Genomics & informatics最新文献_第9页

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

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

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, Jong Lyul Park, Jong-Hwan Kim, Jeong Hwan Kim, Yong Sung Kim, Jin Cheon Kim, 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

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

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

引用次数: 1

Optimization of a microarray for fission yeast 裂变酵母微阵列的优化

Genomics & informatics Pub Date : 2019-09-01 DOI: 10.5808/GI.2019.17.3.e28

Dong-Uk Kim, Minho Lee, Sangjo Han, Miyoung Nam, Sol Lee, Jaewoong Lee, Jihye Woo, Dongsup Kim, K. Hoe

{"title":"Optimization of a microarray for fission yeast","authors":"Dong-Uk Kim, Minho Lee, Sangjo Han, Miyoung Nam, Sol Lee, Jaewoong Lee, Jihye Woo, Dongsup Kim, K. Hoe","doi":"10.5808/GI.2019.17.3.e28","DOIUrl":"https://doi.org/10.5808/GI.2019.17.3.e28","url":null,"abstract":"Bar-code (tag) microarrays of yeast gene-deletion collections facilitate the systematic identification of genes required for growth in any condition of interest. Anti-sense strands of amplified bar-codes hybridize with ~10,000 (5,000 each for up- and down-tags) different kinds of sense-strand probes on an array. In this study, we optimized the hybridization processes of an array for fission yeast. Compared to the first version of the array (11 µm, 100K) consisting of three sectors with probe pairs (perfect match and mismatch), the second version (11 µm, 48K) could represent ~10,000 up-/down-tags in quadruplicate along with 1,508 negative controls in quadruplicate and a single set of 1,000 unique negative controls at random dispersed positions without mismatch pairs. For PCR, the optimal annealing temperature (maximizing yield and minimizing extra bands) was 58℃ for both tags. Intriguingly, up-tags required 3× higher amounts of blocking oligonucleotides than down-tags. A 1:1 mix ratio between up- and down-tags was satisfactory. A lower temperature (25℃) was optimal for cultivation instead of a normal temperature (30℃) because of extra temperature-sensitive mutants in a subset of the deletion library. Activation of frozen pooled cells for >1 day showed better resolution of intensity than no activation. A tag intensity analysis showed that tag(s) of 4,316 of the 4,526 strains tested were represented at least once; 3,706 strains were represented by both tags, 4,072 strains by up-tags only, and 3,950 strains by down-tags only. The results indicate that this microarray will be a powerful analytical platform for elucidating currently unknown gene functions.","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":"42657769","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

Identification of neoantigens derived from alternative splicing and RNA modification 选择性剪接和RNA修饰新抗原的鉴定

Genomics & informatics Pub Date : 2019-08-22 DOI: 10.5808/GI.2019.17.3.e23

Jiyeon Park, Y. Chung

引用次数: 17

FusionScan: accurate prediction of fusion genes from RNA-Seq data FusionScan:从RNA-Seq数据中准确预测融合基因

Genomics & informatics Pub Date : 2019-07-23 DOI: 10.5808/GI.2019.17.3.e26

P. Kim, Y. Jang, Sanghyuk Lee

{"title":"FusionScan: accurate prediction of fusion genes from RNA-Seq data","authors":"P. Kim, Y. Jang, Sanghyuk Lee","doi":"10.5808/GI.2019.17.3.e26","DOIUrl":"https://doi.org/10.5808/GI.2019.17.3.e26","url":null,"abstract":"Identification of fusion gene is of prominent importance in cancer research field because of their potential as carcinogenic drivers. RNA sequencing (RNA-Seq) data have been the most useful source for identification of fusion transcripts. Although a number of algorithms have been developed thus far, most programs produce too many false-positives, thus making experimental confirmation almost impossible. We still lack a reliable program that achieves high precision with reasonable recall rate. Here, we present FusionScan, a highly optimized tool for predicting fusion transcripts from RNA-Seq data. We specifically search for split reads composed of intact exons at the fusion boundaries. Using 269 known fusion cases as the reference, we have implemented various mapping and filtering strategies to remove false-positives without discarding genuine fusions. In the performance test using three cell line datasets with validated fusion cases (NCI-H660, K562, and MCF-7), FusionScan outperformed other existing programs by a considerable margin, achieving the precision and recall rates of 60% and 79%, respectively. Simulation test also demonstrated that FusionScan recovered most of true positives without producing an overwhelming number of false-positives regardless of sequencing depth and read length. The computation time was comparable to other leading tools. We also provide several curative means to help users investigate the details of fusion candidates easily. We believe that FusionScan would be a reliable, efficient and convenient program for detecting fusion transcripts that meet the requirements in the clinical and experimental community. FusionScan is freely available at http://fusionscan.ewha.ac.kr/.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46412581","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: 9

Towards cross-platform interoperability for machine-assisted text annotation 面向机器辅助文本注释的跨平台互操作性

Genomics & informatics Pub Date : 2019-06-01 DOI: 10.5808/GI.2019.17.2.e19

Richard Eckart de Castilho, Nancy Ide, Jin-Dong Kim, Jan-Christoph Klie, Keith Suderman

引用次数: 7