• 대한임상검사과학회지
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• 제44권4호
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• pp.167-177
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• 2012

Next-Generation Sequencing (NGS) is a term that means post-Sanger sequencing methods with high-throughput sequencing technologies. NGS parallelizes the sequencing process, producing thousands or millions of sequences at once. The latest NGS technologies use even single DNA molecule as a template and measures the DNA sequence directly via measuring electronic signals from the extension or degradation of DNA. NGS is making big impacts on biomedical research, molecular diagnosis and personalized medicine. The hospitals are rapidly adopting the use of NGS to help to patients understand treatment with sequencing data. As NGS equipments are getting smaller and affordable, many hospitals are in the process of setting up NGS platforms. In this review, the progress of NGS technology development and action mechanisms of representative NGS equipments of each generation were discussed. The key technological advances in the commercialized platforms were presented. As NGS platforms are a great concern in the healthcare area, the latest trend in the use of NGS and the prospect of NGS in the future in diagnosis and personalized medicine were also discussed.

• 생명과학회지
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• 제25권3호
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• pp.357-367
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• 2015

매우 빠른 속도로 발전하고 있는 차세대 염기서열 분석 플랫폼과 최신 생물정보학적 분석도구들로 말미암아, 1,000달러 이하의 가격으로 인간 유전체 염기서열을 해독하고자 하는 궁극적인 목표가 조만간 곧 실현될 수 있을 것 같다. 차세대 염기서열 분석 분야의 급속한 기술적 진전은 NGS 데이터의 분석과 관리를 위한 통계적 방법과 생물정보학적 분석도구들에 대한 수요를 꾸준히 증대시키고 있다. NGS 플랫폼이 상용화되어 쓰이기 시작한 초창기부터, NGS 데이터를 분석하고 해석하거나, 가시화 해주는 다수의 응용프로그램이나 도구들이 개발되어 활용되어 왔다. 그러나, NGS 데이터의 엄청난 범람으로 데이터 저장, 데이터 분석 및 관리 등에 있어서 해결해야 할 많은 문제들이 부각되고 있다. NGS 데이터 분석은 단편서열과 참조서열간의 서열정렬, 염기식별, 다형성 발견, 쌍단편 서열이나 비쌍단편 서열 등을 이용한 어셈블리 작업, 구조변이 발견, 유전체 브라우징 등을 본질적으로 포함한다. 본 논문은 주요 차세대 염기서열 결정기술과 NGS 데이터 분석을 위한 생물정보학적 분석도구들에 대해 개관적으로 소개하고자 한다.

• Genomics & Informatics
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• 제13권3호
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• pp.81-85
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• 2015

Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (${\sim}72{\times}coverage$) was sequenced with a $2{\times}150bp$ paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.

• 한국군사과학기술학회지
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• 제27권4호
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• pp.507-515
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• 2024

Microbial forensics is a scientific discipline for analyzing evidence related to biological crimes by identifying the origin of microorganisms. Multiple locus variable number tandem repeat analysis(MLVA) is one of the microbiological analysis methods used to specify subtypes within a species based on the number of tandem repeat in the genome, and advances in next generation sequencing(NGS) technology have enabled in silico anlysis of full-length whole genome sequences. In this paper, we analyzed unknown samples provided by Robert Koch Institute(RKI) through The United Nations Secretary-General's Mechanism(UNSGM)'s external quality assessment exercise(EQAE) project, which we officially participated in 2023. We confirmed that the 3 unknown samples were B. anthracis through nucleic acid isolation and genetic sequence analysis studies. MLVA results on 32 loci of B. anthracis were analysed by using genome sequences obtained from NGS(NextSeq and MinION) and Sanger sequencing. The MLVA typing using short-reads based NGS platform(NextSeq) showed a high probability of causing assembly error when a size of the tandem repeats was grater than 200 bp, while long-reads based NGS platform(MinION) showed higher accuracy than NextSeq, although insertion and deletion was observed. We also showed hybrid assembly can correct most indel error caused by MinION. Based on the MLVA results, genetic identification was performed compared to the 2,975 published MLVA databases of B. anthracis, and MLVA results of 10 strains were identical with 3 unkonwn samples. As a result of whole genome alignment of the 10 strains and 3 unknown samples, all samples were identified as B. anthracis strain A4564 which is associated with injectional anthrax isolates in heroin users.

• 한국항행학회논문지
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• 제13권6호
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• pp.957-963
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• 2009

본 논문은 스토리지 디바이스에 대한 자원관리 시스템의 설계에 관한 것이다. 컴퓨팅 환경의 변화와 복잡화에 따라 자원에 대한 효율적인 관리방안으로 제안되고 있는 표준관리응용프로그램을 설계하기 위해서 객체지향 모델링 기술에 바탕을 둔 공통정보모델을 사용하여 관리객체에 대한 모델링 과정을 수행하였다. 표준화된 관리응용프로그램 구현 방법을 사용하여 사용자에게 시각적인 특성을 제공할 수 있도록 GUI인터페이스를 구현하였으며 시스템의 구성 요소를 자동으로 검색, 관리하고 각 구성 요소의 상태 정보를 주의/경고/긴급의 3단계로 분류하여 사용자에게 제공하였다. 또한 다양한 구성 요소의 운용을 위한 설정기능을 제공하는 관리응용시스템을 구현하였다.

• 한국육종학회지
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• 제50권4호
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• pp.364-377
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• 2018

차세대 염기 서열 분석 기술의 적용은 빠르게 식물 유전체학의 지식을 확장시킴으로 기능유전자 연구의 발전을 도모하고 있다. 특히, 밀의 기능유전체학의 발전은 기존의 염기서열 분석 기술로는 가능성이 없어 보였다. 하지만 NGS의 발전은 고품질 보통밀의 RefSeq를 완성뿐만 아니라 다양한 밀 계통들의 재염기서열분석을 가능하게 한다. 현재 이렇게 얻어진 고품질 유전정보와 유전적 다형성이 밝혀진 유전자원의 이용으로 밀 기능유전체 연구가 새로운 단계로 접어들고 있다. NGS 기술 및 reverse genetics의 발전은 앞으로 전세계에 펼쳐져 있는 야생형 밀과 재배종 밀 계통들의 유전적인 다양성 분석을 가능케 하고 밀의 유전과 진화 과정을 깊게 이해하는데 큰 도움이 될 것이다. NGS 기술의 사용과 생물정보학의 결합은 타 작물에 비해 뒤쳐진 밀의 기능유전체 연구 속도를 가속화할 것이다. 기능유전체 연구를 활용한 밀 육종의 시대가, 애기장대 및 벼 분야와 같이, 다가오고 있다.

• 한국축산시설환경학회지
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• 제21권3호
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• pp.93-98
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• 2015

The objective of this study was to review application of next-generation sequencing (NGS) to investigate microbiome in the livestock sector. Since the 16S rRNA gene is used as a phylogenetic marker, unculturable members of microbiome in nature or managed environments have been investigated using the NGS technique based on 16S rRNA genes. However, few NGS studies have been conducted to investigate microbiome in the livestock sector. The 16S rRNA gene sequences obtained from NGS are classified to microbial taxa against the 16S rRNA gene reference database such as RDP, Greengenes and Silva databases. The sequences also are clustered into species-level OTUs at 97% sequence similarity. Microbiome similarity among treatment groups is visualized using principal coordinates analysis, while microbiome shared among treatment groups is visualized using a venn diagram. The use of the NGS technique will contribute to elucidating roles of microbiome in the livestock sector.

• 한국동물위생학회지
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• 제42권4호
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• pp.217-225
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• 2019

To detect Single nucleotide polymorphisms (SNP) markers associated with Bovine viral diarrhea virus (BVDV) and Bovine respiratory syncytial virus (BRSV) S/P ratio in Korean Holstein dairy cattle, Genome-wide association study (GWAS) was performed using Illumina BovineSNP50 Beadchip. The number of phenotype data and genotype data were 107, and 294. respectively. Phenotype data were collected for four periods (0 week, 1 week, 4 week, 24 week) after having vaccinated (0 week no vaccinated period). A total of 36,257 SNPs was remained after quality control had been done by PLINK. The result of GWAS showed 6 SNP markers (BTB-01704243, BTB-01594395, ARS-BFGL-NGS-118070, ARS-BFGL-NGS-111365, BTA-65410-no-rs, Hapmap38331-BTA-61256) under BVDV and 4 SNP markers (ARS-BFGL-NGS-109861, Hapmap53701-rs29017064, ARS-BFGL-NGS-71055, BTA-11232-no-rs) under BRSV. And also, 10 candidate genes found through 10 SNP markers (TBX18, CEP162, PAFAH1B1, METTL16, BRCA1, RND2, POLK, ENSBTAG00000051724, ADAM18, NRG3).

• 식품과학과 산업
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• 제52권3호
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• pp.220-228
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• 2019

Rapid development of next-generation sequencing (NGS) technology is available to study microbes in genomic level. This NGS has been widely used in DNA/RNA sequencing for genome sequencing, metagenomics, and transcriptomics. The food microbiology area could be categorized into three groups. Food microbes including probiotics and food-borne pathogens are studied in genomic level using NGS for microbial genomics. While food fermentation or food spoilage are more complicated, their genomic study needs to be done with metagenomics using NGS for compositional analysis. Furthermore, because microbial response in food environments are also important to understand their roles in food fermentation or spoilage, pattern analysis of RNA expression in the specific food microbe is conducted using RNA-Seq. These microbial genomics, metagenomics, and transcriptomics for food fermentation and spoilage would extend our knowledge on effective utilization of fermenting bacteria for health promotion as well as efficient control of food-borne pathogens for food safety.

• Plant Breeding and Biotechnology
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• 제5권4호
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• pp.269-281
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• 2017

With the continual development of genetically modified (GM) crops, it has become necessary to develop detailed and effective molecular characterization methods to select candidate events from a large pool of transformation events. Relative to traditional molecular analysis methods such as the polymerase chain reaction (PCR) and Southern blot hybridization, next generation sequencing (NGS) technology for whole-genome sequencing of complex crop genomes had proven comparatively useful for in-depth molecular characterization. In this study, four transformation events, including one in Bacillus thuringiensis (Bt)-resistant rice, one in resveratrol-producing rice, and two in beta-carotene-enhanced soybeans, were selected for molecular characterization. To merge NGS analysis and Southern blot-hybridization results, we confirmed the transgene insertion sites, insertion construction, and insertion numbers of these four transformation events. In addition, the read-coverage depth assessed by NGS analysis for inserted genes might provide consistent results in terms of inserted T-DNA numbers in case of complex insertion structures and highly duplicated donor genomes; however, PCR-based methods can produce incorrect conclusions. Our combined method provides an effective and complete analytical approach for whole-genome visual inspection of transformation events that require biosafety assessment.