• Korean Journal of Ecology and Environment
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• v.56 no.1
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• pp.104-125
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• 2023

The predator-prey interaction in freshwater ecosystems is a crucial area in the ecological study field and one of example to find such interaction is to investigate stomach contents. However, traditional method through visual inspection often induce misidentification, as it depends critically on intactness of physically visible data. In this study, we utilized Next-Generations Sequencing (NGS) technology to test the applicability stomach content analysis and overcome such limitation. NGS was applied to analyze the stomach contents of the Hemibarbus labeo, Tachysurus fulvidraco, and Plecoglossus altivelis collected in the lower part of Nakdong River. As a result, T. fulvidraco had a higher number of Animalia operational taxonomic units (OTUs) intake rate than H. labeo. At the same time, P. altivelis had higher number of Plantae OTUs intake rate than T. fulvidraco and higher Protozoa OTUs intake rate than H. labeo respectively. Therefore, NGS technology application enable to overcome traditional method's limitation and discover hidden interspecific interaction which can further be used in appropriate habitat assessment.

• Genomics & Informatics
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• v.10 no.2
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• pp.69-73
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• 2012

The explosive development of genomics technologies including microarrays and next generation sequencing (NGS) has provided comprehensive maps of cancer genomes, including the expression of mRNAs and microRNAs, DNA copy numbers, sequence variations, and epigenetic changes. These genome-wide profiles of the genetic aberrations could reveal the candidates for diagnostic and/or prognostic biomarkers as well as mechanistic insights into tumor development and progression. Recent efforts to establish the huge cancer genome compendium and integrative omics analyses, so-called "integromics", have extended our understanding on the cancer genome, showing its daunting complexity and heterogeneity. However, the challenges of the structured integration, sharing, and interpretation of the big omics data still remain to be resolved. Here, we review several issues raised in cancer omics data analysis, including NGS, focusing particularly on the study design and analysis strategies. This might be helpful to understand the current trends and strategies of the rapidly evolving cancer genomics research.

• Genomics & Informatics
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• v.12 no.4
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• pp.289-292
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• 2014

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 of single-nucleotide variant (SNV)-calling algorithms are available; however, there is no tool for visualizing the recurrent and phenotype-specific mutations for general researchers. In this study, in order to support defining the recurrent mutations or phenotype-specific mutations from NGS data of a group of cancers with diverse phenotypes, we aimed to develop a user-friendly tool, named mutation arranger for defining phenotype-related SNV (MAP). MAP is a user-friendly program with multiple functions that supports the determination of recurrent or phenotype-specific mutations and provides graphic illustration images to the users. Its operation environment, the Microsoft Windows environment, enables more researchers who cannot operate Linux to define clinically meaningful mutations with NGS data from cancer cohorts.

• Proceedings of the Korea Contents Association Conference
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• 2019.05a
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• pp.469-470
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• 2019

차세대염기서열분석법(NGS, Next Generation Sequencing) 기술은 하나의 유전체를 무수히 많은 조각으로 분해하여 각 조각을 동시에 읽어낸 뒤, 전산기술을 이용하여 조합함으로써 방대한 유전체 정보를 빠르게 해독하는 방법이다. 한편, 액체 생검(LB, liquid biopsy)이란 암세포가 깨지면서 생기는 미량의 DNA 조각을 말초혈액 속에서 찾아내 암을 진단하는 기술로 조직 생검(tissue biopsy)에 비해 비침습적이다. 본 논문은 NGS와 LB 기술을 접목했을 때 확진이 가능하고 예후 및 치료경과의 예측이 가능함을 제언하였다.

• BMB Reports
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• v.54 no.7
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• pp.386-391
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• 2021

Owing to rapid advancements in NGS (next generation sequencing), genomic alteration is now considered an essential predictive biomarkers that impact the treatment decision in many cases of cancer. Among the various predictive biomarkers, tumor mutation burden (TMB) was identified by NGS and was considered to be useful in predicting a clinical response in cancer cases treated by immunotherapy. In this study, we directly compared the lab-developed-test (LDT) results by target sequencing panel, K-MASTER panel v3.0 and whole-exome sequencing (WES) to evaluate the concordance of TMB. As an initial step, the reference materials (n = 3) with known TMB status were used as an exploratory test. To validate and evaluate TMB, we used one hundred samples that were acquired from surgically resected tissues of non-small cell lung cancer (NSCLC) patients. The TMB of each sample was tested by using both LDT and WES methods, which extracted the DNA from samples at the same time. In addition, we evaluated the impact of capture region, which might lead to different values of TMB; the evaluation of capture region was based on the size of NGS and target sequencing panels. In this pilot study, TMB was evaluated by LDT and WES by using duplicated reference samples; the results of TMB showed high concordance rate (R² = 0.887). This was also reflected in clinical samples (n = 100), which showed R² of 0.71. The difference between the coding sequence ratio (3.49%) and the ratio of mutations (4.8%) indicated that the LDT panel identified a relatively higher number of mutations. It was feasible to calculate TMB with LDT panel, which can be useful in clinical practice. Furthermore, a customized approach must be developed for calculating TMB, which differs according to cancer types and specific clinical settings.

• Biomedical Science Letters
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• v.22 no.4
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• pp.150-159
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• 2016

Knowledge of the distribution and biodiversity of environmental bacteria and the ecosystem that influences them is crucial for predicting an ecosystem. However, bacterial culture methods can only analyze approximately 0.1% of the existing microorganisms, those that are readily cultured under laboratory conditions. By contrast, next-generation sequencing (NGS) has generally been known to obtain more diverse profiling of bacterial composition. We compared the bacterial communities using both a culture-dependent (MALDI-TOF) and culture-independent (NGS) methods. Environmental specimens were obtained from both freshwater and seawater. Water samples were also analyzed by both pyrosequencing and MiSeq sequencing, in order to select one NGS platform which could analyze comparatively more diverse microbiota. Bacterial distribution analyzed with MALDI-TOF showed no difference between the microbiota of freshwater and seawater, whereas the results analyzed with NGS distinguished between the two. The diversity indexes of MiSeq sequencing were higher than for Pyrosequencing. This indicated that MiSeq sequencing is capable of analyzing a comparatively wider diversity of bacteria. The genus of Flavobacterium and Planktophila were identified as being unique to freshwater, whereas EU801223 and OM43 were found in the seawater. Difference between the bacterial composition of the freshwater and seawater environments was identified by MiSeq sequencing analysis.

• Journal of Life Science
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• v.24 no.11
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• pp.1258-1267
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• 2014

Developing economic traits with a high growth rate, robustness, and disease resistance in livestock is an important challenge. RFLP and AFLP are the classical methods used to develop economic traits. Whole-genome-based economic traits have recently been detected with the advent of next-generation sequencing (NGS) technologies. However, NGS technologies are rather costly for use in studies, and RNA-seq, RAD-Seq, RRL, MSG, and GBS have been used to overcome the issue of high costs. In this study, recent NGS-based studies were reviewed, particularly those that focused on minimum costs and maximum effects. Then, we presented further prospects on how to apply for selection of high economic-trait livestock.

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

• Journal of Genetic Medicine
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• v.12 no.1
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• pp.12-18
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• 2015

Malformations of cortical development (MCD) cover a broad spectrum of developmental disorders which cause the various clinical manifestations including epilepsy, developmental delay, and intellectual disability. MCD have been clinically classified based on the disruption of developmental processes such as proliferation, migration, and organization. Molecular genetic studies of MCD have improved our understanding of these disorders at a molecular level beyond the clinical classification. These recent advances are resulted from the development of massive parallel sequencing technology, also known as next-generation sequencing (NGS), which has allowed researchers to uncover novel molecular genetic pathways associated with inherited or de novo mutations. Although an increasing number of disease-related genes or genetic variations have been identified, genotype-phenotype correlation is hampered when the biological or pathological functions of identified genetic variations are not fully understood. To elucidate the causality of genetic variations, in vivo disease models that reflect these variations are required. In the current review, we review the use of NGS technology to identify genes involved in MCD, and discuss how the functions of these identified genes can be validated through in vivo disease modeling.

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