• Genomics & Informatics
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• v.16 no.4
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• pp.29.1-29.5
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• 2018

Hybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing polymerase chain reaction biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various study groups for their own purposes. Due to this provincial usage of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared and pooled together, and an 8-plexed capture library was processed to the enrichment step before 150-bp paired-end sequencing with Illumina HiSeq series. For the analysis, we evaluated several published tools. We focused mainly on the compatibility of the input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of the quality and efficiency of conducted experiments.

• BMB Reports
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• v.55 no.11
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• pp.553-558
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• 2022

Hepatocellular carcinoma (HCC) is dangerous cancer that often evades early detection because it is asymptomatic and an effective detection method is lacking. For people with chronic liver inflammation who are at high risk of developing HCC, a sensitive detection method for HCC is needed. In a meta-analysis of The Cancer Genome Atlas pan-cancer methylation database, we identified a CpG island in the USP44 promoter that is methylated specifically in HCC. We developed methylation-sensitive high-resolution melting (MS-HRM) analysis to measure the methylation levels of the USP promoter in cell-free DNA isolated from patients. Our MS-HRM assay correctly identified 40% of patients with early-stage HCC, whereas the α-fetoprotein test, which is currently used to detect HCC, correctly identified only 25% of early-stage HCC patients. These results demonstrate that USP44 MS-HRM analysis is suitable for HCC surveillance.

• Mass Spectrometry Letters
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• v.11 no.2
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• pp.30-35
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• 2020

Schisandra chinensis is a traditional herbal medicine that is widely spread in Korea, Japan, and China. The fruits of S. chinensis Bailon, known as omija in Korea, have traditionally been used for the treatment of coughs, fatigues, and insomnia. Up to now, there have been several reports for the identification of major lignan compounds and their quantitation in S. chinensis extracts. To the best of our knowledge, however, there is no report on the analysis of lignans in omija wine and omija cheong (sugared omija or omija sugar syrup). In the present study, seven dibenzocyclooctadiene lignans (gomisin A, gomisin B, gomisin C, gomisin N, schisandrin, deoxyschisandrin, and wuweizisu C) in omija wine and omija cheong were analyzed and quantitated using liquid chromatography-tandem mass spectrometry. Among seven lignans, pharmacologically active gomisin A, schisandrin, and deoxyschisandrin, which are major components in fruits of S. chinensis, were the most abundant lignans in omija wine and cheong. The content of lignan in omija wine was in the order: schisandrin > gomisin A > deoxyschisandrin > gomisin N > gomisin B > gomisin C > wuweizisu C. The concentration of deoxyschisandrin and gomisin N in omija wine was approximately 2.0- and 6.0-fold higher than for omija cheong. Additionally, this study provided a systematic identification of lignans in omija wine and cheong and indicated that the omija wine and cheong might be of value for their dietary application.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.10a
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• pp.8-8
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• 2017

• KOGO NEWS
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• v.6 no.4
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• pp.8-13
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• 2006

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4229-4233
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• 2012

With the advances in modern diagnostic expertise for cancer, certain approaches allowing scanning of the complete genome and the proteome are becoming very useful for researchers. These high throughput techniques have already proven power, over traditional detection methods, in differentiating disease sub-types and identifying specific genetic events during progression of cancer. This paper introduces major branches of omics-technology and their applications in the field of cancer. It also addresses current road blocks that need to be overcome and future possibilities of these methods in oncogenic detection.

• BMB Reports
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• v.44 no.3
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• pp.182-186
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• 2011

Exogenous stimuli such as nerve growth factor (NGF) exert their effects on neurite outgrowth via Trk neurotrophin receptors. TrkA receptors are known to be ubiquitinated via proteasome inhibition in the presence of NGF. However, the effect of proteasome inhibition on neurite outgrowth has not been studied extensively. To clarify these issues, we investigated signaling events in PC12 cells treated with NGF and the proteasome inhibitor MG132. We found that MG132 facilitated NGF-induced neurite outgrowth and potentiated the phosphorylation of the extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) and phosphatidylinositol-3-kinase (PI3K)/AKT pathways and TrkA receptors. MG132 stimulated internalization of surface TrkA receptor and stabilized intracellular TrkA receptor, and the $Ub^{K63}$ chain was found to be essential for stability. These results indicate that the ubiquitin-proteasome system potentiated neurite formation by regulating the stability of TrkA receptors.

• Mass Spectrometry Letters
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• v.9 no.1
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• pp.1-16
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• 2018

Microfluidic technologies hold high promise and emerge as a potential molecular tool to facilitate the progress of fundamental and applied biomedical researches by enabling miniaturization and upgrading current biological research tools. In this review, we summarize the state of the art of existing microfluidic technologies and its' application for characterizing biophysical properties of individual cells. Microfluidic devices offer significant advantages and ability to handle in integrating sample processes, minimizing sample and reagent volumes, and increased analysis speed. Therefore, we first present the basic concepts and summarize several achievements in new coupling between microfluidic devices and mass spectrometers. Secondly, we discuss the recent applications of microfluidic chips in various biological research field including cellular and molecular level. Finally, we present the current challenge of microfluidic technologies and future perspective in this study field.

• Journal of Preventive Medicine and Public Health
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• v.54 no.4
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• pp.259-264
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• 2021

Traditional epidemiological studies have identified a number of risk factors for various diseases using regression-based methods that examine the association between an exposure and an outcome (i.e., one-to-one correspondences). One of the major limitations of this approach is the "black-box" aspect of the analysis, in the sense that this approach cannot fully explain complex relationships such as biological pathways. With high-throughput data in current epidemiology, comprehensive analyses are needed. The network approach can help to integrate multi-omics data, visualize their interactions or relationships, and make inferences in the context of biological mechanisms. This review aims to introduce network analysis for systems epidemiology, its procedures, and how to interpret its findings.

• Genomics & Informatics
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• v.18 no.4
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• pp.46.1-46.4
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• 2020

We developed the BaSDAS (Barcode-Seq Data Analysis System), a GUI-based pooled knockout screening data analysis system, to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information.