首页 > 最新文献

Genomics and Informatics最新文献

英文 中文
Comparative co-expression analysis of RNA-Seq transcriptome revealing key genes, miRNA and transcription factor in distinct metabolic pathways in diabetic nerve, eye, and kidney disease. RNA-Seq转录组的比较共表达分析揭示了糖尿病神经、眼睛和肾脏疾病中不同代谢途径的关键基因、miRNA和转录因子。
Q2 Agricultural and Biological Sciences Pub Date : 2022-09-01 Epub Date: 2022-09-30 DOI: 10.5808/gi.22029
Veeran Kutty Subaida Shafna Asmy, Jeyakumar Natarajan

Diabetes and its related complications are associated with long term damage and failure of various organ systems. The microvascular complications of diabetes considered in this study are diabetic retinopathy, diabetic neuropathy, and diabetic nephropathy. The aim is to identify the weighted co-expressed and differentially expressed genes (DEGs), major pathways, and their miRNA, transcription factors (TFs) and drugs interacting in all the three conditions. The primary goal is to identify vital DEGs in all the three conditions. The overlapped five genes (AKT1, NFKB1, MAPK3, PDPK1, and TNF) from the DEGs and the co-expressed genes were defined as key genes, which differentially expressed in all the three cases. Then the protein-protein interaction network and gene set linkage analysis (GSLA) of key genes was performed. GSLA, gene ontology, and pathway enrichment analysis of the key genes elucidates nine major pathways in diabetes. Subsequently, we constructed the miRNA-gene and transcription factorgene regulatory network of the five gene of interest in the nine major pathways were studied. hsa-mir-34a-5p, a major miRNA that interacted with all the five genes. RELA, FOXO3, PDX1 and SREBF1 were the TFs interacting with the major five gene of interest. Finally, drug-gene interaction network elucidates five potential drugs to treat the genes of interest. This research reveals biomarker genes, miRNA, TFs, and therapeutic drugs in the key signaling pathways, which may help us, understand the processes of all three secondary microvascular problems and aid in disease detection and management.

糖尿病及其相关并发症与多种器官系统的长期损害和衰竭有关。本研究考虑的糖尿病微血管并发症包括糖尿病视网膜病变、糖尿病神经病变和糖尿病肾病。目的是确定加权共表达和差异表达基因(deg)、主要途径及其miRNA、转录因子(tf)和药物在这三种情况下的相互作用。主要目标是确定所有三种情况下的重要deg。将deg中重叠的5个基因(AKT1、NFKB1、MAPK3、PDPK1、TNF)和共表达基因定义为关键基因,在3例病例中均有差异表达。然后对关键基因进行蛋白-蛋白相互作用网络和基因集连锁分析(GSLA)。关键基因的GSLA、基因本体和通路富集分析阐明了糖尿病的9个主要通路。随后,我们构建了mirna基因和转录因子基因调控网络,对5个感兴趣基因的9个主要通路进行了研究。hsa-mir-34a-5p,一个与所有五个基因相互作用的主要miRNA。RELA、FOXO3、PDX1和SREBF1是与主要5个感兴趣基因相互作用的TFs。最后,药物-基因相互作用网络阐明了治疗感兴趣基因的五种潜在药物。这项研究揭示了关键信号通路中的生物标志物基因、miRNA、tf和治疗药物,这可能有助于我们了解这三种继发性微血管问题的过程,并有助于疾病的检测和管理。
{"title":"Comparative co-expression analysis of RNA-Seq transcriptome revealing key genes, miRNA and transcription factor in distinct metabolic pathways in diabetic nerve, eye, and kidney disease.","authors":"Veeran Kutty Subaida Shafna Asmy,&nbsp;Jeyakumar Natarajan","doi":"10.5808/gi.22029","DOIUrl":"https://doi.org/10.5808/gi.22029","url":null,"abstract":"<p><p>Diabetes and its related complications are associated with long term damage and failure of various organ systems. The microvascular complications of diabetes considered in this study are diabetic retinopathy, diabetic neuropathy, and diabetic nephropathy. The aim is to identify the weighted co-expressed and differentially expressed genes (DEGs), major pathways, and their miRNA, transcription factors (TFs) and drugs interacting in all the three conditions. The primary goal is to identify vital DEGs in all the three conditions. The overlapped five genes (AKT1, NFKB1, MAPK3, PDPK1, and TNF) from the DEGs and the co-expressed genes were defined as key genes, which differentially expressed in all the three cases. Then the protein-protein interaction network and gene set linkage analysis (GSLA) of key genes was performed. GSLA, gene ontology, and pathway enrichment analysis of the key genes elucidates nine major pathways in diabetes. Subsequently, we constructed the miRNA-gene and transcription factorgene regulatory network of the five gene of interest in the nine major pathways were studied. hsa-mir-34a-5p, a major miRNA that interacted with all the five genes. RELA, FOXO3, PDX1 and SREBF1 were the TFs interacting with the major five gene of interest. Finally, drug-gene interaction network elucidates five potential drugs to treat the genes of interest. This research reveals biomarker genes, miRNA, TFs, and therapeutic drugs in the key signaling pathways, which may help us, understand the processes of all three secondary microvascular problems and aid in disease detection and management.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":" ","pages":"e26"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9576479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33538775","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}
引用次数: 0
In silico genome wide identification and expression analysis of the WUSCHEL-related homeobox gene family in Medicago sativa. 紫花苜蓿(Medicago sativa) wuscher相关同源盒基因家族的全基因组鉴定与表达分析。
Q2 Agricultural and Biological Sciences Pub Date : 2022-06-01 Epub Date: 2022-05-30 DOI: 10.5808/gi.22013
Tianhui Yang, Ting Gao, Chuang Wang, Xiaochun Wang, Caijin Chen, Mei Tian, Weidi Yang

Alfalfa (Medicago sativa) is an important food and feed crop which rich in mineral sources. The WUSCHEL-related homeobox (WOX) gene family plays important roles in plant development and identification of putative gene families, their structure, and potential functions is a primary step for not only understanding the genetic mechanisms behind various biological process but also for genetic improvement. A variety of computational tools, including MAFFT, HMMER, hidden Markov models, Pfam, SMART, MEGA, ProtTest, BLASTn, and BRAD, among others, were used. We identified 34 MsWOX genes based on a systematic analysis of the alfalfa plant genome spread in eight chromosomes. This is an expansion of the gene family which we attribute to observed chromosomal duplications. Sequence alignment analysis revealed 61 conserved proteins containing a homeodomain. Phylogenetic study sung reveal five evolutionary clades with 15 motif distributions. Gene structure analysis reveals various exon, intron, and untranslated structures which are consistent in genes from similar clades. Functional analysis prediction of promoter regions reveals various transcription binding sites containing key growth, development, and stress-responsive transcription factor families such as MYB, ERF, AP2, and NAC which are spread across the genes. Most of the genes are predicted to be in the nucleus. Also, there are duplication events in some genes which explain the expansion of the family. The present research provides a clue on the potential roles of MsWOX family genes that will be useful for further understanding their functional roles in alfalfa plants.

紫花苜蓿(Medicago sativa)是一种富含矿物质的重要食物和饲料作物。wuschell相关同源盒(WOX)基因家族在植物发育过程中起着重要的作用,鉴定可能的基因家族及其结构和潜在功能是了解各种生物过程背后的遗传机制和进行遗传改良的首要步骤。使用了多种计算工具,包括MAFFT、hmm、隐马尔可夫模型、Pfam、SMART、MEGA、ProtTest、BLASTn和BRAD等。通过对苜蓿8条染色体基因组的系统分析,鉴定出34个MsWOX基因。这是基因家族的扩展,我们将其归因于观察到的染色体复制。序列比对分析显示61个保守蛋白含有同源结构域。系统发育研究揭示了5个进化支系有15个基序分布。基因结构分析表明,在相似进化支的基因中,各种外显子、内含子和非翻译结构是一致的。启动子区域的功能分析预测揭示了各种转录结合位点包含关键的生长、发育和应激应答转录因子家族,如MYB、ERF、AP2和NAC,这些转录因子家族分布在基因中。据预测,大多数基因都在细胞核中。此外,在一些基因中存在重复事件,这解释了家族的扩张。本研究为进一步了解MsWOX家族基因在苜蓿植物中的功能作用提供了线索。
{"title":"In silico genome wide identification and expression analysis of the WUSCHEL-related homeobox gene family in Medicago sativa.","authors":"Tianhui Yang,&nbsp;Ting Gao,&nbsp;Chuang Wang,&nbsp;Xiaochun Wang,&nbsp;Caijin Chen,&nbsp;Mei Tian,&nbsp;Weidi Yang","doi":"10.5808/gi.22013","DOIUrl":"https://doi.org/10.5808/gi.22013","url":null,"abstract":"<p><p>Alfalfa (Medicago sativa) is an important food and feed crop which rich in mineral sources. The WUSCHEL-related homeobox (WOX) gene family plays important roles in plant development and identification of putative gene families, their structure, and potential functions is a primary step for not only understanding the genetic mechanisms behind various biological process but also for genetic improvement. A variety of computational tools, including MAFFT, HMMER, hidden Markov models, Pfam, SMART, MEGA, ProtTest, BLASTn, and BRAD, among others, were used. We identified 34 MsWOX genes based on a systematic analysis of the alfalfa plant genome spread in eight chromosomes. This is an expansion of the gene family which we attribute to observed chromosomal duplications. Sequence alignment analysis revealed 61 conserved proteins containing a homeodomain. Phylogenetic study sung reveal five evolutionary clades with 15 motif distributions. Gene structure analysis reveals various exon, intron, and untranslated structures which are consistent in genes from similar clades. Functional analysis prediction of promoter regions reveals various transcription binding sites containing key growth, development, and stress-responsive transcription factor families such as MYB, ERF, AP2, and NAC which are spread across the genes. Most of the genes are predicted to be in the nucleus. Also, there are duplication events in some genes which explain the expansion of the family. The present research provides a clue on the potential roles of MsWOX family genes that will be useful for further understanding their functional roles in alfalfa plants.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 2","pages":"e19"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9299560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40589088","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}
引用次数: 4
Integrated bioinformatics analysis of validated and circulating miRNAs in ovarian cancer. 卵巢癌中已验证和循环mirna的综合生物信息学分析。
Q2 Agricultural and Biological Sciences Pub Date : 2022-06-01 Epub Date: 2022-06-30 DOI: 10.5808/gi.21067
Berkcan Dogan, Ece Gumusoglu, Ege Ulgen, Osman Ugur Sezerman, Tuba Gunel

Recent studies have focused on the early detection of ovarian cancer (OC) using tumor materials by liquid biopsy. The mechanisms of microRNAs (miRNAs) to impact OC and signaling pathways are still unknown. This study aims to reliably perform functional analysis of previously validated circulating miRNAs' target genes by using pathfindR. Also, overall survival and pathological stage analyses were evaluated with miRNAs' target genes which are common in the The Cancer Genome Atlas and GTEx datasets. Our previous studies have validated three downregulated miRNAs (hsa-miR-885-5p, hsa-miR-1909-5p, and hsalet7d-3p) having a diagnostic value in OC patients' sera, with high-throughput techniques. The predicted target genes of these miRNAs were retrieved from the miRDB database (v6.0). Active-subnetwork-oriented Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted by pathfindR using the target genes. Enrichment of KEGG pathways assessed by the analysis of pathfindR indicated that 24 pathways were related to the target genes. Ubiquitin-mediated proteolysis, spliceosome and Notch signaling pathway were the top three pathways with the lowest p-values (p < 0.001). Ninety-three common genes were found to be differentially expressed (p < 0.05) in the datasets. No significant genes were found to be significant in the analysis of overall survival analyses, but 24 genes were found to be significant with pathological stages analysis (p < 0.05). The findings of our study provide in-silico evidence that validated circulating miRNAs' target genes and enriched pathways are related to OC and have potential roles in theranostics applications. Further experimental investigations are required to validate our results which will ultimately provide a new perspective for translational applications in OC management.

近年来的研究主要集中在利用肿瘤材料进行液体活检来早期检测卵巢癌。microRNAs (miRNAs)影响OC和信号通路的机制尚不清楚。本研究旨在通过pathfindR对先前验证的循环miRNAs靶基因进行可靠的功能分析。此外,总体生存期和病理分期分析也用在the Cancer Genome Atlas和GTEx数据集中常见的mirna靶基因进行评估。我们之前的研究已经通过高通量技术验证了三种下调的mirna (hsa-miR-885-5p, hsa-miR-1909-5p和hsalet7d-3p)在OC患者血清中具有诊断价值。这些mirna的预测靶基因从miRDB数据库(v6.0)中检索。利用pathfindR对目标基因进行了面向主动子网的京都基因与基因组百科全书(KEGG)通路富集分析。通过pathfindR分析评估KEGG通路的富集程度,发现24条通路与靶基因有关。泛素介导的蛋白水解、剪接体和Notch信号通路是p值最低的前3条通路(p < 0.001)。共有93个基因存在差异表达(p < 0.05)。总生存分析中无显著基因,病理分期分析中有24个基因显著(p < 0.05)。我们的研究结果提供了验证循环mirna的靶基因和富集途径与OC相关的硅证据,并在治疗应用中具有潜在的作用。需要进一步的实验研究来验证我们的结果,这将最终为OC管理的翻译应用提供一个新的视角。
{"title":"Integrated bioinformatics analysis of validated and circulating miRNAs in ovarian cancer.","authors":"Berkcan Dogan,&nbsp;Ece Gumusoglu,&nbsp;Ege Ulgen,&nbsp;Osman Ugur Sezerman,&nbsp;Tuba Gunel","doi":"10.5808/gi.21067","DOIUrl":"https://doi.org/10.5808/gi.21067","url":null,"abstract":"<p><p>Recent studies have focused on the early detection of ovarian cancer (OC) using tumor materials by liquid biopsy. The mechanisms of microRNAs (miRNAs) to impact OC and signaling pathways are still unknown. This study aims to reliably perform functional analysis of previously validated circulating miRNAs' target genes by using pathfindR. Also, overall survival and pathological stage analyses were evaluated with miRNAs' target genes which are common in the The Cancer Genome Atlas and GTEx datasets. Our previous studies have validated three downregulated miRNAs (hsa-miR-885-5p, hsa-miR-1909-5p, and hsalet7d-3p) having a diagnostic value in OC patients' sera, with high-throughput techniques. The predicted target genes of these miRNAs were retrieved from the miRDB database (v6.0). Active-subnetwork-oriented Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted by pathfindR using the target genes. Enrichment of KEGG pathways assessed by the analysis of pathfindR indicated that 24 pathways were related to the target genes. Ubiquitin-mediated proteolysis, spliceosome and Notch signaling pathway were the top three pathways with the lowest p-values (p < 0.001). Ninety-three common genes were found to be differentially expressed (p < 0.05) in the datasets. No significant genes were found to be significant in the analysis of overall survival analyses, but 24 genes were found to be significant with pathological stages analysis (p < 0.05). The findings of our study provide in-silico evidence that validated circulating miRNAs' target genes and enriched pathways are related to OC and have potential roles in theranostics applications. Further experimental investigations are required to validate our results which will ultimately provide a new perspective for translational applications in OC management.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 2","pages":"e20"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9299562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40589089","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}
引用次数: 2
Comparison of survival prediction models for pancreatic cancer: Cox model versus machine learning models. 胰腺癌生存预测模型的比较:Cox模型与机器学习模型。
Q2 Agricultural and Biological Sciences Pub Date : 2022-06-01 Epub Date: 2022-06-30 DOI: 10.5808/gi.22036
Hyunsuk Kim, Taesung Park, Jinyoung Jang, Seungyeoun Lee

A survival prediction model has recently been developed to evaluate the prognosis of resected nonmetastatic pancreatic ductal adenocarcinoma based on a Cox model using two nationwide databases: Surveillance, Epidemiology and End Results (SEER) and Korea Tumor Registry System-Biliary Pancreas (KOTUS-BP). In this study, we applied two machine learning methods-random survival forests (RSF) and support vector machines (SVM)-for survival analysis and compared their prediction performance using the SEER and KOTUS-BP datasets. Three schemes were used for model development and evaluation. First, we utilized data from SEER for model development and used data from KOTUS-BP for external evaluation. Second, these two datasets were swapped by taking data from KOTUS-BP for model development and data from SEER for external evaluation. Finally, we mixed these two datasets half and half and utilized the mixed datasets for model development and validation. We used 9,624 patients from SEER and 3,281 patients from KOTUS-BP to construct a prediction model with seven covariates: age, sex, histologic differentiation, adjuvant treatment, resection margin status, and the American Joint Committee on Cancer 8th edition T-stage and N-stage. Comparing the three schemes, the performance of the Cox model, RSF, and SVM was better when using the mixed datasets than when using the unmixed datasets. When using the mixed datasets, the C-index, 1-year, 2-year, and 3-year time-dependent areas under the curve for the Cox model were 0.644, 0.698, 0.680, and 0.687, respectively. The Cox model performed slightly better than RSF and SVM.

最近开发了一种生存预测模型,用于评估切除的非转移性胰腺导管腺癌的预后,该模型基于Cox模型,使用两个全国性数据库:监测,流行病学和最终结果(SEER)和韩国肿瘤登记系统-胆道胰腺(KOTUS-BP)。在这项研究中,我们应用了两种机器学习方法-随机生存森林(RSF)和支持向量机(SVM)-进行生存分析,并使用SEER和KOTUS-BP数据集比较了它们的预测性能。采用三种方案进行模型开发和评价。首先,我们利用来自SEER的数据进行模型开发,并使用来自KOTUS-BP的数据进行外部评估。其次,通过从KOTUS-BP获取用于模型开发的数据和从SEER获取用于外部评估的数据来交换这两个数据集。最后,我们将这两个数据集对半混合,并利用混合数据集进行模型开发和验证。我们使用来自SEER的9624例患者和来自KOTUS-BP的3281例患者构建了一个包含7个协变量的预测模型:年龄、性别、组织学分化、辅助治疗、切除边缘状态和美国癌症联合委员会第8版t期和n期。对比三种方案,混合数据集下Cox模型、RSF和SVM的性能优于未混合数据集下的性能。当使用混合数据集时,Cox模型的c指数、1年、2年和3年曲线下的时间依赖面积分别为0.644、0.698、0.680和0.687。Cox模型的表现略好于RSF和SVM。
{"title":"Comparison of survival prediction models for pancreatic cancer: Cox model versus machine learning models.","authors":"Hyunsuk Kim,&nbsp;Taesung Park,&nbsp;Jinyoung Jang,&nbsp;Seungyeoun Lee","doi":"10.5808/gi.22036","DOIUrl":"https://doi.org/10.5808/gi.22036","url":null,"abstract":"<p><p>A survival prediction model has recently been developed to evaluate the prognosis of resected nonmetastatic pancreatic ductal adenocarcinoma based on a Cox model using two nationwide databases: Surveillance, Epidemiology and End Results (SEER) and Korea Tumor Registry System-Biliary Pancreas (KOTUS-BP). In this study, we applied two machine learning methods-random survival forests (RSF) and support vector machines (SVM)-for survival analysis and compared their prediction performance using the SEER and KOTUS-BP datasets. Three schemes were used for model development and evaluation. First, we utilized data from SEER for model development and used data from KOTUS-BP for external evaluation. Second, these two datasets were swapped by taking data from KOTUS-BP for model development and data from SEER for external evaluation. Finally, we mixed these two datasets half and half and utilized the mixed datasets for model development and validation. We used 9,624 patients from SEER and 3,281 patients from KOTUS-BP to construct a prediction model with seven covariates: age, sex, histologic differentiation, adjuvant treatment, resection margin status, and the American Joint Committee on Cancer 8th edition T-stage and N-stage. Comparing the three schemes, the performance of the Cox model, RSF, and SVM was better when using the mixed datasets than when using the unmixed datasets. When using the mixed datasets, the C-index, 1-year, 2-year, and 3-year time-dependent areas under the curve for the Cox model were 0.644, 0.698, 0.680, and 0.687, respectively. The Cox model performed slightly better than RSF and SVM.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 2","pages":"e23"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9299568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40589092","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}
引用次数: 4
A novel mutation in GJC2 associated with hypomyelinating leukodystrophy type 2 disorder. 与低髓鞘性白质营养不良2型疾病相关的GJC2新突变
Q2 Agricultural and Biological Sciences Pub Date : 2022-06-01 Epub Date: 2022-06-30 DOI: 10.5808/gi.22008
Sajad Rafiee Komachali, Mozhgan Sheikholeslami, Mansoor Salehi

Hypomyelinating leukodystrophy type 2 (HLD2), is an inherited genetic disease of the central nervous system caused by recessive mutations in the gap junction protein gamma 2 (GJC2/GJA12). HLD2 is characterized by nystagmus, developmental delay, motor impairments, ataxia, severe speech problem, and hypomyelination in the brain. The GJC2 sequence encodes connexin 47 protein (Cx47). Connexins are a group of membrane proteins that oligomerize to construct gap junctions protein. In the present study, a novel missense mutation gene c.760G>A (p.Val254Met) was identified in a patient with HLD2 by performing whole exome sequencing. Following the discovery of the new mutation in the proband, we used Sanger sequencing to analyze his affected sibling and parents. Sanger sequencing verified homozygosity of the mutation in the proband and his affected sibling. The autosomal recessive inheritance pattern was confirmed since Sanger sequencing revealed both healthy parents were heterozygous for the mutation. PolyPhen2, SIFT, PROVEAN, and CADD were used to evaluate the function prediction scores of detected mutations. Cx47 is essential for oligodendrocyte function, including adequate myelination and myelin maintenance in humans. Novel mutation p.Val254Met is located in the second extracellular domain of Cx47, both extracellular loops are highly conserved and probably induce intramolecular disulfide interactions. This novel mutation in the Cx47 gene causes oligodendrocyte dysfunction and HLD2 disorder.

2型低髓鞘性白质营养不良症(HLD2)是一种由间隙连接蛋白γ 2 (GJC2/GJA12)隐性突变引起的中枢神经系统遗传性疾病。HLD2的特点是眼球震颤、发育迟缓、运动障碍、共济失调、严重的语言问题和大脑髓鞘发育低下。GJC2序列编码连接蛋白47 (Cx47)。连接蛋白是一组寡聚形成间隙连接蛋白的膜蛋白。在本研究中,通过对HLD2患者进行全外显子组测序,发现了一种新的错义突变基因c.760G> a (p.Val254Met)。在先证者身上发现新的突变后,我们用桑格测序法分析了他受影响的兄弟姐妹和父母。桑格测序证实了先证者及其患病兄弟姐妹突变的纯合性。常染色体隐性遗传模式被证实,因为Sanger测序显示健康的父母都是杂合突变。使用PolyPhen2、SIFT、PROVEAN和CADD评估检测到的突变的功能预测评分。Cx47对人类少突胶质细胞功能至关重要,包括充分的髓鞘形成和髓磷脂维持。新突变p.Val254Met位于Cx47的第二个胞外结构域,两个胞外环高度保守,可能诱导分子内二硫相互作用。Cx47基因的这种新突变导致少突胶质细胞功能障碍和HLD2疾病。
{"title":"A novel mutation in GJC2 associated with hypomyelinating leukodystrophy type 2 disorder.","authors":"Sajad Rafiee Komachali,&nbsp;Mozhgan Sheikholeslami,&nbsp;Mansoor Salehi","doi":"10.5808/gi.22008","DOIUrl":"https://doi.org/10.5808/gi.22008","url":null,"abstract":"<p><p>Hypomyelinating leukodystrophy type 2 (HLD2), is an inherited genetic disease of the central nervous system caused by recessive mutations in the gap junction protein gamma 2 (GJC2/GJA12). HLD2 is characterized by nystagmus, developmental delay, motor impairments, ataxia, severe speech problem, and hypomyelination in the brain. The GJC2 sequence encodes connexin 47 protein (Cx47). Connexins are a group of membrane proteins that oligomerize to construct gap junctions protein. In the present study, a novel missense mutation gene c.760G>A (p.Val254Met) was identified in a patient with HLD2 by performing whole exome sequencing. Following the discovery of the new mutation in the proband, we used Sanger sequencing to analyze his affected sibling and parents. Sanger sequencing verified homozygosity of the mutation in the proband and his affected sibling. The autosomal recessive inheritance pattern was confirmed since Sanger sequencing revealed both healthy parents were heterozygous for the mutation. PolyPhen2, SIFT, PROVEAN, and CADD were used to evaluate the function prediction scores of detected mutations. Cx47 is essential for oligodendrocyte function, including adequate myelination and myelin maintenance in humans. Novel mutation p.Val254Met is located in the second extracellular domain of Cx47, both extracellular loops are highly conserved and probably induce intramolecular disulfide interactions. This novel mutation in the Cx47 gene causes oligodendrocyte dysfunction and HLD2 disorder.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 2","pages":"e24"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9299563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40589093","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}
引用次数: 1
Bayesian analysis of longitudinal traits in the Korea Association Resource (KARE) cohort. 对韩国协会资源(KARE)队列中的纵向特征进行贝叶斯分析。
Q2 Agricultural and Biological Sciences Pub Date : 2022-06-01 Epub Date: 2022-06-30 DOI: 10.5808/gi.22022
Wonil Chung, Hyunji Hwang, Taesung Park

Various methodologies for the genetic analysis of longitudinal data have been proposed and applied to data from large-scale genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with traits of interest and to detect SNP-time interactions. We recently proposed a grid-based Bayesian mixed model for longitudinal genetic data and showed that our Bayesian method increased the statistical power compared to the corresponding univariate method and well detected SNP-time interactions. In this paper, we further analyze longitudinal obesity-related traits such as body mass index, hip circumference, waist circumference, and waist-hip ratio from Korea Association Resource data to evaluate the proposed Bayesian method. We first conducted GWAS analyses of cross-sectional traits and combined the results of GWAS analyses through a meta-analysis based on a trajectory model and a random-effects model. We then applied our Bayesian method to a subset of SNPs selected by meta-analysis to further discover SNPs associated with traits of interest and SNP-time interactions. The proposed Bayesian method identified several novel SNPs associated with longitudinal obesity-related traits, and almost 25% of the identified SNPs had significant p-values for SNP-time interactions.

人们提出了各种用于纵向数据遗传分析的方法,并将其应用于大规模全基因组关联研究(GWAS)的数据,以确定与相关性状相关的单核苷酸多态性(SNP),并检测 SNP-时间交互作用。我们最近针对纵向遗传数据提出了一种基于网格的贝叶斯混合模型,结果表明,与相应的单变量方法相比,我们的贝叶斯方法提高了统计能力,并能很好地检测 SNP-时间交互作用。在本文中,我们进一步分析了韩国协会资源数据中的纵向肥胖相关性状,如体重指数、臀围、腰围和腰臀比,以评估所提出的贝叶斯方法。我们首先对横断面性状进行了 GWAS 分析,并通过基于轨迹模型和随机效应模型的荟萃分析合并了 GWAS 分析的结果。然后,我们将贝叶斯方法应用于通过荟萃分析选出的 SNPs 子集,以进一步发现与相关性状和 SNP 时间交互作用相关的 SNPs。所提出的贝叶斯方法发现了几个与纵向肥胖相关性状有关的新的SNPs,在所发现的SNPs中,近25%的SNPs具有显著的SNP-时间交互作用P值。
{"title":"Bayesian analysis of longitudinal traits in the Korea Association Resource (KARE) cohort.","authors":"Wonil Chung, Hyunji Hwang, Taesung Park","doi":"10.5808/gi.22022","DOIUrl":"10.5808/gi.22022","url":null,"abstract":"<p><p>Various methodologies for the genetic analysis of longitudinal data have been proposed and applied to data from large-scale genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with traits of interest and to detect SNP-time interactions. We recently proposed a grid-based Bayesian mixed model for longitudinal genetic data and showed that our Bayesian method increased the statistical power compared to the corresponding univariate method and well detected SNP-time interactions. In this paper, we further analyze longitudinal obesity-related traits such as body mass index, hip circumference, waist circumference, and waist-hip ratio from Korea Association Resource data to evaluate the proposed Bayesian method. We first conducted GWAS analyses of cross-sectional traits and combined the results of GWAS analyses through a meta-analysis based on a trajectory model and a random-effects model. We then applied our Bayesian method to a subset of SNPs selected by meta-analysis to further discover SNPs associated with traits of interest and SNP-time interactions. The proposed Bayesian method identified several novel SNPs associated with longitudinal obesity-related traits, and almost 25% of the identified SNPs had significant p-values for SNP-time interactions.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 2","pages":"e16"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9299561/pdf/gi-22022.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40567503","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}
引用次数: 0
Associations between single-nucleotide polymorphisms of the interleukin-18 gene and breast cancer in Iraqi women. 伊拉克妇女白细胞介素-18基因单核苷酸多态性与乳腺癌之间的关系
Q2 Agricultural and Biological Sciences Pub Date : 2022-06-01 Epub Date: 2022-06-30 DOI: 10.5808/gi.22026
Bilal Fadıl Zakariya, Asmaa M Salih Almohaidi, Seçil Akilli Şimşek, Areege Mustafa Kamal, Wijdan H Al-Dabbagh, Safaa A Al-Waysi

According to long-term projections, by 2030, the world's population is predicted to reach 7.5 billion individuals, and there will be roughly 27 million new cancer cases diagnosed. The global burden of breast cancer (BC) is expected to rise. According to the Ministry of Health-Iraqi Cancer Registry, cancer is the second largest cause of death after cardiovascular disease. This study investigated the interleukin-18 (IL18) single-nucleotide polymorphisms (SNPs) -607C/A rs1946518 and -137G/C rs187238 using the sequence-specific amplification-polymerase chain reaction approach. Regarding the position -607C/A, there was a highly significant difference between the observed and expected frequencies in patients and controls (χ 2 = 3.16 and χ 2 = 16.5), respectively. The AA and CA genotypes were associated with significantly increased BC risk (odds ratio [OR], 3.68; p = 0.004 and OR, 2.83; p = 0.04, respectively). Women with the A allele had a 5.03-fold increased susceptibility to BC. The C allele may be a protective allele against BC (OR, 0.19). Although position -137G/C showed no significant differences in the CC genotype distribution (p = 0.18), the frequency of the CC genotype was significantly higher in patients than in controls. In contrast, patients had a significantly higher frequency of GC genotypes than controls (p = 0.04), which was associated with an increased risk of developing BC (OR, 2.63). The G allele frequency was significantly lower in patients than in controls (55.0% vs. 76.2%, respectively). This SNP may be considered a common genotype in the Iraqi population, with the wild-type G allele having a protective function (OR, 0.19) and the mutant C allele having an environmental effect (OR, 2.63).

根据长期预测,到2030年,世界人口预计将达到75亿人,新诊断的癌症病例约为2700万例。乳腺癌(BC)的全球负担预计将上升。根据伊拉克卫生部癌症登记处的资料,癌症是继心血管疾病之后的第二大死因。本研究采用序列特异性扩增-聚合酶链反应方法对白细胞介素-18 (il -18)单核苷酸多态性-607C/A rs1946518和-137G/C rs187238进行了研究。对于-607C/A位置,患者和对照组的观察频率和预期频率差异极显著(χ 2 = 3.16和χ 2 = 16.5)。AA和CA基因型与BC风险显著增加相关(优势比[OR], 3.68;p = 0.004, OR为2.83;P = 0.04)。携带A等位基因的女性对BC的易感性增加了5.03倍。C等位基因可能是抗BC的保护性等位基因(OR, 0.19)。虽然-137G/C位置的CC基因型分布差异无统计学意义(p = 0.18),但患者的CC基因型频率明显高于对照组。相比之下,患者的GC基因型频率明显高于对照组(p = 0.04),这与发生BC的风险增加有关(OR, 2.63)。患者的G等位基因频率明显低于对照组(分别为55.0%和76.2%)。该SNP可能被认为是伊拉克人群中常见的基因型,野生型G等位基因具有保护功能(OR, 0.19),突变型C等位基因具有环境影响(OR, 2.63)。
{"title":"Associations between single-nucleotide polymorphisms of the interleukin-18 gene and breast cancer in Iraqi women.","authors":"Bilal Fadıl Zakariya,&nbsp;Asmaa M Salih Almohaidi,&nbsp;Seçil Akilli Şimşek,&nbsp;Areege Mustafa Kamal,&nbsp;Wijdan H Al-Dabbagh,&nbsp;Safaa A Al-Waysi","doi":"10.5808/gi.22026","DOIUrl":"https://doi.org/10.5808/gi.22026","url":null,"abstract":"<p><p>According to long-term projections, by 2030, the world's population is predicted to reach 7.5 billion individuals, and there will be roughly 27 million new cancer cases diagnosed. The global burden of breast cancer (BC) is expected to rise. According to the Ministry of Health-Iraqi Cancer Registry, cancer is the second largest cause of death after cardiovascular disease. This study investigated the interleukin-18 (IL18) single-nucleotide polymorphisms (SNPs) -607C/A rs1946518 and -137G/C rs187238 using the sequence-specific amplification-polymerase chain reaction approach. Regarding the position -607C/A, there was a highly significant difference between the observed and expected frequencies in patients and controls (χ 2 = 3.16 and χ 2 = 16.5), respectively. The AA and CA genotypes were associated with significantly increased BC risk (odds ratio [OR], 3.68; p = 0.004 and OR, 2.83; p = 0.04, respectively). Women with the A allele had a 5.03-fold increased susceptibility to BC. The C allele may be a protective allele against BC (OR, 0.19). Although position -137G/C showed no significant differences in the CC genotype distribution (p = 0.18), the frequency of the CC genotype was significantly higher in patients than in controls. In contrast, patients had a significantly higher frequency of GC genotypes than controls (p = 0.04), which was associated with an increased risk of developing BC (OR, 2.63). The G allele frequency was significantly lower in patients than in controls (55.0% vs. 76.2%, respectively). This SNP may be considered a common genotype in the Iraqi population, with the wild-type G allele having a protective function (OR, 0.19) and the mutant C allele having an environmental effect (OR, 2.63).</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 2","pages":"e18"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9299566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40589087","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}
引用次数: 0
Genome characterization and mutation analysis of human influenza A virus in Thailand. 泰国甲型流感病毒的基因组特征和突变分析。
Q2 Agricultural and Biological Sciences Pub Date : 2022-06-01 Epub Date: 2022-06-30 DOI: 10.5808/gi.21077
Somruthai Rattanaburi, Vorthon Sawaswong, Pattaraporn Nimsamer, Oraphan Mayuramart, Pavaret Sivapornnukul, Ariya Khamwut, Prangwalai Chanchaem, Kritsada Kongnomnan, Nungruthai Suntronwong, Yong Poovorawan, Sunchai Payungporn

The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/ H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in hemagglutinin (HA) and neuraminidase (NA) genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, HA, and NA genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.

甲型流感病毒具有很高的突变率,在世界范围内造成严重的健康问题。因此,本研究的重点是基于下一代测序技术对泰国患者分离的病毒进行基因组表征。鼻拭子采集自2017-2018年泰国流感样疾病患者。采用逆转录-定量聚合酶链反应检测甲型流感病毒,并用MDCK细胞分离甲型流感病毒。利用Illumina MiSeq平台对病毒基因组进行扩增和测序。利用全基因组序列对病毒进行鉴定、系统发育构建、突变分析和核苷酸多样性分析。结果显示,90份样本呈病毒阳性,其中A/ H1N1病毒44份,A/H3N2病毒46份。其中43份成功分离,25份病毒基因组扩增完成。最终,成功测序了17个病毒全基因组(A/H1N1, n=12, A/H3N2, n=5),平均每个样本有232,578个测序序列和1,720个基因组覆盖率。系统发育分析表明,甲型H1N1流感病毒可与推荐的疫苗株区分开来。然而,本研究的A/H3N2病毒与推荐的疫苗株密切相关。在两种病毒的所有基因中均发现了非同义突变,特别是在血凝素(HA)和神经氨酸酶(NA)基因中。核苷酸多样性分析显示甲型H1N1流感病毒的PB1、PA、HA和NA基因存在负选择。本研究中的高通量数据允许对流行流感病毒进行遗传表征,这将对将来预防大流行和流行病爆发至关重要。
{"title":"Genome characterization and mutation analysis of human influenza A virus in Thailand.","authors":"Somruthai Rattanaburi,&nbsp;Vorthon Sawaswong,&nbsp;Pattaraporn Nimsamer,&nbsp;Oraphan Mayuramart,&nbsp;Pavaret Sivapornnukul,&nbsp;Ariya Khamwut,&nbsp;Prangwalai Chanchaem,&nbsp;Kritsada Kongnomnan,&nbsp;Nungruthai Suntronwong,&nbsp;Yong Poovorawan,&nbsp;Sunchai Payungporn","doi":"10.5808/gi.21077","DOIUrl":"https://doi.org/10.5808/gi.21077","url":null,"abstract":"<p><p>The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/ H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in hemagglutinin (HA) and neuraminidase (NA) genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, HA, and NA genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 2","pages":"e21"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9299564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40589090","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}
引用次数: 1
Identification of the associations between genes and quantitative traits using entropy-based kernel density estimation. 利用基于熵的核密度估计鉴定基因与数量性状之间的关联。
Q2 Agricultural and Biological Sciences Pub Date : 2022-06-01 Epub Date: 2022-06-30 DOI: 10.5808/gi.22033
Jaeyong Yee, Taesung Park, Mira Park

Genetic associations have been quantified using a number of statistical measures. Entropy-based mutual information may be one of the more direct ways of estimating the association, in the sense that it does not depend on the parametrization. For this purpose, both the entropy and conditional entropy of the phenotype distribution should be obtained. Quantitative traits, however, do not usually allow an exact evaluation of entropy. The estimation of entropy needs a probability density function, which can be approximated by kernel density estimation. We have investigated the proper sequence of procedures for combining the kernel density estimation and entropy estimation with a probability density function in order to calculate mutual information. Genotypes and their interactions were constructed to set the conditions for conditional entropy. Extensive simulation data created using three types of generating functions were analyzed using two different kernels as well as two types of multifactor dimensionality reduction and another probability density approximation method called m-spacing. The statistical power in terms of correct detection rates was compared. Using kernels was found to be most useful when the trait distributions were more complex than simple normal or gamma distributions. A full-scale genomic dataset was explored to identify associations using the 2-h oral glucose tolerance test results and γ-glutamyl transpeptidase levels as phenotypes. Clearly distinguishable single-nucleotide polymorphisms (SNPs) and interacting SNP pairs associated with these phenotypes were found and listed with empirical p-values.

遗传关联已经用一些统计方法进行了量化。基于熵的互信息可能是估计关联的更直接的方法之一,因为它不依赖于参数化。为此,需要同时获得表型分布的熵和条件熵。然而,数量特征通常不允许熵的精确评估。熵的估计需要一个概率密度函数,这个概率密度函数可以用核密度估计近似。为了计算互信息,我们研究了将核密度估计和熵估计与概率密度函数相结合的适当程序顺序。构建基因型及其相互作用,为条件熵设置条件。使用三种类型的生成函数创建的大量模拟数据使用两种不同的核以及两种类型的多因素降维和另一种称为m-spacing的概率密度近似方法进行了分析。比较正确检出率方面的统计能力。当性状分布比简单的正态分布或伽玛分布更复杂时,使用核函数是最有用的。利用2小时口服葡萄糖耐量试验结果和γ-谷氨酰转肽酶水平作为表型,研究了一个完整的基因组数据集,以确定两者之间的关联。发现了与这些表型相关的明显可区分的单核苷酸多态性(SNP)和相互作用的SNP对,并列出了经验p值。
{"title":"Identification of the associations between genes and quantitative traits using entropy-based kernel density estimation.","authors":"Jaeyong Yee,&nbsp;Taesung Park,&nbsp;Mira Park","doi":"10.5808/gi.22033","DOIUrl":"https://doi.org/10.5808/gi.22033","url":null,"abstract":"<p><p>Genetic associations have been quantified using a number of statistical measures. Entropy-based mutual information may be one of the more direct ways of estimating the association, in the sense that it does not depend on the parametrization. For this purpose, both the entropy and conditional entropy of the phenotype distribution should be obtained. Quantitative traits, however, do not usually allow an exact evaluation of entropy. The estimation of entropy needs a probability density function, which can be approximated by kernel density estimation. We have investigated the proper sequence of procedures for combining the kernel density estimation and entropy estimation with a probability density function in order to calculate mutual information. Genotypes and their interactions were constructed to set the conditions for conditional entropy. Extensive simulation data created using three types of generating functions were analyzed using two different kernels as well as two types of multifactor dimensionality reduction and another probability density approximation method called m-spacing. The statistical power in terms of correct detection rates was compared. Using kernels was found to be most useful when the trait distributions were more complex than simple normal or gamma distributions. A full-scale genomic dataset was explored to identify associations using the 2-h oral glucose tolerance test results and γ-glutamyl transpeptidase levels as phenotypes. Clearly distinguishable single-nucleotide polymorphisms (SNPs) and interacting SNP pairs associated with these phenotypes were found and listed with empirical p-values.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 2","pages":"e17"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9299569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40589086","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}
引用次数: 0
Mathematical modeling of the impact of Omicron variant on the COVID-19 situation in South Korea. 欧米茄变种对韩国 COVID-19 情况影响的数学建模。
Q2 Agricultural and Biological Sciences Pub Date : 2022-06-01 Epub Date: 2022-06-22 DOI: 10.5808/gi.22025
Jooha Oh, Catherine Apio, Taesung Park

The rise of newer coronavirus disease 2019 (COVID-19) variants has brought a challenge to ending the spread of COVID-19. The variants have a different fatality, morbidity, and transmission rates and affect vaccine efficacy differently. Therefore, the impact of each new variant on the spread of COVID-19 is of interest to governments and scientists. Here, we proposed mathematical SEIQRDVP and SEIQRDV3P models to predict the impact of the Omicron variant on the spread of the COVID-19 situation in South Korea. SEIQEDVP considers one vaccine level at a time while SEIQRDV3P considers three vaccination levels (only one dose received, full doses received, and full doses + booster shots received) simultaneously. The omicron variant's effect was contemplated as a weighted sum of the delta and omicron variants' transmission rate and tuned using a hyperparameter k. Our models' performances were compared with common models like SEIR, SEIQR, and SEIQRDVUP using the root mean square error (RMSE). SEIQRDV3P performed better than the SEIQRDVP model. Without consideration of the variant effect, we don't see a rapid rise in COVID-19 cases and high RMSE values. But, with consideration of the omicron variant, we predicted a continuous rapid rise in COVID-19 cases until maybe herd immunity is developed in the population. Also, the RMSE value for the SEIQRDV3P model decreased by 27.4%. Therefore, modeling the impact of any new risen variant is crucial in determining the trajectory of the spread of COVID-19 and determining policies to be implemented.

2019年冠状病毒病(COVID-19)新变种的出现为终止COVID-19的传播带来了挑战。这些变种的致死率、发病率和传播率各不相同,对疫苗效力的影响也不尽相同。因此,每个新变种对 COVID-19 传播的影响都引起了政府和科学家的关注。在此,我们提出了 SEIQRDVP 和 SEIQRDV3P 数学模型来预测 Omicron 变种对韩国 COVID-19 传播情况的影响。SEIQEDVP 一次只考虑一种疫苗接种水平,而 SEIQRDV3P 则同时考虑三种疫苗接种水平(只接种一剂、接种全剂和接种全剂+加强针)。奥米克变体的影响被视为德尔塔变体和奥米克变体传播率的加权和,并使用超参数 k 进行调整。我们使用均方根误差 (RMSE) 将模型的性能与 SEIR、SEIQR 和 SEIQRDVUP 等常见模型进行了比较。SEIQRDV3P 的表现优于 SEIQRDVP 模型。在不考虑变异效应的情况下,我们不会看到 COVID-19 病例的迅速增加和高 RMSE 值。但是,如果考虑到奥米克龙变异,我们预测 COVID-19 病例会持续快速上升,直到人群中可能形成群体免疫。此外,SEIQRDV3P 模型的 RMSE 值降低了 27.4%。因此,对任何新的立氏变异体的影响进行建模对于确定 COVID-19 的传播轨迹和确定应实施的政策至关重要。
{"title":"Mathematical modeling of the impact of Omicron variant on the COVID-19 situation in South Korea.","authors":"Jooha Oh, Catherine Apio, Taesung Park","doi":"10.5808/gi.22025","DOIUrl":"10.5808/gi.22025","url":null,"abstract":"<p><p>The rise of newer coronavirus disease 2019 (COVID-19) variants has brought a challenge to ending the spread of COVID-19. The variants have a different fatality, morbidity, and transmission rates and affect vaccine efficacy differently. Therefore, the impact of each new variant on the spread of COVID-19 is of interest to governments and scientists. Here, we proposed mathematical SEIQRDVP and SEIQRDV3P models to predict the impact of the Omicron variant on the spread of the COVID-19 situation in South Korea. SEIQEDVP considers one vaccine level at a time while SEIQRDV3P considers three vaccination levels (only one dose received, full doses received, and full doses + booster shots received) simultaneously. The omicron variant's effect was contemplated as a weighted sum of the delta and omicron variants' transmission rate and tuned using a hyperparameter k. Our models' performances were compared with common models like SEIR, SEIQR, and SEIQRDVUP using the root mean square error (RMSE). SEIQRDV3P performed better than the SEIQRDVP model. Without consideration of the variant effect, we don't see a rapid rise in COVID-19 cases and high RMSE values. But, with consideration of the omicron variant, we predicted a continuous rapid rise in COVID-19 cases until maybe herd immunity is developed in the population. Also, the RMSE value for the SEIQRDV3P model decreased by 27.4%. Therefore, modeling the impact of any new risen variant is crucial in determining the trajectory of the spread of COVID-19 and determining policies to be implemented.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 2","pages":"e22"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9299565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40589091","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}
引用次数: 0
期刊
Genomics and Informatics
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1