Current Genomics最新文献

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Pan-Genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges 泛基因组学:洞察功能基因组、应用、进步与挑战
IF 2.6 4区 生物学
Current Genomics Pub Date : 2024-07-04 DOI: 10.2174/0113892029311541240627111506
Akansha Sarwad, Spoorti Hosgoudar, Prachi Parvatikar
{"title":"Pan-Genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges","authors":"Akansha Sarwad, Spoorti Hosgoudar, Prachi Parvatikar","doi":"10.2174/0113892029311541240627111506","DOIUrl":"https://doi.org/10.2174/0113892029311541240627111506","url":null,"abstract":": A pan-genome is a compilation of the common and unique genomes found in a given species. It incorporates the genetic information from all of the genomes sampled, producing a big and diverse set of genetic material. Pan-genomic analysis has various advantages over typical genomics research. It creates a vast and varied spectrum of genetic material by combining the genetic data from all the sampled genomes. Comparing pan-genomics analysis to conventional genomic research, there are a number of benefits. Although the most recent era of pan-genomic studies has used cutting-edge sequencing technology to shed fresh light on biological variety and improvement, the potential uses of pan-genomics in improvement have not yet been fully realized. Pangenome research in various organisms has demonstrated that missing genetic components and the detection of significant Structural Variants (SVs) can be investigated using pan-genomic methods. Many individual-specific sequences have been linked to biological adaptability, phenotypic, and key economic attributes. This study aims to focus on how pangenome analysis uncovers genetic differences in various organisms, including human, and their effects on phenotypes, as well as how this might help us comprehend the diversity of species. The review also concentrated on potential problems and the prospects for future pangenome research.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gene-Knockdown Methods for Silencing Nuclear-Localized Insulin Receptors in Lung Adenocarcinoma Cells: A Bioinformatics Approach 沉默肺腺癌细胞核定位胰岛素受体的基因敲除方法:生物信息学方法
IF 2.6 4区 生物学
Current Genomics Pub Date : 2024-07-04 DOI: 10.2174/0113892029298721240627095839
Qiu Ren, Hui Ma, Lingling Wang, Jiayu Qin, Miao Tian, Wei Zhang
{"title":"Gene-Knockdown Methods for Silencing Nuclear-Localized Insulin Receptors in Lung Adenocarcinoma Cells: A Bioinformatics Approach","authors":"Qiu Ren, Hui Ma, Lingling Wang, Jiayu Qin, Miao Tian, Wei Zhang","doi":"10.2174/0113892029298721240627095839","DOIUrl":"https://doi.org/10.2174/0113892029298721240627095839","url":null,"abstract":"Background: Lung adenocarcinoma, the predominant subtype of lung cancer, presents a significant challenge to public health due to its notably low five-year survival rate. Recent epidemiological data highlights a concerning trend: patients with pulmonary adenocarcinoma and comorbid diabetes exhibit substantially elevated mortality rates compared to those without diabetes, suggesting a potential link between hyperinsulinemia in diabetic individuals and accelerated progression of pulmonary adenocarcinoma. Insulin Receptor (IR) is a tyrosine-protein kinase on the cell surface, and its over-expression is considered the pathological hallmark of hyperinsulinemia in various cancer cell types. Research indicates that IR can translocate to the nucleus of lung adenocarcinoma cells to promote their proliferation, but its precise molecular targets remain unclear. This study aims to silence IRs in lung adenocarcinoma cells and identify key genes within the ERK pathway that may serve as potential molecular targets for intervention. Methods: Gene expression data from lung adenocarcinoma and para cancer tissues were retrieved from the Gene Expression Omnibus (GEO) database and assessed through \"pheatmap\", GO annotation, KEGG analysis, R calculations, Cytoscape mapping, and Hub gene screening. Significant genes were visualized using the ggplot2 tool to compare expression patterns between the two groups. Additionally, survival analysis was performed using the R \"survminer\" and \"survival\" packages, along with the R \"pathview\" package for pathway visualization. Marker genes were identified and linked to relevant signaling pathways. Validation was conducted utilizing real-time quantitative polymerase chain reaction and immunoblotting assays in an A549 lung cancer cell model to determine the roles of these marker genes in associated signaling cascades. Results: The study examined 58 lung adenocarcinoma samples and paired para-neoplastic tissues. Analysis of the GSE32863 dataset from GEO revealed 1040 differentially expressed genes, with 421 up-regulated and 619 down-regulated. Visualization of these differences identified 172 significant alterations, comprising 141 up-regulated and 31 down-regulated genes. Functional enrichment analysis using Gene Ontology (GO) revealed 56 molecular functions, 77 cellular components, and 816 biological processes. KEGG analysis identified 17 strongly enriched functions, including cytokine interactions and tumor necrosis factor signaling. Moreover, the ERK signaling pathway was associated with four Hub genes (FGFR4, ANGPT1, TEK, and IL1B) in cellular biological processes. Further validation demonstrated a positive correlation between IL-1B expression in the ERK signaling pathway and lung cancer through real-time fluorescence quantitative enzyme- linked reaction with immunoblotting assays. Conclusion: In IR-silenced lung adenocarcinoma, the expression of the IL-1B gene exhibited a positive correlation with the ERK signaling pathway.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
FAT4 Mutation is Related to Tumor Mutation Burden and Favorable Prognosis in Gastric Cancer FAT4 基因突变与胃癌的肿瘤突变负担和良好预后有关
IF 2.6 4区 生物学
Current Genomics Pub Date : 2024-06-20 DOI: 10.2174/0113892029300694240612081006
Qingqing Li, Yuxin Chu, Yi Yao, Qibin Song
{"title":"FAT4 Mutation is Related to Tumor Mutation Burden and Favorable Prognosis in Gastric Cancer","authors":"Qingqing Li, Yuxin Chu, Yi Yao, Qibin Song","doi":"10.2174/0113892029300694240612081006","DOIUrl":"https://doi.org/10.2174/0113892029300694240612081006","url":null,"abstract":"Objective: This study aimed to investigate the frequently mutated genes in Gastric Cancer (GC), assess their association with Tumor Mutation Burden (TMB) and the patients’ survival, and identify the potential biomarkers for tailored therapy. Methods: Simple somatic mutation data of GC were collected from the TCGA and ICGC databases. The high-frequency mutated genes were identified from both datasets. The samples were initially dichotomized into wild-type and mutation groups based on the status of overlapping genes. TMB difference between the two groups was evaluated by the Mann-Whitney U-test. Survival difference between the two groups was compared by the Kaplan-Meier method with a log-rank test. The prognostic value of the target gene was assessed by the Cox proportional hazards model. The signaling pathways involved in FAT4 mutation were identified by Gene Set Enrichment Analysis (GSEA). The fractions of different tumor-infiltrating immune cells were calculated by the CIBERSORT algorithm. Results: 21 overlapping genes with frequent mutation were identified in both datasets. Mutation of these genes was significantly associated with higher TMB (P<0.05) in GC. The survival of the FAT4 mutation group was superior to the wild-type group. FAT4 mutation was also identified as an independent favorable prognostic factor for the GC patients. GSEA indicated that FAT4 mutation activated the signaling pathways involved in energy metabolism. Finally, CD4 memory-activated T cells, follicular helper T cells, and gamma delta T cells were significantly more enriched, while naïve B cells and regulatory T cells (Tregs) were significantly less enriched in the FAT4 mutation group (P<0.05). Conclusion: FAT4 mutation is relevant to TMB and favorable prognosis in GC, which may become a useful biomarker for immunotherapy of GC patients.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141509539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Emerging Multi-Omic Approaches to the Molecular Diagnosis of Mitochondrial Disease and Available Strategies for Treatment and Prevention 新出现的线粒体疾病分子诊断多指标方法以及现有的治疗和预防策略
IF 2.6 4区 生物学
Current Genomics Pub Date : 2024-06-20 DOI: 10.2174/0113892029308327240612110334
Faeze Khagani, Mahboube Hemmati, Masoumeh Ebrahimi, Arash Salmaninejad
{"title":"Emerging Multi-Omic Approaches to the Molecular Diagnosis of Mitochondrial Disease and Available Strategies for Treatment and Prevention","authors":"Faeze Khagani, Mahboube Hemmati, Masoumeh Ebrahimi, Arash Salmaninejad","doi":"10.2174/0113892029308327240612110334","DOIUrl":"https://doi.org/10.2174/0113892029308327240612110334","url":null,"abstract":": Mitochondria are semi-autonomous organelles present in several copies within most cells in the human body that are controlled by the precise collaboration of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) encoding mitochondrial proteins. They play important roles in numerous metabolic pathways, such as the synthesis of adenosine triphosphate (ATP), the predominant energy substrate of the cell generated through oxidative phosphorylation (OXPHOS), intracellular calcium homeostasis, metabolite biosynthesis, aging, cell cycles, and so forth. Previous studies revealed that dysfunction of these multi-functional organelles, which may arise due to mutations in either the nuclear or mitochondrial genome, leads to a diverse group of clinically and genetically heterogeneous disorders. These diseases include neurodegenerative and metabolic disorders as well as cardiac and skeletal myopathies in both adults and newborns. The plethora of phenotypes and defects displayed leads to challenges in the diagnosis and treatment of mitochondrial diseases. In this regard, the related literature proposed several diagnostic options, such as high throughput mitochondrial genomics and omics technologies, as well as numerous therapeutic options, such as pharmacological approaches, manipulating the mitochondrial genome, increasing the mitochondria content of the affected cells, and recently mitochondrial diseases transmission prevention. Therefore, the present article attempted to review the latest advances and challenges in diagnostic and therapeutic options for mitochondrial diseases.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141530070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Crosstalk Between Cancer-associated Fibroblasts and Myeloid CellsShapes the Heterogeneous Microenvironment of Gastric Cancer 癌症相关成纤维细胞与髓样细胞之间的相互影响塑造了胃癌的异质性微环境
IF 2.6 4区 生物学
Current Genomics Pub Date : 2024-06-11 DOI: 10.2174/0113892029300608240531111743
Zhiwei Peng, Can Fang, Zhiwei Tong, Qiufan Rao, Zihao Ren, K. Hu
{"title":"Crosstalk Between Cancer-associated Fibroblasts and Myeloid Cells\u0000Shapes the Heterogeneous Microenvironment of Gastric Cancer","authors":"Zhiwei Peng, Can Fang, Zhiwei Tong, Qiufan Rao, Zihao Ren, K. Hu","doi":"10.2174/0113892029300608240531111743","DOIUrl":"https://doi.org/10.2174/0113892029300608240531111743","url":null,"abstract":"\u0000\u0000Targeted therapies have improved the clinical outcomes of most patients\u0000with cancer. However, the heterogeneity of gastric cancer remains a major hurdle for precision\u0000treatment. Further investigations into tumor microenvironment heterogeneity are required to resolve\u0000these problems.\u0000\u0000\u0000\u0000In this study, bioinformatic analyses, including metabolism analysis, pathway enrichment,\u0000differentiation trajectory inference, regulatory network construction, and survival analysis,\u0000were applied to gain a comprehensive understanding of tumor microenvironment biology within\u0000gastric cancer using single-cell RNA-seq and public datasets and experiments were carried out to\u0000confirm the conclusions of these analyses.\u0000\u0000\u0000\u0000We profiled heterogeneous single-cell atlases and identified eight cell populations with\u0000differential expression patterns. We identified two cancer-associated fibroblasts (CAFs) subtypes,\u0000with particular emphasis on the role of inflammatory cancer-associated fibroblasts (iCAFs) in\u0000EMT and lipid metabolic crosstalk within the tumor microenvironment. Notably, we detected two\u0000differentiation states of iCAFs that existed in different tissues with discrepant expression of genes\u0000involved in immuno-inflammation or ECM remodeling. Moreover, investigation of tumor-infiltrating\u0000myeloid cells has revealed the functional diversity of myeloid cell lineages in gastric cancer.\u0000Of which a proliferative cell lineage named C1QC+MKI67+TAMs was recognized with high immunosuppressive\u0000capacities, suggesting it has immune suppression and cell proliferation functions\u0000in the tumor niche. Finally, we explored regulatory networks based on ligand-receptor pairs and\u0000found crucial pro-tumor crosstalk between CAFs and myeloid cells in the tumor microenvironment\u0000(TME).\u0000\u0000\u0000\u0000These findings provide insights for future cancer treatments and drug discovery\u0000","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141359640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deciphering the Genetic Complexity of Classical Hodgkin Lymphoma: Insights and Effective Strategies 解密经典霍奇金淋巴瘤的复杂基因:洞察力和有效策略
IF 2.6 4区 生物学
Current Genomics Pub Date : 2024-05-27 DOI: 10.2174/0113892029301904240513045755
Chaeyoung Lee, Yeeun An
{"title":"Deciphering the Genetic Complexity of Classical Hodgkin Lymphoma: Insights and Effective Strategies","authors":"Chaeyoung Lee, Yeeun An","doi":"10.2174/0113892029301904240513045755","DOIUrl":"https://doi.org/10.2174/0113892029301904240513045755","url":null,"abstract":": Understanding the genetics of susceptibility to classical Hodgkin lymphoma (cHL) is considerably limited compared to other cancers due to the rare Hodgkin and Reed-Sternberg (HRS) tumor cells, which coexist with the predominant non-malignant microenvironment. This article offers insights into genetic abnormalities in cHL, as well as nucleotide variants and their associated target genes, elucidated through recent technological advancements. Oncogenomes in HRS cells highlight the survival and proliferation of these cells through hyperactive signaling in specific pathways (e.g., NF-kB) and their interplay with microenvironmental cells (e.g., CD4+ T cells). In contrast, the susceptibility genes identified from genome-wide association studies and expression quantitative trait locus analyses only vaguely implicate their potential roles in susceptibility to more general cancers. To pave the way for the era of precision oncology, more intensive efforts are imperative, employing the following strategies: exploring genetic heterogeneity by gender and cHL subtype, investigating colocalization with various types of expression quantitative trait loci, and leveraging single-cell analysis. These approaches provide valuable perspectives for unraveling the genetic complexities of cHL.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141168800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Beyond the Genome: Deciphering the Role of MALAT1 in Breast Cancer Progression 超越基因组:解密 MALAT1 在乳腺癌进展中的作用
IF 2.6 4区 生物学
Current Genomics Pub Date : 2024-05-22 DOI: 10.2174/0113892029305656240503045154
Md Sadique Hussain, Mohit Agarwal, Nusrat K. Shaikh, Nikita Saraswat, Gurusha Bahl, Mudasir Maqbool, Navneet Khurrana, Ajay Singh Bisht, Muhammad Tufail, Rajesh Kumar
{"title":"Beyond the Genome: Deciphering the Role of MALAT1 in Breast Cancer Progression","authors":"Md Sadique Hussain, Mohit Agarwal, Nusrat K. Shaikh, Nikita Saraswat, Gurusha Bahl, Mudasir Maqbool, Navneet Khurrana, Ajay Singh Bisht, Muhammad Tufail, Rajesh Kumar","doi":"10.2174/0113892029305656240503045154","DOIUrl":"https://doi.org/10.2174/0113892029305656240503045154","url":null,"abstract":"\u0000\u0000The MALAT1, a huge non-coding RNA, recently came to light as a multifaceted regulator\u0000in the intricate landscape of breast cancer (BC) progression. This review explores the multifaceted\u0000functions and molecular interactions of MALAT1, shedding light on its profound implications\u0000for understanding BC pathogenesis and advancing therapeutic strategies. The article commences\u0000by acknowledging the global impact of BC and the pressing need for insights into its\u0000molecular underpinnings. It is stated that the core lncRNA MALAT1 has a range of roles in both\u0000healthy and diseased cell functions. The core of this review unravels MALAT1's multifaceted role\u0000in BC progression, elucidating its participation in critical processes like resistance, invasion, relocation,\u0000and proliferating cells to therapy. It explores the intricate mechanisms through which\u0000MALAT1 modulates gene expression, interacts with other molecules, and influences signalling\u0000pathways. Furthermore, the paper emphasizes MALAT1's clinical significance as a possible prognostic\u0000and diagnostic biomarker. Concluding on a forward-looking note, the review highlights the\u0000broader implications of MALAT1 in BC biology, such as its connections to therapy resistance and\u0000metastasis. It underscores the significance of deeper investigations into these intricate molecular\u0000interactions to pave the way for precision medicine approaches. This review highlights the pivotal\u0000role of MALAT1 in BC progression by deciphering its multifaceted functions beyond the genome,\u0000offering profound insights into its implications for disease understanding and the potential for targeted\u0000therapeutic interventions.\u0000","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141112742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bioinformatics Approaches in the Development of Antifungal Therapeutics and Vaccines 开发抗真菌治疗剂和疫苗的生物信息学方法
IF 2.6 4区 生物学
Current Genomics Pub Date : 2024-05-16 DOI: 10.2174/0113892029281602240422052210
Vaishali Ahlawat, Kiran Sura, Bharat Singh, Mehak Dangi, A. K. Chhillar
{"title":"Bioinformatics Approaches in the Development of Antifungal Therapeutics and Vaccines","authors":"Vaishali Ahlawat, Kiran Sura, Bharat Singh, Mehak Dangi, A. K. Chhillar","doi":"10.2174/0113892029281602240422052210","DOIUrl":"https://doi.org/10.2174/0113892029281602240422052210","url":null,"abstract":"\u0000\u0000Fungal infections are considered a great threat to human life and are associated with\u0000high mortality and morbidity, especially in immunocompromised individuals. Fungal pathogens\u0000employ various defense mechanisms to evade the host immune system, which causes severe infections.\u0000The available repertoire of drugs for the treatment of fungal infections includes azoles, allylamines,\u0000polyenes, echinocandins, and antimetabolites. However, the development of multidrug\u0000and pandrug resistance to available antimycotic drugs increases the need to develop better treatment\u0000approaches. In this new era of -omics, bioinformatics has expanded options for treating fungal\u0000infections. This review emphasizes how bioinformatics complements the emerging strategies,\u0000including advancements in drug delivery systems, combination therapies, drug repurposing, epitope-\u0000based vaccine design, RNA-based therapeutics, and the role of gut-microbiome interactions\u0000to combat anti-fungal resistance. In particular, we focused on computational methods that can be\u0000useful to obtain potent hits, and that too in a short period.\u0000","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140971617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
HPV16 Genomes: In Silico Analysis of E6 and E7 Oncoproteins in 20 South American Variants HPV16 基因组:对 20 个南美变体中 E6 和 E7 肿瘤蛋白的硅学分析
IF 2.6 4区 生物学
Current Genomics Pub Date : 2024-05-10 DOI: 10.2174/0113892029293113240427065916
Márcio Fabrício Falcão de Paula Filho, Lara Luisa Lopes Chrisóstomo, Isaac Farias Cansanção
{"title":"HPV16 Genomes: In Silico Analysis of E6 and E7 Oncoproteins in 20 South American Variants","authors":"Márcio Fabrício Falcão de Paula Filho, Lara Luisa Lopes Chrisóstomo, Isaac Farias Cansanção","doi":"10.2174/0113892029293113240427065916","DOIUrl":"https://doi.org/10.2174/0113892029293113240427065916","url":null,"abstract":"Background: Human papillomavirus (HPV) is the main risk factor for the development of squamous cell cervical cancer, and E6 oncoprotein and E7 oncoprotein are important components of the viral genome and its oncogenic potential. It is known that different viral variants of HPV16 have different pathology and impact on the development of neoplasia, although few studies have been performed on South American variants. Objective: Therefore, the present study aimed to analyze in silico the genomic diversity of HPV16 in 20 complete genome variants of South America in the National Center for Biotechnology Information (NCBI) database. Methods: We performed a descriptive study to characterize the polymorphic regions of the E6 and E7 genes in HPV16 variants, using software for genomic data and single nucleotide polymorphism (SNP) analysis and others for phylogenetic analysis. Results: The variants analyzed included six SNPs linked to cancer (A131G, G145T, C335T, T350G, C712A, and T732C) and significant variation (798 nucleotide substitutions). Despite this, the variants showed low genetic diversity. Eighteen variants of unclear significance (VUS) were identified, 10 of which were in the coding E6 regions and 8 in the coding E7 regions. The prevalence of lineage D variants is of concern due to their pathology in cervical cancer and requires more research and epidemiological vigilance regarding their prevalence in the population. Conclusion: study may contribute to future research on South American variants of HPV16, their pathogenicity, and the development of treatments.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140931828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Global and Local Ancestry and its Importance: A Mini-Review 全球和地方祖先及其重要性:小型回顾
IF 2.6 4区 生物学
Current Genomics Pub Date : 2024-05-10 DOI: 10.2174/0113892029298909240426094055
Rangasai Chandra Goli, Kiyevi G. Chishi, Indrajit Ganguly, Sanjeev Singh, S.P. Dixit, Pallavi Rathi, Vikas Diwakar, Chandana Sree C, Omkar Maharudra Limbalkar, Nidhi Sukhija, K.K. Kanaka
{"title":"Global and Local Ancestry and its Importance: A Mini-Review","authors":"Rangasai Chandra Goli, Kiyevi G. Chishi, Indrajit Ganguly, Sanjeev Singh, S.P. Dixit, Pallavi Rathi, Vikas Diwakar, Chandana Sree C, Omkar Maharudra Limbalkar, Nidhi Sukhija, K.K. Kanaka","doi":"10.2174/0113892029298909240426094055","DOIUrl":"https://doi.org/10.2174/0113892029298909240426094055","url":null,"abstract":": The fastest way to significantly change the composition of a population is through admixture, an evolutionary mechanism. In animal breeding history, genetic admixture has provided both short-term and long-term advantages by utilizing the phenomenon of complementarity and heterosis in several traits and genetic diversity, respectively. The traditional method of admixture analysis by pedigree records has now been replaced greatly by genome-wide marker data that enables more precise estimations. Among these markers, SNPs have been the popular choice since they are cost-effective, not so laborious, and automation of genotyping is easy. Certain markers can suggest the possibility of a population's origin from a sample of DNA where the source individual is unknown or unwilling to disclose their lineage, which are called Ancestry-Informative Markers (AIMs). Revealing admixture level at the locus-specific level is termed as local ancestry and can be exploited to identify signs of recent selective response and can account for genetic drift. Considering the importance of genetic admixture and local ancestry, in this mini-review, both concepts are illustrated, encompassing basics, their estimation/identification methods, tools/- software used and their applications.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140931827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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