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  • 1
    Online Resource
    Online Resource
    Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations
    Maad Rayan Publishing Company ; 2023
    In:  Archives of Iranian Medicine Vol. 26, No. 2 ( 2023-02-01), p. 69-75
    Details
    In: Archives of Iranian Medicine, Maad Rayan Publishing Company, Vol. 26, No. 2 ( 2023-02-01), p. 69-75
    Abstract: Background: Global real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings. Methods: We used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021. Results: In total, 125 out of 137 samples showed 91.24% concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78% concordance, 65 of which were assigned as VOCs and showed 100% concordance. Of 1028 samples screened by our in-house method, 78 distinct mutations were detected. The most common mutations were: S:D614G (21.91%), S:P681R (12.19%), S:L452R (12.15%), S:T478K (12.15%), S:N501Y (8.91%), S:A570D (8.89%), S:P681H (8.89%), S:T716I (8.74%), S:L699I (3.50%) and S:S477N (0.28%). Of 1028 samples, 980 were attributed as VOCs, which include the Delta (B.1.617.2) and Alpha (B.1.1.7) variants. Conclusion: Our proposed in-house Sanger-based assay for SARS-CoV-2 lineage assignment is an accessible strategy in countries with poor infrastructure facilities. It can be applied in the rapid tracking of SARS-CoV-2 VOCs in the SARS-CoV-2 pandemic.
    Type of Medium: Online Resource
    ISSN: 1029-2977 , 1735-3947
    URL: Article
    DOI: 10.34172/aim.2023.12
    Language: English
    Publisher: Maad Rayan Publishing Company
    Publication Date: 2023
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  • 2
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    Novel Mutation in LARP7 in Two Iranian Consanguineous Families with Syndromic Intellectual Disability and Facial Dysmorphism
    Maad Rayan Publishing Company ; 2020
    In:  Archives of Iranian Medicine Vol. 23, No. 12 ( 2020-12-01), p. 842-847
    Details
    In: Archives of Iranian Medicine, Maad Rayan Publishing Company, Vol. 23, No. 12 ( 2020-12-01), p. 842-847
    Abstract: Background: Recently, we have reported mutations in LARP7 gene, leading to neurodevelopmental disorders (NDDs), the most frequent cause of disability in children with a broad phenotype spectrum and diverse genetic landscape. Methods: Here, we present two Iranian patients from consanguineous families with syndromic intellectual disability, facial dysmorphism, and short stature. Results: Whole-exome sequencing (WES) revealed a novel homozygous stop-gain (c.C925T, p.R309X) variant and a previously known homozygous acceptor splice-site (c.1669-1_1671del) variant in LARP7 gene, indicating the diagnosis of Alazami syndrome. Conclusion: These identified variants in patients with Alazami syndrome were consistent with previously reported loss of function variants in LARP7 and provide further evidence that loss of function of LARP7 is the disease mechanism.
    Type of Medium: Online Resource
    ISSN: 1029-2977 , 1735-3947
    URL: Article
    DOI: 10.34172/aim.2020.112
    Language: English
    Publisher: Maad Rayan Publishing Company
    Publication Date: 2020
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  • 3
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    Online Resource
    Emerging Epidemiological Data on Rare Intellectual Disability Syndromes from Analyzing the Data of a Large Iranian Cohort
    Maad Rayan Publishing Company ; 2023
    In:  Archives of Iranian Medicine Vol. 26, No. 4 ( 2023-04-01), p. 186-197
    Details
    In: Archives of Iranian Medicine, Maad Rayan Publishing Company, Vol. 26, No. 4 ( 2023-04-01), p. 186-197
    Abstract: Background: Intellectual disability (ID) is a genetically heterogeneous condition, and so far, 1679 human genes have been identified for this phenotype. Countries with a high rate of parental consanguinity, such as Iran, provide an excellent opportunity to identify the remaining novel ID genes, especially those with an autosomal recessive (AR) mode of inheritance. This study aimed to investigate the most prevalent ID genes identified via next-generation sequencing (NGS) in a large ID cohort at the Genetics Research Center (GRC) of the University of Social Welfare and Rehabilitation Sciences. Methods: First, we surveyed the epidemiological data of 619 of 1295 families in our ID cohort, who referred to the Genetics Research Center from all over the country between 2004 and 2021 for genetic investigation via the NGS pipeline. We then compared our data with those of several prominent studies conducted in consanguineous countries. Data analysis, including cohort data extraction, categorization, and comparison, was performed using the R program version 4.1.2. Results: We categorized the most common ID genes that were mutated in more than two families into 17 categories. The most common syndromic ID in our cohort was AP4 deficiency syndrome, and the most common non-syndromic autosomal recessive intellectual disability (ARID) gene was ASPM. We identified two unrelated families for the 36 ID genes. We found 14 genes in common between our cohort and the Arab and Pakistani groups, of which three genes (AP4M1, AP4S1, and ADGRG1) were repeated more than once. Conclusion: To date, there has been no comprehensive targeted NGS platform for the detection of ID genes in our country. Due to the large sample size of our study, our data may provide the initial step toward designing an indigenously targeted NGS platform for the diagnosis of ID, especially common ARID in our population.
    Type of Medium: Online Resource
    ISSN: 1029-2977 , 1735-3947
    URL: Article
    DOI: 10.34172/aim.2023.29
    Language: English
    Publisher: Maad Rayan Publishing Company
    Publication Date: 2023
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  • 4
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    Online Resource
    Disease Waves of SARS-CoV-2 in Iran Closely Mirror Global Pandemic Trends
    Maad Rayan Publishing Company ; 2022
    In:  Archives of Iranian Medicine Vol. 25, No. 8 ( 2022-08-01), p. 508-522
    Details
    In: Archives of Iranian Medicine, Maad Rayan Publishing Company, Vol. 25, No. 8 ( 2022-08-01), p. 508-522
    Abstract: Background: Complete SARS-CoV-2 genome sequencing in the early phase of the outbreak in Iran showed two independent viral entries. Subsequently, as part of a genome surveillance project, we aimed to characterize the genetic diversity of SARS-CoV-2 in Iran over one year after emerging. Methods: We provided 319 SARS-CoV-2 whole-genome sequences used to monitor circulating lineages in March 2020-May 2021 time interval. Results: The temporal dynamics of major SARS-CoV-2 clades/lineages circulating in Iran is comparable to the global perspective and represent the 19A clade (B.4) dominating the first disease wave, followed by 20A (B.1.36), 20B (B.1.1.413), 20I (B.1.1.7), leading the second, third and fourth waves, respectively. We observed a mixture of circulating B.1.36, B.1.1.413, B.1.1.7 lineages in winter 2021, paralleled in a fading manner for B.1.36/B.1.1.413 and a growing rise for B.1.1.7, prompting the fourth outbreak. Entry of the Delta variant, leading to the fifth disease wave in summer 2021, was detected in April 2021. This study highlights three lineages as hallmarks of the SARS-CoV-2 outbreak in Iran; B4, dominating early periods of the epidemic, B.1.1.413 (B.1.1 with the combination of [D138Y-S477N-D614G] spike mutations) as a characterizing lineage in Iran, and the co-occurrence of [I100T-L699I] spike mutations in half of B.1.1.7 sequences mediating the fourth peak. It also designates the renowned combination of G and GR clades’ mutations as the top recurrent mutations. Conclusion: In brief, we provided a real-time and comprehensive picture of the SARS-CoV-2 genetic diversity in Iran and shed light on the SARS-CoV-2 transmission and circulation on the regional scale.
    Type of Medium: Online Resource
    ISSN: 1029-2977 , 1735-3947
    URL: Article
    DOI: 10.34172/aim.2022.83
    Language: English
    Publisher: Maad Rayan Publishing Company
    Publication Date: 2022
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  • 5
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    An Extended Iranian Family with Autosomal Dominant Non-syndromic Hearing Loss Associated with A Nonsense Mutation in the DIAPH1 Gene
    Maad Rayan Publishing Company ; 2023
    In:  Archives of Iranian Medicine Vol. 26, No. 3 ( 2023-03-01), p. 176-180
    Details
    In: Archives of Iranian Medicine, Maad Rayan Publishing Company, Vol. 26, No. 3 ( 2023-03-01), p. 176-180
    Abstract: Genetic analysis of non-syndromic hearing loss (NSHL) has been challenged due to marked clinical and genetic heterogeneity. Today, advanced next-generation sequencing (NGS) technologies, such as exome sequencing (ES), have drastically increased the efficacy of gene identification in heterogeneous Mendelian disorders. Here, we present the utility of ES and re-evaluate the phenotypic data for identifying candidate causal variants for previously unexplained progressive moderate to severe NSHL in an extended Iranian family. Using this method, we identified a known heterozygous nonsense variant in exon 26 of the DIAPH1 gene (MIM: 602121), which led to "Deafness, autosomal dominant 1, with or without thrombocytopenia; DFNA1" (MIM: 124900) in this large family in the absence of GJB2 disease-causing variants and also OtoSCOPE-negative results. To the best of our knowledge, this nonsense variant (NM_001079812.3):c.3610C 〉 T (p.Arg1204Ter) is the first report of the DIAPH1 gene variant for autosomal dominant non-syndromic hearing loss (ADNSHL) in Iran.
    Type of Medium: Online Resource
    ISSN: 1029-2977 , 1735-3947
    URL: Article
    DOI: 10.34172/aim.2023.27
    Language: English
    Publisher: Maad Rayan Publishing Company
    Publication Date: 2023
    detail.hit.zdb_id: 2059531-1
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