Folate gene polymorphisms CBS 844ins68 and RFC1 A80G and risk of Down syndrome offspring in young Iranian women: A cross-sectional study.

Background: Cytogenetics and association studies showed that folate gene polymorphisms can increase the risk of chromosomal nondisjunction and aneuploidies. The folate-metabolizing gene polymorphisms in Down syndrome mothers (DSM) have been assessed in a variety of populations. Reduced folate carrier 1 (RFC1) and cystathionine beta-synthase (CBS) are key enzymes in folate metabolism. Objective: 2 common polymorphisms, CBS 844ins68 and RFC1 A80G, were analyzed to determine their probable risk for having Down syndrome (DS) babies in young mothers of Khuzestan province, Iran. Materials and Methods: This study was conducted on 100 mothers who had trisomy 21 DS children. 100 age- and ethnic-matched mothers with at least 2 healthy children and no history of abnormal pregnancies were considered as control. The samples were collected from all the mothers from June 2019 to April 2021. Genomic DNA was extracted from peripheral blood. The CBS-844ins68 and RFC1-A80G were genotyped using polymerase chain reaction-electrophoresis and restriction fragment length polymorphism, respectively. Results: The frequency of RFC1 AG and GG genotypes in DSM was significantly higher than the control mothers (odds ratio [OR] of 2.38 and 3.07, respectively). The heterozygote genotype of CBS 844ins68 was significantly more prevalent among DSM than the control (OR: 2.419). The OR was significantly increased to 6.667 when the homozygote of both variants was found together. Conclusion: Studying polymorphisms possibly increases the susceptibility of having a DS child. However, ethnicity, nutrition, and epistatic interactions are considerable factors to be evaluated in future studies.

Retinitis pigmentosa-1 due to an RP1 mutation in a consanguineous Iranian family: Report of a novel mutation.

Key Clinical Message: The identification of a novel RP1 gene mutation highlights the importance of precise variant identification for retinitis pigmentosa prognosis and genetic consultations, emphasizing comprehensive genetic analysis for personalized care. Abstract: Our study unveils a noteworthy association between retinitis pigmentosa-1 and a newly discovered homozygous mutation (c.5326delC; p.Asp1777Ilefs*32) within the RP1 gene. This highlights the crucial role of accurate variant identification in not only informing prognosis but also improving genetic consultations and influencing future diagnostic approaches for individuals affected by retinitis pigmentosa.

A Novel Deleterious MYO15A Gene Mutation Causes Nonsyndromic Hearing Loss.

Introduction: Hearing loss (HL) is the most frequent sensory neurodeficiency, affecting a broad spectrum of individuals globally. Within this context, the role of genetic factors takes center stage, particularly in cases of hereditary HL. Case Report: Here, we present a nonsyndromic HL (NSHL) case report. The patient is a 21-year-old man with progressive HL. The whole-exome sequencing (WES) demonstrated a novel homozygous missense mutation, c.9908A>C; p.Lys3303Thr, in the proband's exon 61 of the MYO15A gene. Further analysis has revealed that the detected mutation is present in a heterozygous state in the parents. Conclusion: WES analysis in this study revealed a novel mutation in the MYO15A gene. Our data indicates that the MYO15A-p.Lys3303Thr mutation is the likely pathogenic variant associated with NSHL. Additionally, this finding enhances genetic counseling for individuals with NSHL patients, highlighting the value of the WES method in detecting rare genetic variants.

Do NGS-based techniques represent a first-line testing in suspected Duchenne muscular dystrophy?

Duchenne muscular dystrophy (DMD) is caused by mutations in the dystrophin gene, which mostly affects boys. The subject was an 8-year-old child who had typical symptoms of muscle weakness. The NGS may be used as an efficient and cost-effective molecular diagnostic strategy for identifying patients with DMD.

A machine learning technology to improve the risk of non-invasive prenatal tests.

BACKGROUND: Timely and accurate diagnosis of genetic diseases can lead to proper action and prevention of irreparable events. OBJECTIVE: In this work we propose an integrated genetic-neural network (GNN) to improve the prediction risk of trisomy diseases including Down's syndrome (T21), Edwards' syndrome (T18) and Patau's Syndrome (T13). METHODS: A dataset including 561 pregnant were created. In this integrated model, the structure and input parameters of the proposed multilayer feedforward network (MFN) were optimized. RESULTS: The results of execution of the GNN on the testing dataset showed that the developed model can be accurately classify the anomalies from healthy fetus with 97.58% accuracy rate, and 99.44% and 85.65% sensitivity, and specificity, respectively. In the proposed GNN model, the Levenberg Merquident (LM) algorithm, the Radial Basis (Radbas) function from various types of functions were selected by the proposed GA. Moreover, maternal age, Nuchal Translucency (NT), Crown-rump length (CRL), Pregnancy-associated plasma protein A (PAPP-A) were selected by the proposed GA as the most effective factors for classifying the healthfetuses from the cases with fetal disorders. CONCLUSION: The proposed computerized model increases the diagnostic performance of the physicians especially in the accurate detection of healthy fetus with non - invasive and low - cost treatments.

PDigenic Mutations in Junctional Epidermolysis Bullosa in An Iranian Family.

In this study, we describe one Iranian patient who was diagnosed with Epidermolysis Bullosa (EB) because of mutations in three candidate genes, including 3 mutations. Two missense mutations in the LAMA3 (D3134H) and LAMB3 (Y339H) genes and also, a synonymous mutation in the ITGB4 (H422H) gene were identified that leads to the Junctional-EBHerlitz (JEB-Herlitz) clinical phenotype. The patient had a heterozygous LAMA3 mutation combined with a heterozygous mutation in LAMB3. Our results propose that these mutations produce novel protein-coding transcripts which explain the JEB-Herlitz phenotype in the patient. Interestingly, this is the first report indicating that a digenic inheritance in the LAMA3 and LAMB3 which is responsible for JEB-Herlitz. Also, this is the first digenic inheritance recognized in the JEB-Herlitz family. This study provides a new way to clarify the molecular mechanisms of LAMA3 and LAMB3 genes in JEB-Herlitz.

AHI1 gene mutation in a consanguineous Iranian family affected by Joubert syndrome: A case report.

This point of detected mutation could be considered as a novel mutational hotspot point that carried in patient ancestors. Moreover, the obtained results and family history suggest a precise genetic consulting and molecular prenatal evaluation for suspect individuals with a family history of mental and physical abnormalities.

Utilization of Whole Exome Sequencing in Non-Syndromic Premature Ovarian Failure: Ficolin-3 Gene Mutation in an Iranian Family

Background: Premature ovarian failure is a heterogeneous disorder, leading to early menopause. Several genes have been identified as the cause of non-syndromic premature ovarian failure (POF). Our aim was to explore the genetic defects in Iranian patients with POF. Methods: We studied a family with three females exhibiting non-syndromic POF. WES was performed for one of the affected individuals after ruling out the presence of CGG repeat expansion at fragile X mental retardation 1 gene in the family. Sanger sequencing was used to confirm the candidate sequence variants in the proband, and screening of the detected mutation was performed for the other affected and unaffected members of the family. Results: A homozygous frameshift mutation, c.349delC, was identified in ficolin-3 (FCN3) gene in the proband and two other patients. The parents and two healthy brothers were heterozygous for the mutation, and an unaffected sister was homozygous for wild type. Conclusion: This is the first report of a mutation in FCN3 gene in a family with POF. Our findings can lead to the enhancement of genetic databases of patients with POF, specifically for families with high-risk background.

Identification of a Novel Stop Loss Mutation in P2RX2 Gene in an Iranian Family with Autosomal Nonsyndromic Hearing Loss

Background: Hearing loss, a congenital genetic disorder in human, is difficult to diagnose. Whole exome sequencing is a powerful approach for ethiological disgnosis of such disorders. Methods: One Iranian family with two patients were attented in the study. Sequencing of known non-syndromic hearing loss genes was carried out to recognize the genetic causes of HL. Results: Molecular analyses identified a novel stop loss mutation, c.1048T>G (p.Term350Glu), whitin the P2RX2 gene, causing a termination-site modification.This event would lead to continued translation into the 3' UTR of the gene, which in turn may result in a longer protein product. The mutation was segregating with the disease phenotype and predicted to be pathogenic by bioinformatic tools. Conclusion: This study is the first Iranian case report of a diagnosis of autosomal dominant nonsyndromic hearing loss (ADNSHL) caused by P2RX2 mutation. The recognition of other causative mutations in P2RX2 gene more supports the probable function of this gene in causing ADNSHL.

Identification of a Novel WFS1 Mutation Using the Whole Exome Sequencing in an Iranian Pedigree with Autosomal Dominant Hearing Loss.

INTRODUCTION: Sensorineural hearing loss is the most frequent type of hearing impairment in the human population. Genetic factors account for over 60% of hearing loss in patients. This is a genetically heterogeneous sensorineural disorder. CASE REPORT: We carried out whole exome sequencing (WES) to screen hearing loss candidate genes in a member of an Iranian family with hearing loss. The Sanger process was used to sequencing the variant in the family members. A novel mutation (c. 559C > T) was found in the WFS1 gene (in exon 5) in the patient leading to a heterozygous missense mutation (p.L187F). Furthermore, it co-segregated with HL in the family. All affected individuals in the family had severe-to-profound HL. CONCLUSION: This survey is the first to describe WFS1 related HL in the Iranian population. Our data propose that the WFS1-p.L187F mutation is the pathogenic variant for autosomal dominant nonsyndromic hearing loss. Our results extend the range of the WFS1 gene mutations.

The pattern of gene copy number alteration (CNAs) in hepatocellular carcinoma: an in silico analysis.

BACKGROUND: Hepatocellular carcinoma (HCC) is the most common type of liver cancer that occurs predominantly in patients with previous liver conditions. In the absence of an ideal screening modality, HCC is usually diagnosed at an advanced stage. Recent studies show that loss or gain of genomic materials can activate the oncogenes or inactivate the tumor suppressor genes to predispose cells toward carcinogenesis. Here, we evaluated both the copy number alteration (CNA) and RNA sequencing data of 361 HCC samples in order to locate the frequently altered chromosomal regions and identify the affected genes. RESULTS: Our data show that the chr1q and chr8p are two hotspot regions for genomic amplifications and deletions respectively. Among the amplified genes, YY1AP1 (chr1q22) possessed the largest correlation between CNA and gene expression. Moreover, it showed a positive correlation between CNA and tumor grade. Regarding deleted genes, CHMP7 (chr8p21.3) possessed the largest correlation between CNA and gene expression. Protein products of both genes interact with other cellular proteins to carry out various functional roles. These include ASH1L, ZNF496, YY1, ZMYM4, CHMP4A, CHMP5, CHMP2A and CHMP3, some of which are well-known cancer-related genes. CONCLUSIONS: Our in-silico analysis demonstrates the importance of copy number alterations in the pathology of HCC. These findings open a door for future studies that evaluate our results by performing additional experiments.

The worldwide molecular spectrum and distribution of thalassaemia: a systematic review.

CONTEXT: Thalassaemia is one of the most common inherited autosomal recessive disorders around the world. A considerable amount of literature has been published about the type of mutations and the prevalence of thalassaemia, but findings are often contradictory. OBJECTIVE: This systematic review aimed to provide a comprehensive view of the prevalence of thalassaemia-associated mutations in different countries, their effect on haemoglobin (Hb) levels, as well as reporting thalassaemia-associated rare mutations. METHODS: A systematic search of the literature was carried out through major indexing databases (MEDLINE/PubMed, Scopus, EMBASE, Cochrane central, and ISI web of science) using keywords: "Co-inheritance, αα, ß, thalassaemia" and "α-ß thalassaemia, Mediterranean anemia, mutations" from 1998-September 2019. Hand-searching was also performed. There was no language restriction. RESULTS: The initial searches yielded 1059 studies, of which 92 articles were included following inclusion and exclusion criteria. Of these, 3.3% (3) of articles were cohort studies, and 96.7% (89) of the remaining articles were cross-sectional studies. Our findings showed that 45.6% (42) of researchers investigated ß-thalassaemia, 22.9% (21) αα-ß thalassaemia, and 31.5% (29) α thalassaemia. CONCLUSION: The present study provides valuable information about the spectrum of thalassaemia-associated mutations, which can be useful for preventing thalassaemia, reducing costs of care, reducing the treatment-related side effects, and showing the most defective mutations.HighlightEvaluating the increase or decrease in the birth prevalence of thalassaemiaIdentifying the most common and rare mutations in various parts of the worldComparing researchers' findings from various parts of the world.

The antioxidant and anti-inflammatory effects of astaxanthin supplementation on the expression of miR-146a and miR-126 in patients with type 2 diabetes mellitus: A randomised, double-blind, placebo-controlled clinical trial.

BACKGROUND: The pathogenesis of type 2 diabetes mellitus (T2DM) is associated with chronic oxidative stress and inflammation. It is well known that the expression of some miRNAs such as miRNA-146a is upregulated in diabetic and hyperglycaemic patients, whereas circulating miRNA-126 is reduced. Therefore, we aimed to determine the effects of astaxanthin (AST) supplementation on the circulating malondialdehyde (MDA) and interleukin 6 (IL-6) levels, and the expression of miR-146a and miR-126 in patients with T2DM. METHODS: This randomised, double-blind, placebo-controlled clinical trial was conducted in 44 patients with T2DM randomly receiving 8 mg/d of oral AST (n = 22) or placebo (n = 22) for 8 weeks. RESULTS: We observed that AST supplementation could decrease plasma levels of MDA and IL-6 (P < .05) and decrease the expression level of miR-146a over time (fold change: -1/388) (P < .05). CONCLUSION: AST supplementation might be beneficial for improving circulating MDA and IL-6 and the down-regulation of miR-146a. However, future investigations are suggested to confirm these results.

Effect of lipoic acid supplementation on gene expression and activity of glutathione S-transferase enzyme in infertile men.

Oxidative stress has become the focus of interest as a potential cause of male infertility. We evaluate effects of lipoic acid (LA) supplementation on glutathione S-transferase (GST) expression. This randomized, triple-blind, placebo-controlled clinical trial was conducted on 44 infertile males with idiopathic asthenozoospermia. Men were randomized to receive 600 mg LA or placebo once daily for 12 weeks and semen samples and venous blood samples were obtained. GST expression, reactive oxygen species (ROS) levels, GST activity and reproductive hormone profiles were also measured. GST expression in the intervention group were significantly higher than the control group. Also, at the end of the study, GST activity increased, and ROS levels decreased significantly compared to the baseline. Additionally, the intervention group showed an increase in testosterone and decrease in serum follicle-stimulating hormone (FSH), luteinizing hormone (LH) and prolactin after 12 weeks, but this difference was not significant. We conclude a 12-week treatment with LA leads to improvements in reproductive hormones in serum, and significantly reduces the generation of ROS and increases the gene expression and activity of GST in seminal fluid.

Effect of weight-loss diet combined with taurine supplementation on body composition and some biochemical markers in obese women: a randomized clinical trial.

Taurine (Tau), an endogenous non-protein and sulfuric-amino acid, is involved in various biological pathways including anti-inflammatory, anti-oxidation, insulin resistance inhibition, and lipid profile improvement. According to some experimental and clinical studies, insulin resistance and excess body weight are associated with reduced serum level of Tau. Therefore, this study was aimed to evaluate Tau supplementation and a diet-induced weight-loss intervention on body composition and some biochemical indices of obese women. Participants were divided randomly into the intervention (standard weight-loss group + cap Tau 3 g/day for 8 weeks, n = 20) and control (standard weight-loss group + cap placebo for 8 weeks, n = 18) groups. To achieve weight loss, all participants received an individualized diet that included a 30% reduction in their total energy intake. Chi-square test was applied to compare categorical variables between two groups at baseline. Paired t test and independent-sample t test were also used to analyze the parametric continuous data within and between the two groups, respectively. Analysis of covariance was run for controlling the confounding variables. At the post-intervention, the mean changes of total cholesterol (p = 0.03), low-density lipoprotein cholesterol (p = 0.03), leptin (p = 0. 006), total adiponectin (p = 0.04), and high sensitivity C-reactive protein (p = 0.03) decreased significantly in Tau group compared with the control group. No significant results were found in the mean changes of high-density lipoprotein cholesterol, anthropometric measurements, glycemic indices, and liver enzymes between the two groups (p > 0.05). The findings showed that Tau supplementation along with a weight-loss diet may be more effective in improving the lipid profile and metabolic risk factors compared with a weight-loss diet alone.

Ginger in patients with active ulcerative colitis: a study protocol for a randomized controlled trial.

BACKGROUND: As a lifetime disorder, ulcerative colitis (UC) is an inflammatory bowel disease (IBD) that affects quality of life and also demands long-term interventions. In spite of considerable side effects and sometimes restricted uses, efficient medications are available for UC treatment. Some in vitro and in vivo examinations have correspondingly introduced ginger and its active components with antioxidant, anti-inflammatory, and anti-ulcerative properties. Therefore, this trial aims to evaluate the effect of ginger supplementation on patients with active UC. METHODS: This study will be a 12-week, double-blind, parallel-group, randomized, controlled trial (RCT) in which 44 patients will be allocated to ginger and placebo groups receiving basic routine treatments plus ginger or placebo capsules, respectively. The primary outcomes are inflammatory markers (TNF-α and hs-CRP) and total antioxidant capacity. DISCUSSION: The findings of this trial will provide evidence on the effect of ginger on patients with active UC. TRIAL REGISTRATION: Iranian Registry of Clinical Trials, IRCT20190129042552N1. Registered on 21 June 2019.

Exome sequencing revealed a p.G299R mutation in the COMP gene in an Iranian family suffering from pseudoachondroplasia.

BACKGROUND: Short-stature (SS) is multifactorial pathologic condition that originates from either genetic or environmental factors. The diagnosis is based on family history, clinical findings, radiological examination and genetic analysis. A variety of genes have been reported for SS, among which FGFR-3 was the main gene in achondroplasia and hypochondroplasia. In other forms of SS, the gene involved varies from one patient to another. Whole exome sequencing (WES) and comparative genomic hybridization (CGH) have recently introduced a growing body of genes annually. The present study performed a WES analysis on an Iranian family suffering from an inherited form of SS aiming to diagnose the causative gene. The father and all of his four sons were diagnosed as SS. METHODS: The blood samples were collected from the proband and his available family members. Genomic DNA was extracted using salting-out method. The DNA of the proband was analyzed using WES and confirmed through polymerase chain reaction (PCR)-sequencing. The WES-extracted variant was evaluated in silico using software aiming to determine whether this nucleotide change is pathogenic. The presence of the variant was traced in other affected family members using PCR-sequencing. RESULTS: Following segregation analysis, variant c.896 G>A of the COMP gene was found in all of the affected individuals in a heterozygous form. This variant resulted in substitution of glycine 299 with arginine and was previously predicted as pathogenic in the Human Gene Mutation Database dataset, although it represents the first report in Iran. CONCLUSIONS: The findings of the present study suggest consideration of the c.896 G>A variant of the COMP gene with respect to the genetic counseling of inherited skeletal dysplasia in Iran.

A pathogenic variant in SLC26A4 is associated with Pendred syndrome in a consanguineous Iranian family.

Objective: Hearing loss (HL) is a common sensory deficit with high phenotypic and genotypic heterogeneity. A large Iranian family with HL was genetically assessed in this study. Design: A proband from a consanguineous multiplex HL family from Iran was examined via Targeted Next-Generation Sequencing (TNGS). Sanger sequencing allowed the segregation analysis of the variant of interest and the investigation of its presence in a cohort of 50 ethnicity-matched healthy control individuals. The gene was previously associated with HL. Therefore, to determine whether the variant was specifically associated with Pendred Syndrome (PDS) or DFNB4, biochemical analyses, PTA, thyroid scans by Tc99m, perchlorate discharge test and high-resolution CT scan of the temporal bone were carried out on the affected family members. Study sample: Ten members of a large multiplex Iranian family with HL were recruited in this study. In addition, 50 unrelated healthy controls of the same ethnic group were randomly selected to genotype the variant. Results: A homozygous missense variant (NM_000441.1: c.1211C > T/p.Thr404Ile) in exon 10 was found segregating in the family. Based on the ACMG's guidelines, the variant was classified as pathogenic. Conclusion: This study expands the spectrum of SLC26A4 pathogenic variants in hearing loss.

Whole exome sequencing revealed a novel dystrophin-related protein-2 (DRP2) deletion in an Iranian family with symptoms of polyneuropathy.

OBJECTIVES: Charcot-Marie Tooth disease (CMT) is one of the main inherited causes of motor and sensory neuropathies with variable expressivity and age-of onset. Although more than 70 genes have been identified for CMT, more studies are needed to discover other genes involved in CMT. Introduction of whole exome sequencing (WES) to capture all the exons may help to find these genes. MATERIALS AND METHODS: Here, we tried to find the genetic cause of the neuropathy in two Iranian brothers using WES. Blood sample was collected from probands and their family members to extract the genomic DNA. The extracted DNA from one of the affected case was subjected for WES. The variant calls were filtered to reveal the pathogenic variant. Presence of the candidate mutation was confirmed using Sanger sequencing. The pathogenic potential of the variant was examined using in silico software. Using ClustalW multiple alignment, the presence of variant in conserved domain of protein was investigated. The parent and another affected boy were also checked for presence of the variant using PCR-sequencing. RESULTS: The obtained data presented a novel TTC del mutation in CDS 738 of dystrophin related protein 2 (DRP2) gene, which was validated by sequencing. The variant was located in a conserved domain of DRP2 protein and predicted as pathogenic. Two affected boys were hemizygous for the mutation and received the mutation from mother. CONCLUSION: Here, we provided the evidence for the contribution of DRP2 in CMT. Also, the symptoms shed light on molecular aspect of this genetically heterogeneous disease.

Evaluation of the effect of oral taurine supplementation on fasting levels of fibroblast growth factors, ß-Klotho co-receptor, some biochemical indices and body composition in obese women on a weight-loss diet: a study protocol for a double-blind, randomized controlled trial.

BACKGROUND: Taurine (Tau) is involved in many biochemical functions such as regulation of glucose and lipid metabolism, enhancement of energy expenditure, anti-inflammatory effects and appetite control. The most important effect of Tau in obesity is its direct effect on adipose tissue. Some evidence has shown an impaired FGF (fibroblast growth factor) 19 and 21 biosyntheses in obesity. Besides the effects of eicosapentaenoic acid on serum FGF concentrations, the effect of other nutrients on FGFs is not clear. Since obesity as an important health problem is rising around the world and on the other side, Tau biosynthesis is reduced by adipose-tissue-derived factors in obesity, the effects of Tau and a weight-loss diet on obesity need to be investigated further. METHODS: We will conduct an 8-week. double-blind, parallel-group, randomized controlled clinical trial to investigate the effect of Tau supplementation on fasting serum levels of FGFs, ß-Klotho co-receptor, some biochemical indices and body composition in 50 obese women aged between 18 and 49 years on a weight-loss diet. DISCUSSION: We will determine the other advantages of a weight-loss diet on new metabolic risk factors. Since Tau may regulate adipose-tissue-derived factors and a weight-loss diet can promote the useful effects of Tau supplementation; for the first time, the effects of a weight-loss diet along with Tau supplementation on these variables will be assessed. TRIAL REGISTRATION: Iran Clinical Trials Registry, ID: IRCT20131125015542N2 . Registered on 24 November 2018.