Global Medical Genetics最新文献

{"title":"Maternal Transmission of the <i>PAX7</i> Single Nucleotide Polymorphisms among Indian Cleft Trios.","authors":"Mahamad Irfanulla Khan,&nbsp;Prashanth C S,&nbsp;Mohammed S Mustak,&nbsp;Sheikh Nizamuddin","doi":"10.1055/s-0042-1760383","DOIUrl":"https://doi.org/10.1055/s-0042-1760383","url":null,"abstract":"<p><p>Cleft lip and/or cleft palate (CL/P) is one of the most common congenital anomalies of the human face with a complex etiology involving multiple genetic and environmental factors. Several studies have shown the association of the paired box 7 ( <i>PAX7</i> ) gene with CL/P in different populations worldwide. However, the current literature reveals no reported case-parent trio studies to evaluate the association between the <i>PAX7</i> gene and the risk of nonsyndromic cleft lip and/or palate (NSCL/P) in the Indian population. Hence, the purpose of this study was to assess the <i>PAX7</i> gene single nucleotide polymorphisms (SNPs) in the etiology of NSCL/P among the Indian cleft trios. Forty Indian case-parent trios of NSCL/P were included. The cases and their parents' genomic DNA were extracted. The SNPs rs9439714, rs1339062, rs6695765, rs742071, and rs618941of the <i>PAX7</i> gene were genotyped using the Agena Bio MassARRAY analysis. The allelic transmission disequilibrium test was performed using PLINK software while pair-wise linkage disequilibrium by the Haploview program. The SNP rs9439714 showed evidence of association ( <i>p</i> -value = 0.02, odds ratio = 3) with NSCL/P. Considering the parent-of-origin effects, the SNPs rs9439714 and rs618941 showed an excess maternal transmission of allele C at rs9439714 ( <i>p</i> -value = 0.05) and G allele at rs618941 ( <i>p</i> -value = 0.04). The results of the present study suggested that the SNPs rs9439714 and rs618941 showed an excess maternal transmission of alleles suggestive of the possible role of the <i>PAX7</i> gene involvement in the etiology of NSCL/P in the Indian population.</p>","PeriodicalId":40142,"journal":{"name":"Global Medical Genetics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9873478/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10680947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>PMS2</i> Pathogenic Variant in Lynch Syndrome-Associated Colorectal Cancer with Polyps.","authors":"Henriette Poaty,&nbsp;Lauria Batamba Bouya,&nbsp;Aimé Lumaka,&nbsp;Arnaud Mongo-Onkouo,&nbsp;Deby Gassaye","doi":"10.1055/s-0042-1759888","DOIUrl":"https://doi.org/10.1055/s-0042-1759888","url":null,"abstract":"<p><p><b>Background</b>  Lynch syndrome (LS) is an autosomal dominant condition due to the germline mutation in the mismatch repair (MMR) genes including <i>MLH1</i> , <i>MSH2</i> , <i>MSH6,</i> and <i>PMS2</i> (post-meiotic segregation increased 2). The MMR mutation carriers have high risk for cancers. Pathogenic <i>PMS2</i> variants are rarely reported in LS-associated colorectal cancer (CRC) with colorectal polyps. The aim of the study was to investigate the genetic etiology of CRC in an individual with CRC with multiple colorectal polyps and a family history of cancers. <b>Patients and Methods</b>  The index patient was an African male affected by CRC with multiple colorectal polyps. The clinical diagnostic for LS was based on the Amsterdam II criteria and pedigree. Next-generation sequencing with inherited cancer genes panel was used to detect the pathogenic variant. <b>Results</b>  The patient fulfilled the Amsterdam II criteria and the pedigree revealed a family history of recurrent CRC. A deleterious <i>PMS2</i> germline heterozygous mutation c.2192_2196delTAACT was detected. <b>Conclusion</b>  Our study supports the notion that LS may be associated with polyps and shows the predisposition of <i>PMS2</i> heterozygous mutation in LS-associated CRC at young age.</p>","PeriodicalId":40142,"journal":{"name":"Global Medical Genetics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9833889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10536395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mystery Behind Barrett's Esophagus: The Origin and Malignant Transformation of Esophageal Adenocarcinoma.","authors":"Xiayao Diao","doi":"10.1055/s-0042-1758764","DOIUrl":"10.1055/s-0042-1758764","url":null,"abstract":"Esophageal cancer (EC) is the eighth most common cancer in the world, with an estimated 604,100 new cases in 2020, accounting for 3.1% of all cancer cases.1 Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are the two main histologic subtypes of EC. ESCC predominantly affects developing countries and accounts for more than 88.8% in Chinese EC patients,2,3 while EAC predominantly affects developed countries and accounts for 80.1% in EC patients from United States.4,5 Multiple risk factors, such as Barrett’s esophagus, are associated with EC development. Barrett’s esophagus is a typical metaplastic disease that begins at the gastroesophageal junctions with proximal displacement of the squamocolumnar junctions. Intestinal metaplasia increases the propensity for ECs, especially EACs, and may result from transcriptional switches within gastric cell types or products of intestinal cell types, but the exact origin is unclear. However, half of EAC patients were not observed to have Barrett’s esophagus at the time of diagnosis.6,7 Therefore, we cannot help but ask the following question: does Barrett’s esophagus increase the risk of EAC? This question can be answered by determining the origin of Barrett’s esophagus. Most scientists believe that Barrett’s esophagus originates from many sources, such as various specific cell populations in the gastroesophageal junctions and esophageal submucosal glands. Lineage tracing studies in mouse models is the primary method for exploring Barrett’s esophagus origin. However, the squamous pregastric keratinization and lack of esophageal submucosal glands make this animal model unable to fully mimic human gastroesophageal physiology. Additionally, isolation of esophageal submucosal glands from fresh human tissue is particularly difficult. All of these have become the major obstacles to lineage tracing studies. In a study recently published in Science, titled “Molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition,” Nowicki-Osuch et al8 successfully harvested the tissue samples across the gastroesophageal junction and isolated esophageal submucosal glands from patients and healthy individuals to explore the exact source of Barrett’s esophagus. These tissue samples were analyzed by single-cell transcriptomic profiling, in silico lineage tracing of methylation, and somatic mutation/open chromatin array. The functional validation was performed in organoid models. In brief, the authors immuno-stained pan-epithelial tissues, squamous tissues, columnar tissues, and esophageal submucosal glands of fresh human esophagus tissue with cadherin 1 (CDH1), keratin 5 (KRT5), keratin 8 (KRT8), and keratin 7 (KRT7) antibodies, respectively, and then used the three-dimensional confocal microscopy to identify and isolate the ductal cells, oncocytes, mucous cells, and myoepithelial cells. Theyobserved a population of P63þKRT5þKRT7þ cells (transitional basal progenitor) in ","PeriodicalId":40142,"journal":{"name":"Global Medical Genetics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2022-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9771686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10435826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Most Comprehensive Study at Single-Cell Resolution: A Giant Step toward Understanding Gastric Cancer.","authors":"Fei-Yu Diao","doi":"10.1055/s-0042-1758763","DOIUrl":"https://doi.org/10.1055/s-0042-1758763","url":null,"abstract":"In 2020, gastric cancer is thefifthcommoncancerand thefifth leading cause of cancer death in the world.1 It has the highest incidence andmortality rate in Asian countries, such as China, Japan, and South Korea.2,3 Heterogeneity at the histologic, transcriptomic, genomic, and epigenomic levels exists between gastric cancer patients (interpatient heterogeneity) and within individual tumor mass (intertumoral heterogeneity). It leads to different cancer biological behaviors and treatment response.4 Therefore, biomarkers developed based on theheterogeneityofgastric cancer playan important role in guiding clinical treatment and improving patient prognosis.5,6 Although some current cancer genome projects, The Cancer Genome Atlas (TCGA) and Asian Cancer Research Group, have made great progress in facilitating the molecular typing of gastric cancer, their role in improving the prognosis of gastric cancer patients is limited. Therefore, to conduct high-resolution studies at molecular level in a wide range of patients to guide the clinical treatment of gastric cancer is necessary. Previous “bulk-transcriptome” studies have found that each gastric cancer case has a unique expression profile contributed by cancer cells and resident cell types of tumor microenvironment (such as cancer-associatedfibroblasts, immune cells, and endothelial cells, etc.),7 but the underlying molecular mechanisms of how tumor microenvironment resident cells drive tumor phenotype evolution and clinical progression remain unknown. With the advances in bioinformatics, bulk sequencing data has been successfully decomposed into lineage-specific constituent programs, but this approach fails to discern rare cell populations,fine-scale tissue lineages, cell–cell interactions, and relationships between lineages.8 Single-cell RNA sequencing (scRNA-seq) is the primary tool for addressing these issues. It can detect gene expression in thousands of cells simultaneously, enabling comprehensive analysis of different cell types in tumor mass under different conditions. Indeed, scRNA-seq on gastric cancer tissues from various sources has provided unique insights of cancer biology. However, these current scRNAseq studies are limited by the number of samples and cells, aswell as the dissociation requirements for tissues, which had led to the loss of many key information, especially spatial information. Thus, digital spatial analysis, in situ sequencing, and multiplexed error-robust fluorescence in situ hybridization platforms have been developed to maximize the preservation of spatial information, and thereby allowing the indepth analysis of tumor–tumor microenvironment interactions. In a study recently published in Cancer Discovery, titled “Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer,” Kumar et al9 delineated a comprehensive single-cell atlas of gastric cancer specimens across clinical stages and histologic subtypes by scRNA-","PeriodicalId":40142,"journal":{"name":"Global Medical Genetics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9748445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10748701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exosomal microRNAs Targeting <i>TP53</i> Gene as Promising Prognostic Markers for Head and Neck Squamous Cell Carcinoma.","authors":"Vijayashree Priyadharsini Jayaseelan,&nbsp;Paramasivam Arumugam","doi":"10.1055/s-0042-1758204","DOIUrl":"https://doi.org/10.1055/s-0042-1758204","url":null,"abstract":"<p><p><b>Statement of Problem</b>  MicroRNAs are small non-coding RNAs that regulate an array of functions by targeting crucial genes. A significant dysregulation in the <i>TP53</i> profile has been observed in the head and neck squamous cell carcinoma (HNSCC) patients. Hence, the present <i>in silico</i> study was designed to identify those microRNAs which target <i>TP53</i> gene and demonstrate their differential expression in HNSCC cases. <b>Materials and Methods</b>  The study was extended further to explore their exosomal location using database such as EVmiRNA and ExoCarta. The study follows an observational <i>in silico</i> design. Computational tool miRDB was used identify the microRNA targets of <i>TP53</i> gene. The UALCAN server was used to ascertain the expression of microRNA in HNSCC cases derived from the Cancer Gene Atlas dataset. The survival of HNSCC patients based on the differential expression microRNA markers were recorded. Further, each of the microRNA was queried for their exosomal presence using EVmiRNA. <b>Results</b>  About 102 microRNA targets of <i>TP53</i> gene with a target score in the range of 95-50 were identified. The differential expression data for 52 microRNAs was retrieved from the UALCAN database. The microRNAs hsa-miR-421, hsa-miR-548f-5p, and hsa-let-7c-5p were found to be differentially expressed with marked influence over the survival of HNSCC patients. Furthermore, hsa-miR-421 and hsa-let-7c-5p were found to have an exosomal origin especially in body fluids such as blood and saliva. <b>Conclusion</b>  The results accumulated from the present study identified three microRNAs which can affect the functions of <i>TP53</i> gene and bring about serious outcomes in HNSCC patients. The microRNAs of exosomal origin targeting <i>TP53</i> gene in HNSCC patients can be a promising prognostic marker, which can be further used as a therapeutic lead by designing inhibitors.</p>","PeriodicalId":40142,"journal":{"name":"Global Medical Genetics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9750795/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10748705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in Organoid Culture Research.","authors":"Zhiyuan Xie,&nbsp;Linghao Wang,&nbsp;Yan Zhang","doi":"10.1055/s-0042-1756662","DOIUrl":"https://doi.org/10.1055/s-0042-1756662","url":null,"abstract":"<p><p>Organoids are powerful systems to facilitate the study of individuals' disorders and personalized treatments because they mimic the structural and functional characteristics of organs. However, the full potential of organoids in research has remained unrealized and the clinical applications have been limited. One of the reasons is organoids are most efficient grown in reconstituted extracellular matrix hydrogels from mouse-derived, whose poorly defined, batch-to-batch variability and immunogenicity. Another reason is that organoids lack host conditions. As a component of the tumor microenvironment, microbiota and metabolites can regulate the development and treatment in several human malignancies. Here, we introduce several engineering matrix materials and review recent advances in the coculture of organoids with microbiota and their metabolites. Finally, we discuss current trends and future possibilities to build more complex cocultures.</p>","PeriodicalId":40142,"journal":{"name":"Global Medical Genetics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9750796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10748706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differentiation and Immunological Function of MDSC-Derived Dendritic Cells.","authors":"Zequn Ding,&nbsp;Yan Zhang","doi":"10.1055/s-0042-1756659","DOIUrl":"https://doi.org/10.1055/s-0042-1756659","url":null,"abstract":"<p><p>Dendritic cells (DCs) play a key role in initiating and regulating immune responses, and in addition to their roles in vivo, DCs are used as natural adjuvants for various tumor vaccines. In vitro, monocytes can be used to induce DCs, but in tumor patients, due to insufficient bone marrow hematopoiesis, extramedullary hematopoiesis and tumor-associated myeloid cells expand, and monocytes mainly exist in the form of myeloid-derived suppressor cells (MDSCs). The purpose of this experiment was to explore the differences in the differentiation and immune function of DCs induced by MDSCs in tumor patients. In a mouse model, we used normal mouse bone marrow cell-derived DCs as control cells, and in a tumor-bearing model, we induced MDSCs in the spleen to generate DCs (MDSC-DCs). Through flow cytometry, we found that the production of MDSC-DCs was significantly higher than that of control mice, and the secretion of interferon-γ of MDSC-DCs was significantly reduced. Through OVA antigen presentation experiments, we found that the antigen presentation ability of MDSC-DCs was significantly decreased. Through adoptive treatment of tumor-bearing mice cells, we found that the antitumor immune function of MDSC-DCs was significantly reduced. After that, we explored the mechanism of the decrease of immune function activity of MDSC-DCs. We determined that the surface markers of MDSC-DCs were changed by flow cytometry. Through flow sorting and RNA sequencing, we found that some pathways and key gene expression in MDSC-DCs were changed. In conclusion, this study found that the immune function of MDSC-DCs decreased and explored the mechanism of the decreased immune function activity.</p>","PeriodicalId":40142,"journal":{"name":"Global Medical Genetics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9771685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10428187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of FOCAD: An Important Gene in Liver Cirrhosis.","authors":"Jinjin Shao","doi":"10.1055/s-0042-1758351","DOIUrl":"https://doi.org/10.1055/s-0042-1758351","url":null,"abstract":"Liver cirrhosis is the 11th most common cause of death, causing more than 1 million deaths globally each year, and together with liver cancer, it accounts for 3.5% of all deaths worldwide.1 Cirrhosis develops due to long-term chronic liver inflammation, with the replacement of healthy liver parenchyma with diffuse liver fibrosis and regenerative nodules, leading to portal hypertension and various complications and even hepatocellular carcinoma.2–4 The management of cirrhosis is mainly based on the treatment of cause and complications including comprehensive supportive care. However, there are currently no effective drug therapies to cure the disease, and liver transplantation remains the gold standard treatment for cirrhosis.5,6 Given that cirrhosis has brought heavy health and economic burden to many countries, there is an urgent need for in-depth study of the pathogenesis and key factors of cirrhosis to find feasible intervention strategies. Cirrhosis is traditionally considered a late-onset disease that appears in adults following environmental factors, such as viral infection, a high-fat diet, or chronic alcoholism.7,8 Thus, cirrhosis caused by genetic factors appears to have received less attention than environmental factors, and the etiology in infants and young children is far less understood. In a recent study published in Nature Genetics, titled “Loss of FOCAD, manipulated through the SKI messenger RNA surveillance pathway, leads to a pediatric syndrome with cirrhosis,” Traspas and colleagues uncovered the essentiality of the FOCAD gene in maintaining liver health and provided evidence that loss-of-function mutations in FOCAD may contribute to cirrhosis in children.9 The authors reported 14 children from 10 unrelated families in seven countries presenting with a multisystem syndrome characterized by severe neonatal cirrhosis. By combing genome/exome sequencing, a novel animal model of the human disease, and in vitro biological systems, the team identify that the FOCAD gene is indispensable for maintaining human liver health. Mutations in this gene cause a form of early-onset cirrhosis that has not been documented before. Using CRISPR-Cas9 technology, they established in vitro and in vivo FOCAD knockout models to further study the cellular and molecular mechanisms of pediatric cirrhosis. Phenotypic replication of human disease in FOCAD-deficient zebrafish reveals features of altered messenger RNA degradation processes in the liver. FOCAD deficiency in patient primary cells and human liver cell lines impairs the SKI mRNA surveillance pathway by reducing levels of the RNA helicase SKIC2 and its cofactor SKIC3. Compared with other cell types, hepatocytes rely heavily on this mechanism. Hepatocytes exhibited a decrease in albumin expression and overproduction of the cytokine CCL2 following FOCAD knockout, which may play a key role in the progression of cirrhosis. These findings reveal the importance of FOCAD in maintaining liver homeostasis a","PeriodicalId":40142,"journal":{"name":"Global Medical Genetics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9748444/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10765414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epigenetic Alteration in Colorectal Cancer: A Biomarker for Diagnostic and Therapeutic Application.","authors":"Hafsa Yousif Solayman Essa, Gunay Kusaf, Ozel Yuruker, Rasime Kalkan","doi":"10.1055/s-0042-1757404","DOIUrl":"10.1055/s-0042-1757404","url":null,"abstract":"<p><p>Colorectal cancer (CRC) is the leading cause of cancer death worldwide. A crucial process that initiates and progresses CRC is various epigenetic and genetic changes occurring in colon epithelial cells. Recently, huge progress has been made to understand cancer epigenetics, especially regarding DNA methylation changes, histone modifications, dysregulation of miRNAs and noncoding RNAs. In the \"epigenome\" of colon cancer, abnormal methylation of genes that cause gene alterations or expression of miRNA has been reported in nearly all CRC; these findings can be encountered in the average CRC methylome. Epigenetic changes, known as driving events, are assumed to play a dominant part in CRC. Furthermore, as epigenetic changes in CRC become properly understood, these changes are being established as clinical biomarkers for therapeutic and diagnostic purposes. Progression in this area indicates that epigenetic changes will often be utilized in the future to prevent and treat CRC.</p>","PeriodicalId":40142,"journal":{"name":"Global Medical Genetics","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2022-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9522482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40390400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Designing In-House SARS-CoV-2 RT-qPCR Assay for Variant of Concerns.","authors":"Mahmut Cerkez Ergoren,&nbsp;Gulten Tuncel,&nbsp;Cenk Serhan Ozverel,&nbsp;Tamer Sanlidag","doi":"10.1055/s-0042-1756660","DOIUrl":"https://doi.org/10.1055/s-0042-1756660","url":null,"abstract":"<p><p>Variants (Alfa, Gamma, Beta, and Delta) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are circulating worldwide. These variants of concerns share some common mutations but they also have distinguishing mutations. These mutations affect transmissibility of virus and cause evasion from neutralizing antibodies. Monitoring and identification of circulating variants is of great importance for public health. In this study, an in-house SARS-CoV-2 reverse transcription quantitative polymerase chain reaction (RT-qPCR) kit was designed to detect variants of concerns by the World Health Organization. Primer sets and probes were designed to target presence of virus along with mutations for identifying different variants (for N501Y, HV69-70del, K417N, and T478K). Reactions were set by using commercially available master mixes without a reference dye. The RT-qPCR conditions were optimized by using commercially available ribonucleic acid samples of wild-type, Alfa, Beta, Gamma, and Delta variants. Several samples were also analyzed by the in-house kit after optimization studies. All Alfa variant and wild-type samples were also double confirmed with a commercially available variant detection kit demonstrating a 100% consistence with the in-house kit. Beta, Gamma, and Delta variants could not be confirmed with any other commercially available kits as there is not any available one in the market. SARS-CoV-2 variants are gaining importance during the pandemic and shaping the fight against the virus. RT-qPCR kits detecting different variants would provide a significant advantage while screening the population.</p>","PeriodicalId":40142,"journal":{"name":"Global Medical Genetics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2022-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9489470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33477133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}