جستجوی مقالات مرتبط با کلیدواژه « next-generation sequencing » در نشریات گروه « پزشکی »

Danon disease is defined by a clinical trio of cardiomyopathy, skeletal myopathy, and cognitive impairment. It results from the lysosomal-associated membrane protein-2 (LAMP2) gene variants. The aim of study is determination of genotype and phenotype of a newly diagnosed Iranian family with a unique phenotype due to a pathogenic variant of the LAMP2 gene along with a phenotypic comparison of all reported patients.

In this descriptive study, we evaluated the demographic data, clinical features, management procedures, as well as genetic analysis of both patients in this newly diagnosed family. Whole genome sequencing (WGS) and in silico structural and functional predictions were applied. A comprehensive search of the c.877C>T variant in LAMP2 was conducted using the PubMed, Google Scholar, VarSome, ClinVar, Human Gene Mutation Database (HGMD), and Franklin databases to identify any genotype-phenotype correlations.

Nine patients were carriers of the c.877C>T variant. All patients were male, and displayed variable degrees of left ventricular hypertrophy (LVH) that ranged from mild to severe. All patients exhibited typical cardiac conduction abnormalities consistent with Danon disease. Four underwent heart transplants and survived. Skeletal muscle involvement and cognitive impairment were observed in four patients each. The mean age of onset was 14 years. The proband in this study exhibited an earlier onset of cardiac symptoms.

Genetic analysis is the preferred diagnosis approach for Danon disease and can assist families in managing affected patients, identify carriers, and assist with future family planning. This study highlights the intrafamilial phenotypic variability of Danon disease. It is possible that variants of this gene may be frequent in Iran.

Methylmalonic aciduria is a rare inherited metabolic disorder with autosomal recessive inheritance pattern. There are still MMA patients without known mutations in the responsible genes. This study aimed to identify mutations in Iranian MMA families using autozygosity mapping and NGS.

Multiplex PCR was performed on DNAs isolated from 12 unrelated MMA patients and their family members using 19 STR markers flanking MUT, MMAA, and MMAB genes, followed by Sanger sequencing. WES was carried out in the patients with no mutation.

Haplotype analysis and Sanger sequencing revealed two novel, mutations, A252Vf*5 and G87R, within the MMAA and MUT genes, respectively. Three patients showed no mutations in either autozygosity mapping or NGS analysis.

High-frequency mutations within exons 2 and 3 of MUT gene and exon 7 of MMAB gene are consistent with the global expected frequency of genetic variations among MMA patients.

Mucopolysaccharidosis-II (MPSII) is diagnosed based on a deficiency in iduronate 2-sulfatase enzyme activity. Detection of a hemizygous pathogenic variant in the iduronate 2-sulfatase (IDS) gene confirms the diagnosis in a male proband.

We report a five-year-old boy with MPSII in whom no mutation was detected in the IDS gene by next-generation sequencing (Miseq-Illumina) covering the coding regions of the gene. Therefore, we tried to detect the mutation in the IDS gene using RNA sequencing that has recently been used.

In some diseases diagnosed by clinical and biochemical methods, mutations cannot be detected even with advanced genetic methods, such as next-generation sequencing. In these cases, we emphasize that mutations should be investigated using other methods, including RNA sequencing.

Human intestine microbiota are known to be directly and indirectly altered during some diseases such as kidney complications. Bacteroides is considered as the main and the most abundant phylum among human gut microbiota, which has been classified as enterotype 1. This study aimed to assess the abundance of Bacteroides spp. in fecal flora of end-stage renal disease (ESRD) and chronic kidney disease (CKD) patients and compare it with the Bacteroides composition among fecal flora of healthy individual.

Fresh fecal samples were collected from 20 CKD/ESRD patients and 20 healthy individual without any kidney complications. The pure microbial DNA was extracted by QIAamp Stool Mini Kit from stool samples. MiSeq system was used to analyze the intestinal composition by next generation sequencing method.

A number of 651 bacterial strains were isolated and identified from 40 fecal samples of both patients and healthy groups. Bioinformatics analysis defined 18 different types of Bacteroides species which included 2.76% of all strains. Statistical analysis showed no significant difference between study groups (P>0.05). In both healthy and patient groups three species including B. dorei, B. uniformis, and B. ovatus have allocated the most abundance to themselves. The lowest abundance was related to B. eggerthii, A. furcosa and B. barnesiae among CKD/ESRD patients and A. furcosa, B. barnesiae, and B. coprocola had the lowest abundance among healthy people.

This study indicates despite all previous evidence of Bacteroides role in gut microbiota, it had no different distribution between healthy persons and CKD/ESRD patients.

Cigarette smoking has been identified as most perilous risk factor for several health ailments. Increased price may discourage smoking habits. There is limited literature available on impact of price rise on smoking behaviors in Saudi Arabia, which is the fourth largest importer of cigarettes and this study assessed the impact of tax increase (in 2020) on smoking behaviors.

A cross-sectional survey was carried out between July 2021 and December 2021.i.e.one year after new value added tax (VAT) system came into force. Data was collected with 14-item pretested questionnaire from 721 adult smokers in Al-Jouf Region of Saudi Arabia selected through stratified cluster ransom sampling. We measured effects of tax increase on smoking behaviors, its impact on decision to quit and perceived health improvements as outcome variables.

Nearly 40% of the respondents said that increased price lead them to smoke less number of cigarettes per day (P=0.000), decreased smoking improved their health in terms of breathing capacity, mood, ability to exercise and sleep in hierarchy. 67.4% of the participants are currently thinking of quitting smoking due to increased prices (P=0.001) and logistic regression models identified reduced smoking due to tax rise (Odds=5.68), improvement in health (Odds=2.94) and excess spending of above 20% (Odds=1.72) significantly associated with intentions to quit smoking.

Increased price of cigarettes due to VAT significantly decreased smoking behaviors and has impact on smokers’ decision to quit smoking. Future studies needed to assess the long-term effect of increased tax on smoking behaviors and its relapse.

Understanding the microbiota of disease vectors can help for developing new strategies to prevent the transmis sion of vector pathogens. Ixodes ricinus is one of the most notorious tick vectors with increasing importance in Iran and other parts of the world while there is limited data on its microbiota. This study aimed to use metagenomics for identifying the I. ricinus tick’s microbiota of Iran.

A total of 39 adult ticks were collected from Mazandaran (21 females), Gilan (17 females), and Golestan (1 male). Five tick pools prepared from 39 adults of I. ricinus were subjected to metagenomics analysis. The data were analyzed by targeting the V6 region of the 16S rRNA gene by Illumina 4000 Hiseq sequencing.

Among hundreds of intestinal microbiota identified by metagenomics, various pathogenic microorganisms distributed in 30 genera and species including those responsible for tick-borne diseases resided in the genera Coxiella, Rickettsia, and Burkholderia were found.

Our results indicated that metagenomics identifies bacteria genera and species which cannot be easily rec ognized by routine methods. The presence of such pathogenic bacteria indicates the importance of possible zoonotic diseases in this region which could affect public health. These results further substantiate the importance of advanced metagenomics analyses to identify neglected tick-borne pathogens which enable researchers to provide efficient mapping roads for the management of emerging and re-emerging infectious diseases.

More than 80 genes are involved in the pathogenesis of the most common single gene peripheral neuropathies denoted as Charcot-Marie-Tooth (CMT). Only a few studies have investigated the pathological molecular mechanisms of Iranian patients affected with CMT. The aim of this study is to identify the clinical manifestation, mutational spectrum and phenotypic correlation of a cohort of patients with Charcot-Marie-Tooth disease (CMT) in Iran.

We conducted a comprehensive gene panel sequencing consisting of 80 genes in a cohort of 23 patients with CMT referred between January 2015 and March 2021. The recruited samples indicated almost an equal distribution of demyelinating and axonal types of CMT, with practically no difference between AD or AR patterns of inheritance.

Four novel mutations, including c.271C>T in LITAF and c.205+1delG in NDRG1, c.2455A>C in KIF1B and c.1728A>G in FIGF were detected in four patients affected with demyelinating CMT types (CMT1C and CMT4D), and characterized phenotypically.

Our promising results unravel the complicated genetic architecture of Iranian CMT patients and help physicians and researchers achieve earlier diagnosis, better clinical management and recognizing high risk families. Further large-scale studies are needed to improve our understanding of CMT complex genetic architecture

Squamous cell carcinoma (SCC) is the most common human solid tumor and the leading cause of cancer death. SCC of the breast is a very rare type of cancer that has not been well researched. Early identification of the genetic factors involved can lead to early diagnosis and targeted treatment. The present study was conducted in 2018 at Isfahan University of Medical Sciences (Isfahan, Iran). The proband was a 66-year-old woman with SCC of the breast and a positive family history of cancer. Blood DNA samples were used for whole-exome sequencing to identify germline pathogenic variants. Variant annotation and prioritization were done on variant call format files using bioinformatics software tools. The screened variants were confirmed using the Sanger sequencing method. Co-segregation analysis was performed on the blood DNA samples of the first- and second-degree relatives of the proband to assess the presence of the mutation. A novel germline pathogenic variant was identified in the RECQL4 gene of the family. RECQL4 is a known protein in DNA repair and replication. Considering its effect on other types of SCC, it may play an important role in SCC initiation and progression in the breast.

 The CSF1R gene encodes the receptor for colony-stimulating factor-1, the macrophage, and monocyte-specific growth factor. Mutations in this gene cause hereditary diffuse leukoencephalopathy with spheroids (HDLS) with autosomal dominant inheritance and BANDDOS (Brain Abnormalities, Neurodegeneration, and Dysosteosclerosis) with autosomal recessive inheritance.

 Targeted gene sequencing was performed on the genomic DNA samples of the deceased patient and a fetus along with ten healthy members of his family to identify the disease-causing mutation. Bioinformatics tools were used to study the mutation effect on protein function and structure. To predict the effect of the mutation on the protein, various bioinformatics tools were applied.

 A novel homozygous variant was identified in the gene CSF1R, c.2498C>T; p.T833M in exon 19, in the index patient and the fetus. Furthermore, some family members were heterozygous for this variant, while they had not any symptoms of the disease. In silico analysis indicated this variant has a detrimental effect on CSF1R. It is conserved among humans and other similar species. The variant is located within the functionally essential PTK domain of the receptor. However, no structural damage was introduced by this substitution.

 In conclusion, regarding the inheritance pattern in the family and clinical manifestations in the index patient, we propose that the mentioned variant in the CSF1R gene may cause BANDDOS.

Preimplantation genetic diagnosis is recognized as an effective approach to rule out embryos with abnormal chromosomes in hopes of increasing the chances of a successful pregnancy. The objective of this study is to evaluate the association between types of single cell (blastomere) chromosomal aneuploidy and female partner age using Next Generation Sequencing technique. This study showed that 70.80% of tested samples had abnormal chromosomal complementation, regardless of maternal age or complexity of the abnormality present.

Type 2 diabetes mellitus (T2DM) is a multifactorial genetic condition caused by the combination of genes and environmental factors. Several variations linked to T2DM have been discovered in recent genetic investigations, particularly genome -wide association studies (GWAS ). This study aimed to investigate genes involved in T2DM , focusing on the NGS analysis and studying the genetic basis of T2DM to improve diagnosis, prevention, and treatment.

We selected 5 families based on the diagnosis of diabetes at the age of 30 years or earlier in at least 3 consecutive generations for NGS analyses.

For each of the 5 participants tested thus far, a mean of 11 to 21 variants of clinical significance were detected. These variants were located in different genes , which indicate the association of these genes with susceptibility to diabetes. WFS1 and INS gene mutations were present in all five diabetic patients analyzed. Specifically, mutations in WFS1, KCNJ11, ABCC8, HNF1B, INS, GCKR, HNF1A and PCSK1N account for 25%, 13%, 8%, 7%, 7%, 6%, 6% and 6% of patients, respectively.

WFS1 is the most often altered gene in our participants with putative alterations, according to our findings (25 %). WFS1 mutations were discovered in all of the probands.

To explore the transcriptome profiling of the fourth-stage larvae of Angiostrongylus cantonensis.

Two groups of fourth-stage larvae were collected to extract total RNA in Zhejiang, China 2020. Then, mRNA was separated and reverse transcribed into cDNA. Next-generation sequencing was used to explore the transcriptome information. Finally, to obtain the biological annotation information, the transcriptome information was run against the related databases, including Nr, GO, COG, KOG and ORF.

Overall, 128667 unigenes and 193059 transcripts were obtained. The Nr annotations of unigenes and transcripts showed that A. cantonensis was the 5th and 4th most related species, respectively. Meanwhile, the annotation of unigenes and transcripts by querying GO, COG, KOG and ORF showed that L4 was extremely active in gene expression, concerning signal transduction, transcription, posttranslational modification, metabolism, etc.

The fourth-stage larvae of A. cantonensis have their own profiling in the transcriptome, which is related to signal transduction, transcription, posttranslational modification, metabolism, etc.

Autosomal dominant polycystic kidney disease (ADPKD), one of the common inherited disorders in humans, is characterized by the development and enlargement of renal cysts, often leading to end-stage renal disease (ESRD). In this study, Iranian ADPKD families were subjected to high-throughput DNA sequencing to find potential causative variants facilitating the way toward risk assessment and targeted therapy.

Our protocol was based on the targeted next generation sequencing (NGS) panel previously developed in our center comprising 12 genes involved in PKD. This panel has been applied to investigate the genetic causes of 32 patients with a clinical suspicion of ADPKD.

We identified a total of 31 variants for 32 individuals, two of which were each detected in two individuals. Twenty-seven out of 31 detected variants were interpreted as pathogenic/likely pathogenic and the remaining 4 of uncertain significance with a molecular diagnostic success rate of 87.5%. Among these variants, 25 PKD1/2 pathogenic/likely pathogenic variants were detected in 32 index patients (78.1%), and variants of uncertain significance in four individuals (12.5% in PKD1/2). The majority of variants was identified in PKD1 (74.2%). Autosomal recessive PKD was identified in one patient, indicating the similarities between recessive and dominant PKD. In concordance with earlier studies, this biallelic PKD1 variant, p.Arg3277Cys, leads to rapidly progressive and severe disease with very early-onset ADPKD.

Our findings suggest that targeted gene panel sequencing is expected to be the method of choice to improve diagnostic and prognostic accuracy in PKD patients with heterogeneity in genetic background.

Carnitine palmitoyltransferase II (CPT-2) deficiency is a rare and autosomal recessive disorder of long-chains fatty acids oxidation. Here, we report a 10-year-old boy with a bilateral hearing loss and a myopathic form of CPT II deficiency which was confirmed under molecular genetic test analysis. He was admitted to our hospital with unexplained headache, vomiting, and fever. Furthermore, he developed seizures, muscle weakness, neck stiffness and pain, mild respiratory distress, and icteric appearance. The laboratory test results also showed sever elevated levels of lactate dehydrogenase (LDH) and Creatine phosphokinase (CPK). He had also icteric appearance with unexplained hyperbilirubinemia. Further examinations revealed normal heart, liver without neurological disorders. Muscle pathological examination reported normal pathology without neuromuscular and mitochondrial disorders and storage diseases. Finally, molecular test analysis with next generation sequencing (NGS) revealed a homozygous pathogenic variant in the CPT-II gene, c.338C>T p. (Ser113Leu) which was correlated to CPT-II deficiency fatty acid oxidation disorder. Furthermore, we identified a homozygous pathogenic variant in the ADGRV1 gene, c.15736C>T p.(Arg5246*), which suggest the Usher syndrome type 2C and the reason for sensorineural hearing loss in this case. Our finding indicates that CPT-II can be associated with multiple symptoms and clinical features. Therefore, evaluation of CPT-II deficiency with molecular test analysis may be helpful in cases with unexplained icteric appearance, muscle weakness and rhabdomyolysis.

Complex chromosome rearrangements (CCRs) involve more than 2 chromosomal breakpoints and cause the exchanges of chromosomal segments between two or more chromosomes. The carriers of CCRs have normal phenotypes, but they have a higher risk of reproductive failure.

This paper presents a couple with a history of two affected children, one spontaneous abortion, three in vitro fertilization (IVF) failures, and one healthy boy who were referred to our laboratory for preimplantation genetic testing (PGT). The wife had been evaluated as a carrier of 46,XX,t (2;6)(p21;p25); therefore, four IVF treatment cycles supported with PGT for this translocation had been performed in different IVF centers until the couple consulted our laboratory. Only one of these four IVF attempts had resulted in a healthy boy and this IVF study had been performed with fluorescence in situ hybridization (FISH)-based preimplantation genetic testing for structural chromosomal rearrangements (PGT-SR). The fifth IVF study with next-generation sequencing (NGS)-based PGT was performed by our laboratory and no healthy embryo was found in evaluated 6 embryos. During our NGS-based PGT, the cryptic involvement of 12p was firstly detected. FISH with chromosome 2,6, and 12 specific probes revealed that the mother was a carrier of a balanced 3-way translocation of 46,XX,t(2;6;12)(p21;p25;p13).

NGS based PGT-SR method is an accurate method for detecting the copy number variations and is helpful to find out the cryptic CCRs.

Pseudo-TORCH syndrome (PTS) is a group of autosomal reces-sive disorders that clinically and radiologically mimic TORCH congenital infec-tions. The prevalence of pseudo-TORCH syndrome 2 is 1 in 1,000,000 cases worldwide. This novel disorder is extremely rare, and is generally detected by prenatal diagnosis through next generation sequencing (NGS) during pregnancy. In this study, a familial case of pseudo-TORCH syndrome 2 with novel non-sense mutation in the ubiquitin-specific peptidase 18 (USP 18) gene in the par-ents was reported, who are heterozygous asymptomatic carriers; however, all children have inherited a homozygous pathogenic form of USP18, which is an important negative regulator of type I interferon (IFN) signal transduction. To the best of our knowledge, this is the first case of a novel mutation of USP18 seen in a family with pseudo-TORCH syndrome 2 (PTS 2) from India.

A 23-year-old pregnant woman with bad obstetric history, including intrauterine and neonatal mortality was referred to the Institute of Ge-netics in the year 2021 for clinical and genetic evaluation. Advanced clinical exome sequencing of the parents and the fetus revealed heterozygous carrier status in parents and homozygous mutation in USP 18 gene in the progeny lead-ing to pseudo-TORCH-2 syndrome.

The present case highlights the significance of carrier screening, prenatal diagnosis, and genetic counseling in couples with bad obstetric history for the detection of rare genetic disorders with poor prognosis.

Aicardi Goutiere’s syndrome is an autosomal recessive neurodegenerative disorder. Its clinical signs usually mimic TORCH-like clinical signs; which makes the differential diagnosis difficult. Here, we report a case with one homozygous pathogenic mutation c.529G>A p.Ala177Thr on RNASEH2B gene (NM_024570) that relates to Aicardi-Goutieres syndrome type 2  that had been misdiagnosed in about 5 years.

Cardiomyopathies are heterogeneous and critical disorders of cardiovascular diseases. One of the most common inherited cardiomyopathies is DCM (dilated cardiomyopathy). Genetic disorders are found in approximately 50% of DCM cases. We aimed to describe a case of DCM in a 42-year-old woman in 2018 at Farhud Genetic Clinic, Tehran, Iran. To detect genetic involvement, Next-generation sequencing (NGS) was performed and the data were evaluated carefully. Variations in different genes coding crucial proteins in cardiac muscle structure (i.e. Titin, Obscurin, MYH6, and LAMA4) and proteins involved in channels (i.e. CAVNA1C, SCN1B and SCN5A) were detected by whole-exome sequencing (WES). In agreement with the clinical manifestations and molecular analysis, DCM was confirmed. This study provides further evidence on the diagnostic role of NGS in borderline DCM cases. It also shows the recently developed high throughput sequencing can provide clinicians with this approach to diagnosis, treatment, and prevention of such hard-to-diagnose disorders. Furthermore, this study highlights the basis of personalized medicine, namely detection of high-risk individuals by revealing some genetic variants as predictive risk factors, and initial prevention of DCM.

We present a Non-Small Cell Lung Cancer Grade IV patient, diagnosed at 46 years of age, with multiple relapse from the diagnosis and demonstrating a poor prognosis after 3 cycles of treatments. A clinical comprehensive genomic profile was performed with the goal of finding potential actionable molecular alterations. The patient showed significant symptomatic and laboratory improvement with a combination chemotherapy determined by the molecular profiling, which would otherwise not have been considered. The mentioned approach was conducted since no other targeted therapies seemed actionable for him.