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The interaction between gut microbiome and nutrients on development of human disease through epigenetic mechanisms 肠道微生物群和营养物质通过表观遗传机制在人类疾病发展中的相互作用
Genomics & informatics Pub Date : 2019-09-01 DOI: 10.5808/GI.2019.17.3.e24
Ho-Sun Lee
{"title":"The interaction between gut microbiome and nutrients on development of human disease through epigenetic mechanisms","authors":"Ho-Sun Lee","doi":"10.5808/GI.2019.17.3.e24","DOIUrl":"https://doi.org/10.5808/GI.2019.17.3.e24","url":null,"abstract":"Early environmental exposure is recognized as a key factor for long-term health based on the Developmental Origins of Health and Disease hypothesis. It considers that early-life nutrition is now being recognized as a major contributor that may permanently program change of organ structure and function toward the development of diseases, in which epigenetic mechanisms are involved. Recent researches indicate early-life environmental factors modulate the microbiome development and the microbiome might be mediate diet-epigenetic interaction. This review aims to define which nutrients involve microbiome development during the critical window of susceptibility to disease, and how microbiome modulation regulates epigenetic changes and influences human health and future prevention strategies.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42891114","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}
引用次数: 12
Editor’s introduction to this issue (G&I 17:3, 2019) 编者对本期的介绍(G&I 17:3, 2019)
Genomics & informatics Pub Date : 2019-09-01 DOI: 10.5808/GI.2019.17.3.e22
T. Park
{"title":"Editor’s introduction to this issue (G&I 17:3, 2019)","authors":"T. Park","doi":"10.5808/GI.2019.17.3.e22","DOIUrl":"https://doi.org/10.5808/GI.2019.17.3.e22","url":null,"abstract":"","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47288740","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}
引用次数: 0
Direct-to-consumer genetic testing: advantages and pitfalls. 直接面向消费者的基因检测：优点和缺点。
Genomics & informatics Pub Date : 2019-09-01 Epub Date: 2019-09-26 DOI: 10.5808/GI.2019.17.3.e33
Bermseok Oh
{"title":"Direct-to-consumer genetic testing: advantages and pitfalls.","authors":"Bermseok Oh","doi":"10.5808/GI.2019.17.3.e33","DOIUrl":"https://doi.org/10.5808/GI.2019.17.3.e33","url":null,"abstract":"<p><p></p>","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"17 3","pages":"e33"},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6808639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41224610","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: 10
De novo transcriptome sequencing and gene expression profiling with/without B-chromosome plants of Lilium amabile 带/不带B染色体植物的无芒百合从头转录组测序和基因表达谱
Genomics & informatics Pub Date : 2019-09-01 DOI: 10.5808/gi.2019.17.3.e27
Doori Park, Jong-Hwa Kim, Nam-Soo Kim
{"title":"De novo transcriptome sequencing and gene expression profiling with/without B-chromosome plants of Lilium amabile","authors":"Doori Park, Jong-Hwa Kim, Nam-Soo Kim","doi":"10.5808/gi.2019.17.3.e27","DOIUrl":"https://doi.org/10.5808/gi.2019.17.3.e27","url":null,"abstract":"Supernumerary B chromosomes were found in Lilium amabile (2n = 2x = 24), an endemic Korean lily that grows in the wild throughout the Korean Peninsula. The extra B chromosomes do not affect the host-plant morphology; therefore, whole transcriptome analysis was performed in 0B and 1B plants to identify differentially expressed genes. A total of 154,810 transcripts were obtained from over 10 Gbp data by de novo assembly. By mapping the raw reads to the de novo transcripts, we identified 7,852 differentially expressed genes (log2FC > |10|), in which 4,059 and 3,794 were up-and down-regulated, respectively, in 1B plants compared to 0B plants. Functional enrichment analysis revealed that various differentially expressed genes were involved in cellular processes including the cell cycle, chromosome breakage and repair, and microtubule formation; all of which may be related to the occurrence and maintenance of B chromosomes. Our data provide insight into transcriptomic changes and evolution of plant B chromosomes and deliver an informative database for future study of B chromosome transcriptomes in the Korean lily.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45989871","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}
引用次数: 5
Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasets 两组惠康基金会病例控制联盟对照数据的人白细胞抗原差异分析
Genomics & informatics Pub Date : 2019-09-01 DOI: 10.5808/gi.2019.17.3.e29
Chloe Soohyun Jang, Wanson Choi, Seungho Cook, B. Han
{"title":"Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasets","authors":"Chloe Soohyun Jang, Wanson Choi, Seungho Cook, B. Han","doi":"10.5808/gi.2019.17.3.e29","DOIUrl":"https://doi.org/10.5808/gi.2019.17.3.e29","url":null,"abstract":"The Wellcome Trust Case Control Consortium (WTCCC) study was a large genome-wide association study that aimed to identify common variants associated with seven diseases. That study combined two control datasets (58C and UK Blood Services) as shared controls. Prior to using the combined controls, the WTCCC performed analyses to show that the genomic content of the control datasets was not significantly different. Recently, the analysis of human leukocyte antigen (HLA) genes has become prevalent due to the development of HLA imputation technology. In this project, we extended the between-control homogeneity analysis of the WTCCC to HLA. We imputed HLA information in the WTCCC control dataset and showed that the HLA content was not significantly different between the two control datasets, suggesting that the combined controls can be used as controls for HLA fine-mapping analysis based on HLA imputation.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43993747","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}
引用次数: 0
In silico approach to calculate the transcript capacity 计算转录能力的计算机方法
Genomics & informatics Pub Date : 2019-09-01 DOI: 10.5808/GI.2019.17.3.e31
Young-Sup Lee, Kyung-Hye Won, Jae-Don Oh, Donghyun Shin
{"title":"In silico approach to calculate the transcript capacity","authors":"Young-Sup Lee, Kyung-Hye Won, Jae-Don Oh, Donghyun Shin","doi":"10.5808/GI.2019.17.3.e31","DOIUrl":"https://doi.org/10.5808/GI.2019.17.3.e31","url":null,"abstract":"We sought the novel concept, transcript capacity (TC) and analyzed TC. Our approach to estimate TC was through an in silico method. TC refers to the capacity that a transcript exerts in a cell as enzyme or protein function after translation. We used the genome-wide association study (GWAS) beta effect and transcription level in RNA-sequencing to estimate TC. The trait was body fat percent and the transcript reads were obtained from the human protein atlas. The assumption was that the GWAS beta effect is the gene’s effect and TC was related to the corresponding gene effect and transcript reads. Further, we surveyed gene ontology (GO) in the highest TC and the lowest TC genes. The most frequent GOs with the highest TC were neuronal-related and cell projection organization related. The most frequent GOs with the lowest TC were wound-healing related and embryo development related. We expect that our analysis contributes to estimating TC in the diverse species and playing a benevolent role to the new bioinformatic analysis.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49468368","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}
引用次数: 0
Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing. 用于RNA测序的MGISEQ-2000和Illumina HiSeq 4000测序平台的比较。
Genomics & informatics Pub Date : 2019-09-01 Epub Date: 2019-09-27 DOI: 10.5808/GI.2019.17.3.e32
Sol A Jeon, Jong Lyul Park, Jong-Hwan Kim, Jeong Hwan Kim, Yong Sung Kim, Jin Cheon Kim, Seon-Young Kim
{"title":"Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing.","authors":"Sol A Jeon,&nbsp;Jong Lyul Park,&nbsp;Jong-Hwan Kim,&nbsp;Jeong Hwan Kim,&nbsp;Yong Sung Kim,&nbsp;Jin Cheon Kim,&nbsp;Seon-Young Kim","doi":"10.5808/GI.2019.17.3.e32","DOIUrl":"https://doi.org/10.5808/GI.2019.17.3.e32","url":null,"abstract":"<p><p>Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGISEQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGISEQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.</p>","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"17 3","pages":"e32"},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6808641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41224609","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: 28
Direct-to-consumer genetic testing 直接面向消费者的基因检测
Genomics & informatics Pub Date : 2019-09-01 DOI: 10.5808/GI.2019.17.3.e34
Jong-Won Kim
{"title":"Direct-to-consumer genetic testing","authors":"Jong-Won Kim","doi":"10.5808/GI.2019.17.3.e34","DOIUrl":"https://doi.org/10.5808/GI.2019.17.3.e34","url":null,"abstract":"Direct-to-consumer (DTC) genetic testing is a controversial issue although Korean Government is considering to expand DTC genetic testing. Preventing the exaggeration and abusing of DTC genetic testing is an important task considering the early history of DTC genetic testing in Korea. And the DTC genetic testing performance or method has been rarely reported to the scientific and/or medical community and reliability of DTC genetic testing needs to be assessed. Law enforcement needs to improve these issues. Also principle of transparency needs to be applied.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42760572","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}
引用次数: 1
Deep learning for stage prediction in neuroblastoma using gene expression data 利用基因表达数据进行神经母细胞瘤阶段预测的深度学习
Genomics & informatics Pub Date : 2019-09-01 DOI: 10.5808/GI.2019.17.3.e30
Aron Park, S. Nam
{"title":"Deep learning for stage prediction in neuroblastoma using gene expression data","authors":"Aron Park, S. Nam","doi":"10.5808/GI.2019.17.3.e30","DOIUrl":"https://doi.org/10.5808/GI.2019.17.3.e30","url":null,"abstract":"Neuroblastoma is a major cause of cancer death in early childhood, and its timely and correct diagnosis is critical. Gene expression datasets have recently been considered as a powerful tool for cancer diagnosis and subtype classification. However, no attempts have yet been made to apply deep learning using gene expression to neuroblastoma classification, although deep learning has been applied to cancer diagnosis using image data. Taking the International Neuroblastoma Staging System stages as multiple classes, we designed a deep neural network using the gene expression patterns and stages of neuroblastoma patients. Despite a small patient population (n = 280), stage 1 and 4 patients were well distinguished. If it is possible to replicate this approach in a larger population, deep learning could play an important role in neuroblastoma staging.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49302915","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}
引用次数: 5
Trends in Genomics & Informatics: a statistical review of publications from 2003 to 2018 focusing on the most-studied genes and document clusters 基因组学和信息学趋势：2003年至2018年出版物的统计综述，重点关注研究最多的基因和文献集群
Genomics & informatics Pub Date : 2019-09-01 DOI: 10.5808/GI.2019.17.3.e25
Jihyeon Kim, Hee-Jo Nam, Hyun-Seok Park
{"title":"Trends in Genomics & Informatics: a statistical review of publications from 2003 to 2018 focusing on the most-studied genes and document clusters","authors":"Jihyeon Kim, Hee-Jo Nam, Hyun-Seok Park","doi":"10.5808/GI.2019.17.3.e25","DOIUrl":"https://doi.org/10.5808/GI.2019.17.3.e25","url":null,"abstract":"Genomics & Informatics (NLM title abbreviation: Genomics Inform) is the official journal of the Korea Genome Organization. Herein, we conduct a statistical analysis of the publications of Genomics & Informatics over the 16 years since its inception, with a particular focus on issues relating to article categories, word clouds, and the most-studied genes, drawing on recent reviews of the use of word frequencies in journal articles. Trends in the studies published in Genomics & Informatics are discussed both individually and collectively.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44453929","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}
引用次数: 1
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