Genomics and Informatics最新文献

{"title":"Development of reverse-transcription loop-mediated isothermal amplification assays for point-of-care testing of human influenza virus subtypes H1N1 and H3N2.","authors":"Ji-Soo Kang, Mi-Ran Seo, Yeun-Jun Chung","doi":"10.5808/gi.22057","DOIUrl":"10.5808/gi.22057","url":null,"abstract":"<p><p>Influenza A virus (IAV) is the most widespread pathogen causing human respiratory infections. Although polymerase chain reaction (PCR)-based methods are currently the mostcommonly used tools for IAV detection, PCR is not ideal for point-of-care testing. In thisstudy, we aimed to develop a more rapid and sensitive method than PCR-based tools todetect IAV using loop-mediated isothermal amplification (LAMP) technology. We designedreverse-transcriptional (RT)-LAMP primers targeting the hemagglutinin gene. RNAs fromreference H1N1 and H3N2 showed specific RT-LAMP signals with the designed primers.We optimized the reaction conditions and developed universal reaction conditions for bothLAMP assays. Under these conditions, the detection limit was 50 copies for both RT-LAMPassays. There was no non-specific signal to 19 non-IAV respiratory viruses, such as influenza B virus, coronaviruses, and respiratory syncytial viruses. Regarding the reaction time, apositive signal was detected within 25 min after starting the reaction. In conclusion, ourRT-LAMP assay has high sensitivity and specificity for the detection of the H1 and H3 subtypes, making it suitable for point-of-care IAV testing.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e46"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10591858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MP-LASSO chart: a multi-level polar chart for visualizing group LASSO analysis of genomic data.","authors":"Min Song,&nbsp;Minhyuk Lee,&nbsp;Taesung Park,&nbsp;Mira Park","doi":"10.5808/gi.22075","DOIUrl":"https://doi.org/10.5808/gi.22075","url":null,"abstract":"<p><p>Penalized regression has been widely used in genome-wide association studies for jointanalyses to find genetic associations. Among penalized regression models, the least absolute shrinkage and selection operator (Lasso) method effectively removes some coefficientsfrom the model by shrinking them to zero. To handle group structures, such as genes andpathways, several modified Lasso penalties have been proposed, including group Lasso andsparse group Lasso. Group Lasso ensures sparsity at the level of pre-defined groups, eliminating unimportant groups. Sparse group Lasso performs group selection as in group Lasso,but also performs individual selection as in Lasso. While these sparse methods are useful inhigh-dimensional genetic studies, interpreting the results with many groups and coefficients is not straightforward. Lasso's results are often expressed as trace plots of regressioncoefficients. However, few studies have explored the systematic visualization of group information. In this study, we propose a multi-level polar Lasso (MP-Lasso) chart, which caneffectively represent the results from group Lasso and sparse group Lasso analyses. An Rpackage to draw MP-Lasso charts was developed. Through a real-world genetic data application, we demonstrated that our MP-Lasso chart package effectively visualizes the resultsof Lasso, group Lasso, and sparse group Lasso.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e48"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9156897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family.","authors":"Satyabrata Sahoo,&nbsp;Ria Rakshit","doi":"10.5808/gi.22045","DOIUrl":"https://doi.org/10.5808/gi.22045","url":null,"abstract":"<p><p>Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, which are frequently utilized in therapeutic practice. In this study, bioinformaticmethodologies were used to examine the pattern of coding sequences and the factors thatmight influence codon usage bias in the chloroplast genome of Atropa belladonna andother nightshade genomes. The chloroplast engineering being a promising field in modernbiotechnology, the characterization of chloroplast genome is very important. The resultsrevealed that the chloroplast genomes of Nicotiana tabacum, Solanum lycopersicum, Capsicum frutescens, Datura stramonium, Lyciumbarbarum, Solanum melongena, and Solanumtuberosum exhibited comparable codon usage patterns. In these chloroplast genomes, weobserved a weak codon usage bias. According to the correspondence analysis, the genesisof the codon use bias in these chloroplast genes might be explained by natural selection,directed mutational pressure, and other factors. GC12 and GC3S were shown to have nomeaningful relationship. Further research revealed that natural selection primarily shapedthe codon usage in A. belladonna and other nightshade genomes for translational efficiency. The sequencing properties of these chloroplast genomes were also investigated by investing the occurrences of palindromes and inverted repeats, which would be useful forfuture research on medicinal plants.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e43"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10582629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial resistance in Klebsiella pneumoniae: identification of bacterial DNA adenine methyltransferase as a novel drug target from hypothetical proteins using subtractive genomics.","authors":"Umairah Natasya Mohd Omeershffudin,&nbsp;Suresh Kumar","doi":"10.5808/gi.22067","DOIUrl":"https://doi.org/10.5808/gi.22067","url":null,"abstract":"<p><p>Klebsiella pneumoniae is a gram-negative bacterium that is known for causing infection innosocomial settings. As reported by the World Health Organization, carbapenem-resistantEnterobacteriaceae, a category that includes K. pneumoniae, are classified as an urgentthreat, and the greatest concern is that these bacterial pathogens may acquire genetictraits that make them resistant towards antibiotics. The last class of antibiotics, carbapenems, are not able to combat these bacterial pathogens, allowing them to clonally expandantibiotic-resistant strains. Most antibiotics target essential pathways of bacterial cells;however, these targets are no longer susceptible to antibiotics. Hence, in our study, we focused on a hypothetical protein in K. pneumoniae that contains a DNA methylation proteindomain, suggesting a new potential site as a drug target. DNA methylation regulates theattenuation of bacterial virulence. We integrated computational-aided drug design by using a bioinformatics approach to perform subtractive genomics, virtual screening, and fingerprint similarity search. We identified a new potential drug, koenimbine, which could bea novel antibiotic.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e47"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9156896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The relationship of E-selectin singlenucleotide polymorphisms with breast cancer in Iraqi Arab women.","authors":"Bilal Fadıl Zakariya,&nbsp;Asmaa M Salih Almohaidi,&nbsp;Seçil Akıllı Şimşek,&nbsp;Safaa A Al-Waysi,&nbsp;Wijdan H Al-Dabbagh,&nbsp;Areege Mustafa Kamal","doi":"10.5808/gi.22042","DOIUrl":"https://doi.org/10.5808/gi.22042","url":null,"abstract":"<p><p>Breast cancer (BC) is a significant threat to female health, with both modifiable andnon-modifiable risk factors. It is essential to monitor patients regularly and to raise population awareness. Increasing research also suggests that E-selectin (SELE) may increase tumor angiogenesis and the development of cancer. This study investigated SELE single-nucleotide polymorphisms (SNPs) in the following positions: rs5367T/C, rs5368C/T, rs5362T/G,and rs5362T/C. Using polymerase chain reaction, significant differences in allele and genotype frequencies were found between BC patients and controls. Position rs5368 was associated with an increased risk of BC for the CT and TT genotypes, with odds ratios (ORs) of16.3 and 6.90 (Fisher probability = 0.0001, p = 0.005). Women with the T allele had a 19.3-fold higher incidence of BC, while allele C may be a protective allele against BC (OR, 0.05).Heterozygous genotypes at rs5367, rs5362, and rs5362 were significantly more common inBC patients, with ORs of 5.70, 4.50, and 3.80, respectively. These SNPs may be associatedwith the risk of BC, because the frequency of mutant alleles was significantly higher in patients (OR: 4.26, 3.83, and 4.30, respectively) than in controls (OR: 0.23, 0.30, and 0.20, respectively). These SNPs may be considered a common genotype in the Iraqi population,with the wild-type allele having a protective fraction and the mutant allele having an environmental fraction. The results also revealed a 2-fold increase in gene expression in BCpatients compared to controls, with a significant effect (p = 0.017). This study's findingsconfirm the importance of SELE polymorphisms in cancer risk prediction.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e42"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10591859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editor's introduction to this issue (G&I 20:4, 2022).","authors":"Taesung Park","doi":"10.5808/gi.20.4.e1","DOIUrl":"https://doi.org/10.5808/gi.20.4.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, and one application note. Three of these articles are related to genetic association studies. The first review article, by J. Ott (Rockefeller University, New York, USA) and T. Park (Seoul National University, Seoul, Korea), is about frequent pattern mining (FPM) analysis. FPM has been widely applied to genetic problems, specifically to the combined association of two genotypes at different DNA variants with diseases. FPM methods have the ability to select genotype patterns that are distinct between cases and controls. In particular, FPM has been quite effective for gene-gene interaction (GGI) analysis. For example, the multifactor dimensionality reduction (MDR) method is a representative FPM method for detecting GGIs. Since its first introduction, MDR has been popularly used for GGI analyses. One of the challenges in FPM is to assess the statistical significance of these selected patterns, which requires a heavy computational burden and suffers from the issue of multiple comparisons. This review discussed these issues in a reasonable way. The second article, by M. Park’s group (Eulji University, Daejeon, Korea), proposes the multi-level polar Lasso (MP-Lasso) chart, which is a visualization tool to summarize the results of group Lasso and sparse group Lasso. In large-scale genetic association studies a set of important markers should be selected simultaneously. In these cases, penalized regression has been widely used in genome-wide association studies (GWAS). Among penalized regression models, Lasso effectively selects some important markers for the model by shrinking unimportant markers toward zero. Group Lasso and sparse group Lasso have been proposed to take into account the structures of groups, such as genes and pathways. Group Lasso selects some important groups of markers from the model and eliminates unimportant groups, thereby ensuring sparsity at the level of pre-defined groups. As in group Lasso, sparse group Lasso performs group selection, but also individual selection as well. Although these sparse methods are useful for high-dimensional genetic studies, interpreting the results with many groups and coefficients is not easy. Trace plots of the regression coefficients are commonly used to present Lasso results. However, studies that systematically visualize group information are rare. In this article, the authors propose an MP-Lasso chart that can effectively express the results of group Lasso and sparse group Lasso analyses. An R package for drawing MP-Lasso charts was developed. Through real data applications, the authors demonstrate the usefulness of the MP-La","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e38"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10582626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of data fusion modeling for the prediction of auxin response elements in Zea mays for food security purposes.","authors":"Nesrine Sghaier,&nbsp;Rayda Ben Ayed,&nbsp;Ahmed Rebai","doi":"10.5808/gi.22056","DOIUrl":"https://doi.org/10.5808/gi.22056","url":null,"abstract":"<p><p>Food security will be affected by climate change worldwide, particularly in the developingworld, where the most important food products originate from plants. Plants are often exposed to environmental stresses that may affect their growth, development, yield, and foodquality. Auxin is a hormone that plays a critical role in improving plants' tolerance of environmental conditions. Auxin controls the expression of many stress-responsive genes inplants by interacting with specific cis-regulatory elements called auxin-responsive elements (AuxREs). In this work, we performed an in silico prediction of AuxREs in promotersof five auxin-responsive genes in Zea mays. We applied a data fusion approach based onthe combined use of Dempster-Shafer evidence theory and fuzzy sets. Auxin has a directimpact on cell membrane proteins. The short-term auxin response may be represented bythe regulation of transmembrane gene expression. The detection of an AuxRE in the promoter of prolyl oligopeptidase (POP) in Z. mays and the 3-fold overexpression of this geneunder auxin treatment for 30 min indicated the role of POP in maize auxin response. POP isregulated by auxin to perform stress adaptation. In addition, the detection of two AuxRETGTCTC motifs in the upstream sequence of the bx1 gene suggests that bx1 can be regulated by auxin. Auxin may also be involved in the regulation of dehydration-responsive element-binding and some members of the protein kinase superfamily.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e45"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847374/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10591855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overview of frequent pattern mining.","authors":"Jurg Ott,&nbsp;Taesung Park","doi":"10.5808/gi.22074","DOIUrl":"https://doi.org/10.5808/gi.22074","url":null,"abstract":"<p><p>Various methods of frequent pattern mining have been applied to genetic problems, specifically, to the combined association of two genotypes (a genotype pattern, or diplotype) at different DNA variants with disease. These methods have the ability to come up with a selection of genotype patterns that are more common in affected than unaffected individuals, and the assessment of statistical significance for these selected patterns poses some unique problems, which are briefly outlined here.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 4","pages":"e39"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9847378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10582628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NBLAST: a graphical user interface-based two-way BLAST software with a dot plot viewer.","authors":"Jatindra Nath Mohanty, Swayamprabha Sahoo, Puspanjali Mishra","doi":"10.5808/gi.21075","DOIUrl":"10.5808/gi.21075","url":null,"abstract":"<p><p>BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as \"query\" or \"target\" in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.</p>","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"20 3","pages":"e40"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9576473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10494940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editor's introduction to this issue (G&I 20:3, 2022).","authors":"Taesung Park","doi":"10.5808/gi.20.3.e1","DOIUrl":"https://doi.org/10.5808/gi.20.3.e1","url":null,"abstract":"miRNAs and genes, sig-nificantly involved in the etiology of early-stage OSCC. The authors identified a total of 23 differentially expressed miRNAs in patients with primary OSCC compared to the healthy controls, which targeted genes including CALM1, CYCS, THBS1, MYC, GATA6, SPRED3, PIK3R3, GIGYF1 , and BCL2L11 . The present study revealed a possible mech-anism mediating primary OSCC and may be useful for predicting the prognosis of patients with early-stage OSCC. Dr. presented a clinical, laboratory, and genetic study of a pathogenic variant of the CYP1B1 gene using whole-exome sequencing data from a rare case of primary congenital glaucoma. Dr. Rha (Yonsei University College of Medicine, Korea) and colleagues evaluated the frequencies of UGT1A polymorphisms and their relationship with clinicopathologic parameters in 382 Korean gastric cancer patients. Polymorphisms of UGT1A1*6, UGT1A1*27, UGT1A1*28, UGT1A1*60, UG-T1A7*2, UGT1A7*3 , and UGT1A9*22 were genotyped. While many clinically important findings were made, the most clinically important finding was about UGT1A9*22 . The genotype of UGT1A9*22 polymorphisms was shown to identify high-risk patients, among gastric cancer patients receiving irinotecan-containing chemotherapy and suffering severe","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":" ","pages":"e25"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9576477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33538774","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}