Teck Yew Wong, S. Menaga, Chi-Ying F. Huang, S. H. Ho, S. Gan, Y. Lim
2-Methoxy-1,4-naphthoquinone (MNQ) has been shown to cause cytotoxic towards various cancer cell lines. This study is designed to investigate the regulatory effect of MNQ on the key cancer genes in mitogen-activated protein kinase, phosphoinositide 3-kinase, and nuclear factor кB signaling pathways. The expression levels of the genes were compared at different time point using polymerase chain reaction arrays and Ingenuity Pathway Analysis was performed to identify gene networks that are most significant to key cancer genes. A total of 43 differentially expressed genes were identified with 21 up-regulated and 22 down-regulated genes. Up-regulated genes were involved in apoptosis, cell cycle and act as tumor suppressor while down-regulated genes were involved in anti-apoptosis, angiogenesis, cell cycle and act as transcription factor as well as proto-oncogenes. MNQ exhibited multiple regulatory effects on the cancer key genes that targeting at cell proliferation, cell differentiation, cell transformation, apoptosis, reduce inflammatory responses, inhibits angiogenesis and metastasis.
{"title":"2-Methoxy-1,4-naphthoquinone (MNQ) regulates cancer key genes of MAPK, PI3K, and NF-κB pathways in Raji cells","authors":"Teck Yew Wong, S. Menaga, Chi-Ying F. Huang, S. H. Ho, S. Gan, Y. Lim","doi":"10.5808/gi.21041","DOIUrl":"https://doi.org/10.5808/gi.21041","url":null,"abstract":"2-Methoxy-1,4-naphthoquinone (MNQ) has been shown to cause cytotoxic towards various cancer cell lines. This study is designed to investigate the regulatory effect of MNQ on the key cancer genes in mitogen-activated protein kinase, phosphoinositide 3-kinase, and nuclear factor кB signaling pathways. The expression levels of the genes were compared at different time point using polymerase chain reaction arrays and Ingenuity Pathway Analysis was performed to identify gene networks that are most significant to key cancer genes. A total of 43 differentially expressed genes were identified with 21 up-regulated and 22 down-regulated genes. Up-regulated genes were involved in apoptosis, cell cycle and act as tumor suppressor while down-regulated genes were involved in anti-apoptosis, angiogenesis, cell cycle and act as transcription factor as well as proto-oncogenes. MNQ exhibited multiple regulatory effects on the cancer key genes that targeting at cell proliferation, cell differentiation, cell transformation, apoptosis, reduce inflammatory responses, inhibits angiogenesis and metastasis.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41964367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sk Injamamul Islam, Moslema Jahan Mou, Saloa Sanjida, Muhammad Tariq, Saad Nasir, Sarower Mahfuj
Vibrio harveyi belongs to the family Vibrionaceae of class Gammaproteobacteria. Around 12 Vibrio species can cause gastroenteritis (gastrointestinal illness) in humans. A large number of bacterial particles can be found in the infected cells, which may cause death. Despite these devastating complications, there is still no cure or vaccine for the bacteria. As a result, we used an immunoinformatics approach to develop a multi-epitope vaccine against the most pathogenic hemolysin gene of V. harveyi. The immunodominant T- and B-cell epitopes were identified using the hemolysin protein. We developed a vaccine employing three possible epitopes: cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocyte epitopes, after thorough testing. The vaccine was developed to be antigenic, immunogenic, and non-allergenic, as well as have a better solubility. Molecular dynamics simulation revealed significant structural stiffness and binding stability. In addition, the immunological simulation generated by computers revealed that the vaccination might elicit immune reactions Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher codon adaptation index value, which was then included in the cloning vector pET2+ (a). Altogether, our experiment implies that the proposed peptide vaccine might be a good option for vibriosis prophylaxis.
{"title":"Designing a novel mRNA vaccine against Vibrio harveyi infection in fish: an immunoinformatics approach","authors":"Sk Injamamul Islam, Moslema Jahan Mou, Saloa Sanjida, Muhammad Tariq, Saad Nasir, Sarower Mahfuj","doi":"10.5808/gi.21065","DOIUrl":"https://doi.org/10.5808/gi.21065","url":null,"abstract":"Vibrio harveyi belongs to the family Vibrionaceae of class Gammaproteobacteria. Around 12 Vibrio species can cause gastroenteritis (gastrointestinal illness) in humans. A large number of bacterial particles can be found in the infected cells, which may cause death. Despite these devastating complications, there is still no cure or vaccine for the bacteria. As a result, we used an immunoinformatics approach to develop a multi-epitope vaccine against the most pathogenic hemolysin gene of V. harveyi. The immunodominant T- and B-cell epitopes were identified using the hemolysin protein. We developed a vaccine employing three possible epitopes: cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocyte epitopes, after thorough testing. The vaccine was developed to be antigenic, immunogenic, and non-allergenic, as well as have a better solubility. Molecular dynamics simulation revealed significant structural stiffness and binding stability. In addition, the immunological simulation generated by computers revealed that the vaccination might elicit immune reactions Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher codon adaptation index value, which was then included in the cloning vector pET2+ (a). Altogether, our experiment implies that the proposed peptide vaccine might be a good option for vibriosis prophylaxis.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43799386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
NorJasmin Hussin, I. A. Azmir, Y. Esa, A. Ahmad, Faezah Mohd Salleh, P. N. S. Jahari, K. Munian, H. Gan
The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.
对世界上最小的鲤科鱼——原基因幼鱼(Paedocypris progenetica)的两个线粒体全基因组进行了测序和组装。有丝分裂基因组P1-P的环状DNA分子。progenetica和S3-P。原基因体长度分别为16,827和16,616 bp，编码13个蛋白质编码基因、22个转移RNA基因、2个核糖体RNA基因和1个控制区。progenetica的基因排列与其他Paedocypris种相同。BLAST和系统发育分析显示，来自霹雳州和雪兰莪州的两种Paedocypris有丝分裂基因组序列存在差异。P. progenetica的环状DNA分子产生标准的脊椎动物基因排列，总核苷酸组成为a 33.0%， T 27.2%， C 23.5%， G 15.5%。该种的总AT含量与其他属其他种一致。黄杨对照区gc -负偏和AT-正偏分别显示丰富的遗传变异性和AT核苷酸偏倚。本研究结果提供了基因组变异信息，增强了对原遗传假单胞虫有丝分裂基因组的认识。之后，它们可以为系统发育分析和群体遗传学数据提供非常有价值的新见解。
{"title":"Characterization of the first mitogenomes of the smallest fish in the world, Paedocypris progenetica, from peat swamp of Peninsular Malaysia, Selangor, and Perak","authors":"NorJasmin Hussin, I. A. Azmir, Y. Esa, A. Ahmad, Faezah Mohd Salleh, P. N. S. Jahari, K. Munian, H. Gan","doi":"10.5808/gi.21081","DOIUrl":"https://doi.org/10.5808/gi.21081","url":null,"abstract":"The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46106618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Human exposure to pollutants has been on the rise. Thus, researchers have been focused on understanding the effect of these compounds on human health, especially on the genetic information by using various tests, among them the somatic mutation and recombination tests (SMARTs). It is a sensitive and accurate method applicable to genotoxicity analysis. Here, a comprehensive bibliometric analysis of SMART assays in genotoxicity studies was performed to assess publication trends of this field. Data were extracted from the Web of Science database and analyzed by the bibliometric tools HistCite, Biblioshiny (RStudio), VOSViewer, and CiteSpace. Results have shown an increase in the last 10 years in terms of publication. A total of 392 records were published in 96 sources mainly from Brazil, Spain, and Turkey. Research collaboration networks between countries and authors were performed. Based on document co-citation, five large research clusters were identified and analyzed. The youngest research frontier emphasized on nanoparticles. With this study, how research trends evolve over years was demonstrated. Thus, international collaboration could be enhanced, and a promising field could be developed.
人类接触污染物的程度一直在上升。因此，研究人员一直致力于通过各种测试了解这些化合物对人类健康的影响，特别是对遗传信息的影响，其中包括体细胞突变和重组测试(SMARTs)。它是一种灵敏、准确的遗传毒性分析方法。本文对遗传毒性研究中的SMART分析进行了全面的文献计量学分析，以评估该领域的发表趋势。数据从Web of Science数据库中提取，并通过文献计量工具HistCite、Biblioshiny (RStudio)、VOSViewer和CiteSpace进行分析。结果显示，在过去10年里，论文发表量有所增加。共发表了392条记录，主要来自巴西、西班牙和土耳其的96个来源。在国家和作者之间建立了研究协作网络。基于文献共被引，确定并分析了5个大型研究集群。最年轻的研究前沿是纳米颗粒。这项研究展示了多年来研究趋势的演变。因此，可以加强国际合作，并可以发展一个有前途的领域。
{"title":"Publication trends of somatic mutation and recombination tests research: a bibliometric analysis (1984‒2020)","authors":"Ghada Tagorti, B. Kaya","doi":"10.5808/gi.21083","DOIUrl":"https://doi.org/10.5808/gi.21083","url":null,"abstract":"Human exposure to pollutants has been on the rise. Thus, researchers have been focused on understanding the effect of these compounds on human health, especially on the genetic information by using various tests, among them the somatic mutation and recombination tests (SMARTs). It is a sensitive and accurate method applicable to genotoxicity analysis. Here, a comprehensive bibliometric analysis of SMART assays in genotoxicity studies was performed to assess publication trends of this field. Data were extracted from the Web of Science database and analyzed by the bibliometric tools HistCite, Biblioshiny (RStudio), VOSViewer, and CiteSpace. Results have shown an increase in the last 10 years in terms of publication. A total of 392 records were published in 96 sources mainly from Brazil, Spain, and Turkey. Research collaboration networks between countries and authors were performed. Based on document co-citation, five large research clusters were identified and analyzed. The youngest research frontier emphasized on nanoparticles. With this study, how research trends evolve over years was demonstrated. Thus, international collaboration could be enhanced, and a promising field could be developed.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48753660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
2022 Korea Genome Organization This is an open-access article distributed under the terms of the Creative Commons Attribution license (http://creativecommons. org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In this issue, there are two review articles, eight original articles, one genome archive, and two application notes. In this editorial, I would like to focus on the two review articles, as well as two original articles and one application note on genome-wide association studies (GWAS). Recent rapid advances in single-cell RNA sequencing have made it possible to recognize a variety of previously unidentified subpopulations and rare cell states in tumors and the immune system based on single-cell gene expression profiles. Single-cell RNA sequencing is the topic of the first review article, by Dr. Jong-Il Kim’s group (Seoul National University College of Medicine, Korea). This review addresses the current development of methods for constructing single-cell epigenomic libraries, including multi-omics tools with important elements and additional requirements for the future, focusing on DNA methylation, chromatin accessibility, and histone post-translational modification. Single-cell epigenomic libraries help to understand the principles of comprehensive gene regulation that determine cell fate through transcripts alone and the resulting output of gene expression programs. The corresponding single-cell epigenome is expected to elucidate the mechanisms involved in the origin and maintenance of a comprehensive single-cell transcriptome. This review insightfully summarizes current research trends in the field of cellular differentiation and disease development at the single-cell level, moving toward the single-cell epigenome. The second review, led by Dr. Tung (Dagon University, Myanmar), deals with recent developments in whole-genome sequencing technologies. While the analysis of whole-genome sequencing data requires highly sophisticated bioinformatics tools, many researchers do not have the bioinformatics capabilities to analyze the genomic data and are therefore unable to take maximum advantage of whole-genome sequencing. This review provides a practical guide on a set of bioinformatics tools available online to analyze whole-genome sequence data of bacterial genomes and presents a description of their web interfaces. Now, I would like to turn to three articles about GWAS. The main goal of GWAS is the identification of causal variants associated with the phenotype of interest. All GWAS introduce appropriate statistical models to explain the phenotype and then to perform statistical tests. An important challenge in this post-GWAS era is to increase statistical power by using better statistical models and tests, and to investigate the causal effects between modifiable risk factors and the phenotypes via Mendelian randomization (MR). The first article, t
{"title":"Editor’s introduction to this issue (G&I 20:1, 2022)","authors":"Taesung Park","doi":"10.5808/gi.20.1.e1","DOIUrl":"https://doi.org/10.5808/gi.20.1.e1","url":null,"abstract":"2022 Korea Genome Organization This is an open-access article distributed under the terms of the Creative Commons Attribution license (http://creativecommons. org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In this issue, there are two review articles, eight original articles, one genome archive, and two application notes. In this editorial, I would like to focus on the two review articles, as well as two original articles and one application note on genome-wide association studies (GWAS). Recent rapid advances in single-cell RNA sequencing have made it possible to recognize a variety of previously unidentified subpopulations and rare cell states in tumors and the immune system based on single-cell gene expression profiles. Single-cell RNA sequencing is the topic of the first review article, by Dr. Jong-Il Kim’s group (Seoul National University College of Medicine, Korea). This review addresses the current development of methods for constructing single-cell epigenomic libraries, including multi-omics tools with important elements and additional requirements for the future, focusing on DNA methylation, chromatin accessibility, and histone post-translational modification. Single-cell epigenomic libraries help to understand the principles of comprehensive gene regulation that determine cell fate through transcripts alone and the resulting output of gene expression programs. The corresponding single-cell epigenome is expected to elucidate the mechanisms involved in the origin and maintenance of a comprehensive single-cell transcriptome. This review insightfully summarizes current research trends in the field of cellular differentiation and disease development at the single-cell level, moving toward the single-cell epigenome. The second review, led by Dr. Tung (Dagon University, Myanmar), deals with recent developments in whole-genome sequencing technologies. While the analysis of whole-genome sequencing data requires highly sophisticated bioinformatics tools, many researchers do not have the bioinformatics capabilities to analyze the genomic data and are therefore unable to take maximum advantage of whole-genome sequencing. This review provides a practical guide on a set of bioinformatics tools available online to analyze whole-genome sequence data of bacterial genomes and presents a description of their web interfaces. Now, I would like to turn to three articles about GWAS. The main goal of GWAS is the identification of causal variants associated with the phenotype of interest. All GWAS introduce appropriate statistical models to explain the phenotype and then to perform statistical tests. An important challenge in this post-GWAS era is to increase statistical power by using better statistical models and tests, and to investigate the causal effects between modifiable risk factors and the phenotypes via Mendelian randomization (MR). The first article, t","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49173955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kyunghyuk Park, Min Chul Jeon, Bokyung Kim, Bukyoung Cha, Jong-Il Kim
The method of single-cell RNA sequencing has been rapidly developed, and numerous experiments have been conducted over the past decade. Their results allow us to recognize various subpopulations and rare cell states in tissues, tumors, and immune systems that are previously unidentified, and guide us to understand fundamental biological processes that determine cell identity based on single-cell gene expression profiles. However, it is still challenging to understand the principle of comprehensive gene regulation that determines the cell fate only with transcriptome, a consequential output of the gene expression program. To elucidate the mechanisms related to the origin and maintenance of comprehensive single-cell transcriptome, we require a corresponding single-cell epigenome, which is a differentiated information of each cell with an identical genome. This review deals with the current development of single-cell epigenomic library construction methods, including multi-omics tools with crucial factors and additional requirements in the future focusing on DNA methylation, chromatin accessibility, and histone post-translational modifications. The study of cellular differentiation and the disease occurrence at a single-cell level has taken the first step with single-cell transcriptome and is now taking the next step with single-cell epigenome.
{"title":"Experimental development of the epigenomic library construction method to elucidate the epigenetic diversity and causal relationship between epigenome and transcriptome at a single-cell level","authors":"Kyunghyuk Park, Min Chul Jeon, Bokyung Kim, Bukyoung Cha, Jong-Il Kim","doi":"10.5808/gi.21078","DOIUrl":"https://doi.org/10.5808/gi.21078","url":null,"abstract":"The method of single-cell RNA sequencing has been rapidly developed, and numerous experiments have been conducted over the past decade. Their results allow us to recognize various subpopulations and rare cell states in tissues, tumors, and immune systems that are previously unidentified, and guide us to understand fundamental biological processes that determine cell identity based on single-cell gene expression profiles. However, it is still challenging to understand the principle of comprehensive gene regulation that determines the cell fate only with transcriptome, a consequential output of the gene expression program. To elucidate the mechanisms related to the origin and maintenance of comprehensive single-cell transcriptome, we require a corresponding single-cell epigenome, which is a differentiated information of each cell with an identical genome. This review deals with the current development of single-cell epigenomic library construction methods, including multi-omics tools with crucial factors and additional requirements in the future focusing on DNA methylation, chromatin accessibility, and histone post-translational modifications. The study of cellular differentiation and the disease occurrence at a single-cell level has taken the first step with single-cell transcriptome and is now taking the next step with single-cell epigenome.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44772237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Loss of heterozygosity (LOH) is a genomic aberration. In some cases, LOH can be generated without changing the copy number, which is called copy-neutral LOH (CN-LOH). CN-LOH frequently occurs in various human diseases, including cancer. However, the biological and clinical implications of CN-LOH for human diseases have not been well studied. In this study, we compared the performance of CN-LOH determination using three commonly used tools. For an objective comparison, we analyzed CN-LOH profiles from single-nucleotide polymorphism array data from 10 colon adenocarcinoma patients, which were used as the reference for comparison with the CN-LOHs obtained through whole-exome sequencing (WES) data of the same patients using three different analysis tools (FACETS, Nexus, and Sequenza). The majority of the CN-LOHs identified from the WES data were consistent with the reference data. However, some of the CN-LOHs identified from the WES data were not consistent between the three tools, and the consistency with the reference CN-LOH profile was also different. The Jaccard index of the CN-LOHs using FACETS (0.84 ± 0.29; mean value, 0.73) was significantly higher than that of Nexus (0.55 ± 0.29; mean value, 0.50; p = 0.02) or Sequenza (0 ± 0.41; mean value, 0.34; p = 0.04). FACETS showed the highest area under the curve value. Taken together, of the three CN-LOH analysis tools, FACETS showed the best performance in identifying CN-LOHs from The Cancer Genome Atlas colon adenocarcinoma WES data. Our results will be helpful in exploring the biological or clinical implications of CN-LOH for human diseases.
{"title":"Comparison of the copy-neutral loss of heterozygosity identified from whole-exome sequencing data using three different tools","authors":"Gang-Taik Lee, Y. Chung","doi":"10.5808/gi.21066","DOIUrl":"https://doi.org/10.5808/gi.21066","url":null,"abstract":"Loss of heterozygosity (LOH) is a genomic aberration. In some cases, LOH can be generated without changing the copy number, which is called copy-neutral LOH (CN-LOH). CN-LOH frequently occurs in various human diseases, including cancer. However, the biological and clinical implications of CN-LOH for human diseases have not been well studied. In this study, we compared the performance of CN-LOH determination using three commonly used tools. For an objective comparison, we analyzed CN-LOH profiles from single-nucleotide polymorphism array data from 10 colon adenocarcinoma patients, which were used as the reference for comparison with the CN-LOHs obtained through whole-exome sequencing (WES) data of the same patients using three different analysis tools (FACETS, Nexus, and Sequenza). The majority of the CN-LOHs identified from the WES data were consistent with the reference data. However, some of the CN-LOHs identified from the WES data were not consistent between the three tools, and the consistency with the reference CN-LOH profile was also different. The Jaccard index of the CN-LOHs using FACETS (0.84 ± 0.29; mean value, 0.73) was significantly higher than that of Nexus (0.55 ± 0.29; mean value, 0.50; p = 0.02) or Sequenza (0 ± 0.41; mean value, 0.34; p = 0.04). FACETS showed the highest area under the curve value. Taken together, of the three CN-LOH analysis tools, FACETS showed the best performance in identifying CN-LOHs from The Cancer Genome Atlas colon adenocarcinoma WES data. Our results will be helpful in exploring the biological or clinical implications of CN-LOH for human diseases.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41856398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Non-syndromic hearing loss (NSHL) is a common hereditary disorder. Both clinical and genetic heterogeneity has created many obstacles to understanding the causes of NSHL. The present study has attempted to ravel the genetic aetiology in NSHL progression and to screen out potential target genes using computational approaches. The reported NSHL target genes (2009‒2020) have been studied by analyzing different biochemical and signaling pathways, interpretation of their functional association network, and discovery of important regulatory interactions with three previously established miRNAs in the human inner ear as well as in NSHL such as miR-183, miR-182, and miR-96. This study has identified SMAD4 and SNAI2 as the most putative target genes of NSHL. But pathogenic and deleterious non-synonymous single nucleotide polymorphisms discovered within SMAD4 is anticipated to have an impact on NSHL progression. Additionally, the identified deleterious variants in the functional domains of SMAD4 added a supportive clue for further study. Thus, the identified deleterious variant i.e., rs377767367 (G491V) in SMAD4 needs further clinical validation. The present outcomes would provide insights into the genetics of NSHL progression.
{"title":"Presentation of potential genes and deleterious variants associated with non-syndromic hearing loss: a computational approach","authors":"Manisha Ray, S. Rath, S. Sarkar, M. Sable","doi":"10.5808/gi.21070","DOIUrl":"https://doi.org/10.5808/gi.21070","url":null,"abstract":"Non-syndromic hearing loss (NSHL) is a common hereditary disorder. Both clinical and genetic heterogeneity has created many obstacles to understanding the causes of NSHL. The present study has attempted to ravel the genetic aetiology in NSHL progression and to screen out potential target genes using computational approaches. The reported NSHL target genes (2009‒2020) have been studied by analyzing different biochemical and signaling pathways, interpretation of their functional association network, and discovery of important regulatory interactions with three previously established miRNAs in the human inner ear as well as in NSHL such as miR-183, miR-182, and miR-96. This study has identified SMAD4 and SNAI2 as the most putative target genes of NSHL. But pathogenic and deleterious non-synonymous single nucleotide polymorphisms discovered within SMAD4 is anticipated to have an impact on NSHL progression. Additionally, the identified deleterious variants in the functional domains of SMAD4 added a supportive clue for further study. Thus, the identified deleterious variant i.e., rs377767367 (G491V) in SMAD4 needs further clinical validation. The present outcomes would provide insights into the genetics of NSHL progression.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46711857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.
{"title":"Whole-genome sequence analysis through online web interfaces: a review","authors":"A. Gunasekara, L. Rajapaksha, T. Tung","doi":"10.5808/gi.20038","DOIUrl":"https://doi.org/10.5808/gi.20038","url":null,"abstract":"The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48200666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Despite the success of recent genome-wide association studies investigating longitudinal traits, a large fraction of overall heritability remains unexplained. This suggests that some of the missing heritability may be accounted for by gene-gene and gene-time/environment interactions. In this paper, we develop a Bayesian variable selection method for longitudinal genetic data based on mixed models. The method jointly models the main effects and interactions of all candidate genetic variants and non-genetic factors and has higher statistical power than previous approaches. To account for the within-subject dependence structure, we propose a grid-based approach that models only one fixed-dimensional covariance matrix, which is thus applicable to data where subjects have different numbers of time points. We provide the theoretical basis of our Bayesian method and then illustrate its performance using data from the 1000 Genome Project with various simulation settings. Several simulation studies show that our multivariate method increases the statistical power compared to the corresponding univariate method and can detect gene-time/environment interactions well. We further evaluate our method with different numbers of individuals, variants, and causal variants, as well as different trait-heritability, and conclude that our method performs reasonably well with various simulation settings.
{"title":"Bayesian mixed models for longitudinal genetic data: theory, concepts, and simulation studies","authors":"Wonil Chung, Youngkwan Cho","doi":"10.5808/gi.21080","DOIUrl":"https://doi.org/10.5808/gi.21080","url":null,"abstract":"Despite the success of recent genome-wide association studies investigating longitudinal traits, a large fraction of overall heritability remains unexplained. This suggests that some of the missing heritability may be accounted for by gene-gene and gene-time/environment interactions. In this paper, we develop a Bayesian variable selection method for longitudinal genetic data based on mixed models. The method jointly models the main effects and interactions of all candidate genetic variants and non-genetic factors and has higher statistical power than previous approaches. To account for the within-subject dependence structure, we propose a grid-based approach that models only one fixed-dimensional covariance matrix, which is thus applicable to data where subjects have different numbers of time points. We provide the theoretical basis of our Bayesian method and then illustrate its performance using data from the 1000 Genome Project with various simulation settings. Several simulation studies show that our multivariate method increases the statistical power compared to the corresponding univariate method and can detect gene-time/environment interactions well. We further evaluate our method with different numbers of individuals, variants, and causal variants, as well as different trait-heritability, and conclude that our method performs reasonably well with various simulation settings.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41453021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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