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MAP: Mutation Arranger for Defining Phenotype-Related Single-Nucleotide Variant
백인표,정연준,정영복,정승현 한국유전체학회 2014 Genomics & informatics Vol.12 No.4
Next-generation sequencing (NGS) is widely used to identify the causative mutations underlying diverse human diseases,including cancers, which can be useful for discovering the diagnostic and therapeutic targets. Currently, a number ofsingle-nucleotide variant (SNV)-calling algorithms are available; however, there is no tool for visualizing the recurrent andphenotype-specific mutations for general researchers. In this study, in order to support defining the recurrent mutations orphenotype-specific mutations from NGS data of a group of cancers with diverse phenotypes, we aimed to develop auser-friendly tool, named mutation arranger for defining phenotype-related SNV (MAP). MAP is a user-friendly program withmultiple functions that supports the determination of recurrent or phenotype-specific mutations and provides graphicillustration images to the users. Its operation environment, the Microsoft Windows environment, enables more researcherswho cannot operate Linux to define clinically meaningful mutations with NGS data from cancer cohorts.
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오미내,김정곤,백인표,주지현 대한류마티스학회 2023 대한류마티스학회지 Vol.30 No.1
A subset of spondyloarthritis (SpA) called ‘reactive arthritis’ is triggered by causal pathogens, usually bacteria related to venereal disease or gastrointestinal infection. During the outbreak of coronavirus disease 2019 (COVID-19), there have been case reports about SpA after COVID-19, but the causality is still elusive. We described cases of 23-year-old monozygotic twins both diagnosed with SpA after COVID-19. The probable linkage between SpA and COVID-19 was elaborated with our cases as well as literature reviews. Of note, shared genetic traits by monozygotic twins, particularly HLA-B27 positivity, might have contributed to their susceptibility to COVID-19-induced SpA. Moreover, single-cell transcriptome analysis revealed that the transcriptomic profile of peripheral compartment of SpA after COVID-19 was distinctive from that of typical radiographic axial SpA as shown by differential expression of ribosomal protein S26 (RPS26) and small nucleolar RNA host gene 5 (SNHG5) in nearly all subsets of peripheral blood mononuclear cells.
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안용주,Kesavan Markkandan,백인표,문세영,이우석,김희수,한규동 한국유전학회 2018 Genes & Genomics Vol.40 No.1
Next generation sequencing (NGS) has traditionally been performed in various fields including agricultural to clinical and there are so many sequencing platforms available in order to obtain accurate and consistent results. However, these platforms showed amplification bias when facilitating variant calls in personal genomes. Here, we sequenced whole genomes and whole exomes from ten Korean individuals using Illumina and Ion Proton, respectively to find the vulnerability and accuracy of NGS platform in the GC rich/poor area. Overall, a total of 1013 Gb reads from Illumina and ~39.1 Gb reads from Ion Proton were analyzed using BWA-GATK variant calling pipeline. Furthermore, conjunction with the VQSR tool and detailed filtering strategies, we achieved high-quality variants. Finally, each of the ten variants from Illumina only, Ion Proton only, and intersection was selected for Sanger validation. The validation results revealed that Illumina platform showed higher accuracy than Ion Proton. The described filtering methods are advantageous for large population-based whole genome studies designed to identify common and rare variations associated with complex diseases.
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