were generated, and compared to wild-type, LAM- (rtM204I, rtL180M/rtM204V) and ADV-resistant (rtN236T) clones., Results: In an Iranian cohort of 249 HBV infected patients, 14.5% (36/249) showed mutations in the rtQ215 locus, namely 6.8% rtQ215S, 3.6% rtQ215P and 4.1% rtQ215H. The frequency of rtQ215 substitutions was higher in LAM-treated than treatment-nai ve patients (25% vs. 11%), but not associated with clinical complications. In phenotypic assays, rtQ215S, rtQ215P and rtQ215H constructs showed equivalent levels of viral replication as wild-type HBV, whereas LAM- and ADV-resistant mutants had significantly impaired replicative capacities. Furthermore, rtQ215S, rtQ215P and rtQ215H harbouring constructs remained susceptible towards treatment with LAM or ADV in vitro., Conclusions: Our study reveals that rtQ215 substitutions in the HBV polymerase frequently occur in chronic hepatitis B, even without exogenous selection pressures. As these substitutions do neither impair the viral replication efficiency nor susceptibility to LAM or ADV in vitro, rtQ215 substitutions likely represent background polymorphisms rather than resistance mutations with clinical implications.

Background: In Iran, co-infections of Plasmodium vivax and Plasmodium falciparum are common and P. vivax infections are often exposed to sulphadoxine-pyrimethamine (SP). In the present study, the frequency distribution of mutations associated to SP resistance was investigated in pvdhfr and pvdhps genes from field isolates., Methods: Clinical isolates of P. vivax were collected in two different malaria endemic regions in northern and south-eastern Iran, between 2001 and 2006. All 189 collected isolates were analysed for SNP/haplotypes at positions 13, 33, 57, 58, 61, 117 and 173 of the pvdhfr and 383 and 553 of pvdhps genes using nested PCR-RFLP methods, Results: All 189 examined isolates were found to carry wild-type amino acids at positions 13, 33, 61 and 173, while 57L and 58R and 117N mutations in pure form was detected among 1.1%, 17.5% and 26% examined samples, respectively, with no polymorphisms in different loci of dhps genes. Based on size polymorphism of pvdhfr genes at repeat region, among northern isolates, the frequency distribution for type A and B were 2.2% and 97.8% respectively. However, in southern samples the prevalence of type A, B and C were 7%, 89.5% and 7.7%, respectively. Mixed genotype infections (type B and C) were detected in only 4.2% (6/143) of southern, but in none of the northern isolates. The combination of pvdhfr and pvdhps haplotypes among all 189 samples demonstrated six distinct haplotypes. The two most prevalent haplotypes among all examined samples were I13P33F57S58T61S117I173/A383A553 (65.6%) and I13P33F57S58T61N117I173 (16.4%). Two other alleles with one point mutation I13P33F57R58T61S117I173/A383A553 and two mutations I13P33F57R58T61N117I173/A383A553 accounted for 7.4% and 9.5% of the total isolates., Conclusion: The present molecular data provide important information for making decisions on population based drug use in Iran. In addition, since October 2005, with more availability of SP as first-line treatment, P. vivax isolates are more exposed to SP and the selection or spread of resistant pvdhfr and pvdhps alleles might increase in the near future in this region.

The C-terminal region of the merozoite surface protein 1 (MSP-1) of Plasmodium falciparum is a strong vaccine candidate as it is associated with immunity to the parasite. This corresponds approximately to the conserved 17th block of the gene and is composed of two EGF- like domains. These domains exhibit only four single amino acid substitutions which show several potential variants in this region of the gene. As the variations might be important for a regional vaccine design, a study was carried out to determine the variations present in P. falciparum isolates from southern Iran. Besides the usual E-T-S-R-L and the Q-K-N-G-F types, we found Q-T-S-R-L, E-K-N-G-F, E-T-S-G-L, Z-T-S-G-L and Z-T-S-R-L types, where Z was E or Q signifying the presence of mixed clones in single isolates.