• Genomics & Informatics
• /
• v.15 no.1
• /
• pp.48-50
• /
• 2017

Tumor tissues from biopsies or surgery are major sources for the next generation sequencing (NGS) study, but these procedures are invasive and have limitation to overcome intratumor heterogeneity. Recent studies have shown that driver alterations in tumor tissues can be detected by liquid biopsy which is a less invasive technique capable of both capturing the tumor heterogeneity and overcoming the difficulty in tissue sampling. However, it is still unclear whether the driver alterations in liquid biopsy can be detected by targeted NGS and how those related to the tissue biopsy. In this study, we performed whole-exome sequencing for a breast cancer tissue and identified PTEN p.H259fs*7 frameshift mutation. In the plasma DNA (liquid biopsy) analysis by targeted NGS, the same variant initially identified in the tumor tissue was also detected with low variant allele frequency. This mutation was subsequently validated by digital polymerase chain reaction in liquid biopsy. Our result confirm that driver alterations identified in the tumor tissue were detected in liquid biopsy by targeted NGS as well, and suggest that a higher depth of sequencing coverage is needed for detection of genomic alterations in a liquid biopsy.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2013.08a
• /
• pp.297.2-297.2
• /
• 2013

Scavenging electricity from wasteful energy resources is currently an important issue and piezoelectric nanogenerators (NGs) based on zinc oxide (ZnO) are promising energy harvesters that can be adapted to various portable, wearable, self-powered electronic devices. Although ZnO has several advantages for NGs, the piezoelectric semiconductor material ZnO generate an intrinsic piezoelectric potential of a few volts as a result of its mechanical deformation. As grown, ZnO is usually n-type, a property that was historically ascribed to native defects. Oxygen vacancies (Vo) that work as donors exist in ZnO thin film and usually screen some parts of the piezoelectric potential. Consequently, the ZnO NGs' piezoelectric power cannot reach to its theoretical value, and thus decreasing the effect from Vo is essential. In the present study, c-axis oriented insulator-like sputtered ZnO thin films were grown in various temperatures to fabricate an optimized nanogenerator (NGs). The purity and crystalinity of ZnO were investigated with photoluminescence (PL). Moreover, by introducing a p-type polymer usually used in organic solar cell, it was discussed how piezoelectric passivation effect works in ZnO thin films having different types of defects. Prepared ZnO thin films have both Zn vacancies (accepter like) and oxygen vacancies (donor like). It generates output voltage 20 time lager than n-type dominant semiconducting ZnO thin film without p-type polymer conjugating. The enhancement is due to the internal accepter like point defects, zinc vacancies (VZn). When the more VZn concentration increases, the more chances to prevent piezoelectric potential screening effects are occurred, consequently, the output voltage is enhanced. Moreover, by passivating remained effective oxygen vacancies by p-type polymers, we demonstrated further power enhancement.

• Journal of Oriental Neuropsychiatry
• /
• v.30 no.4
• /
• pp.327-340
• /
• 2019

Objectives: Alzheimer's disease (AD) is a complex disease accompanied by slow impairment of memory and coordination leading to behavioral changes. To date, the only treatment option is to delay the progress of the disease. The purpose of this study was to investigate the synergistic effects of combination treatment with donepezil and three herbal extracts SIP-3 in the AD mouse model induced by amyloid-β (Aβ). Methods: We tested SIP-3 extracts for the cytotoxicity on Aβ-treated SH-SY5Y cells. Then the synergistic effects of SIP-3 and donepezil were evaluated in the AD mouse model using animal experiments and the next generation sequencing (NGS) study. Results: We found that co-treatment with SIP-3 extracts and donepezil increased the viability in Aβ-treated SH-SY5Y cells. The beneficial effects of the co-treatment were also observed in the Aβ-induced AD mouse model. The NGS study was performed to show that the co-treatment of SIP-3 and donepezil restored the disease phenotype closely to the normal level in the AD mouse model in terms of mRNA expression. However, the phenotypes were only partially restored. Conclusions: This study suggests that the combination treatment has a potential to be used for the treatment of AD. However, longer periods of treatment may be required.

• The Plant Pathology Journal
• /
• v.37 no.6
• /
• pp.521-532
• /
• 2021

Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions.

• Journal of the Korean Institute of Intelligent Systems
• /
• v.15 no.3
• /
• pp.369-374
• /
• 2005

Currently, ECDIS and GPS plotters are much used as equipment providing operators with route information, but they do not have any function of automatic route creation and route explanation, so available for only experienced operators. Especially, the present situation is that no study is made of the automatic route creation and route explanation using ENC for ECDIS, substitution system of paper chart. ENC is the electronic navigation chart that is produced using S-52, 5-57 standard format required by IHO. In this paper, an Navigation Guiding System(NGS) is proposed to generate an optimal route where ENC and GPS data is fusioned including the wind direction and speed of an anemometer. The proposed system was testified by a simulation, and its effectiveness was verified.

• Genomics & Informatics
• /
• v.12 no.4
• /
• pp.165-170
• /
• 2014

Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.

• Neonatal Medicine
• /
• v.28 no.2
• /
• pp.89-93
• /
• 2021

Nemaline myopathy is a genetically heterogeneous neuromuscular disorder and one of the most common congenital myopathies. The clinical manifestations usually vary depending on the age of onset. Neonatal nemaline myopathy has the worst prognosis, primarily due to respiratory failure. Several genes associated with nemaline myopathy have been identified, including NEB, ACTA1, TPM3, TPM2, TNNT1, CFL2, KBTBD13, KLHL40, KLHL41, LMOD3, and KBTBD13. Here, we report a neonatal Korean female patient with nemaline myopathy carrying compound heterozygous mutations in the gene KLHL40 as revealed using next generation sequencing (NGS). The patient presented with postnatal cyanosis, respiratory failure, dysphagia, and hypotonia just after birth. To identify the genetic cause underlying the neonatal myopathy, NGS-based gene panel sequencing was performed. Compound heterozygous pathogenic variants were detected in KLHL40: c.[1405G>T];[1582G>A] (p. [Gly469cys];[Glu528Lys]). NGS allows quick and accurate diagnosis at a lower cost compared to traditional serial single gene sequencing, which is greatly advantageous in genetically heterogeneous disorders such as myopathies. Rapid diagnosis will facilitate efficient and timely genetic counseling, prediction of disease prognosis, and establishment of treatments.

• Food Science and Industry
• /
• v.50 no.1
• /
• pp.2-10
• /
• 2017

Human have eaten various traditional fermented foods for a numbers of million years for health benefit as well as survival. The beneficial effects of fermented foods have been resulted from complex microbial communications within the fermented foods. Therefore, the holistic approaches for individual identification and complete microbial profiling involved in their communications have been of interest to food microbiology fields. Microbiome is the ecological community of microorganisms that literally share our environments including foods as well as human body. However, due to the limitation of culture-dependent methods such as simple isolations of just culturable microorganisms, the culture-independent methods have been consistently developed, resulting in new light on the diverse non-culturable and hitherto unknown microorganisms, and even microbial communities in the fermented foods. For the culture-independent approaches, the food microbiome has been deciphered by employing various molecular analysis tools such as fluorescence in situ hybridization, quantitative PCR, and denaturing gradient gel-electrophoresis. More recently, next-generation-sequencing (NGS) platform-based microbiome analysis has been of interest, because NGS is a powerful analytical tool capable of resolving the microbiome in respect to community structures, dynamics, and activities. In this overview, the development status of analysis tools for the fermented food microbiome is covered and research trend for NGS-based food microbiome analysis is also discussed.

• Korean Journal of Veterinary Service
• /
• v.46 no.1
• /
• pp.93-106
• /
• 2023

Emerging and re-emerging zoonotic viruses become critical public health, economic, societal, and cultural burdens. The Coronavirus disease-19 (COVID-19) pandemic reveals needs for effective preparedness and responsiveness against the emergence of variants and the next virus outbreak. The targeted next-generation sequencing (NGS) significantly contributes to the acquisition of viral genome sequences directly from clinical specimens. Using this advanced NGS technology, the genomic epidemiology and surveillance play a critical role in identifying of infectious source and origin, tracking of transmission chains and virus evolution, and characterizing the virulence and developing of vaccines during the outbreak. In this review, we highlight the platforms and preparation of targeted NGS for the viral genomics. We also demonstrate the application of this strategy to take advantage of the responsiveness and prevention of emerging zoonotic viruses. This article provides broad and deep insights into the preparedness and responsiveness for the next zoonotic virus outbreak.

• Journal of The Korean Society of Inherited Metabolic disease
• /
• v.23 no.2
• /
• pp.1-7
• /
• 2023

Inherited metabolic disorders (IMD) are a group of disorders involving various metabolic pathways. Genetic diagnosis of IMD has been challenging because of extremely heterogeneous nature and extensive laboratory and/or phenotype overlap. Conventional genetic diagnosis was a gene-by-gene approach that needs a priori information on the causative genes that might underlie the IMD. Recent implementation of next-generation sequencing (NGS) technologies has changed the process of genetic diagnosis from a gene-by-gene approach to simultaneous analysis of targeted genes possibly associated with the IMD using gene panels or using whole exome/genome sequencing (WES/WGS) covering entire human genes. Clinical NGS tests can be a cost-effective approach for the rapid diagnosis of IMD with genetic heterogeneity and are becoming standard diagnostic procedures.