• Asian Pacific Journal of Cancer Prevention
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• 제15권19호
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• pp.8035-8040
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• 2014

Gastric cancer is the second after lung cause of cancer-related mortality in the world. Early detection and treatment can lead to a long survival time. Recently microarrays and next generation sequencing (NGS) have become very useful tools of comprehensive research into gastric cancer, facilitating the identification of treatment targets and personalized treatments. However, there are numerous challenges from cancer target discovery to practical clinical benefits. Although there are many biomarkers and target agents, only a minority of patients are tested and treated accordingly. Microarray technology with maturity was established more than 10 years ago, and has been widely used in the study of functional genomics, systems biology, and genomes in medicine. Second generation sequencing technology is more recent, but development is very fast, and it has been applied to the genome, including sequencing and epigenetics and many aspects of functional genomics. Here we review insights gained from these studies regarding the technology of microarray and NGS, how to elucidate the molecular basis of gastric cancer and identify potential therapeutic targets, and how to analyse candidate genes. We also discuss the challenges and future directions of such efforts.

• Genomics & Informatics
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• 제14권2호
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• pp.42-45
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• 2016

Since next-generation sequencing (NGS) technique was adopted into clinical practices, revolutionary advances in diagnosing rare genetic diseases have been achieved through translating genomic medicine into precision or personalized management. Indeed, several successful cases of molecular diagnosis and treatment with personalized or targeted therapies of rare genetic diseases have been reported. Still, there are several obstacles to be overcome for wider application of NGS-based precision medicine, including high sequencing cost, incomplete variant sensitivity and accuracy, practical complexities, and a shortage of available treatment options.

• Genomics & Informatics
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• 제8권2호
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• pp.97-99
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• 2010

To allow for a quick conversion of the proprietary sequence data from various sequencing platforms, sequence format conversion toolkits are required that can be easily integrated into workflow systems. In this respect, a format conversion tool, as well as quality conversion tool would be the minimum requirements to integrate reads from different platforms. We have developed the Pyrus NGS Sequencing Format Converter, a simple software toolkit which allows to convert three kinds of Next Generation Sequencing reads, into commonly used fasta or fastq formats. The converter modules are all implemented, uniformly, in Java GUI modules that can be integrated in software applications for displaying the data content in the same format.

• 대한수혈학회지
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• 제29권3호
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• pp.310-319
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• 2018

배경: 최근 차세대염기서열분석법(Next Generation Sequencing: NGS)을 이용한 HLA 형별 분석에 대한 연구가 활발히 진행되고 있다. 이에 HLA 고해상도 분석법의 내재적 한계인 위상 모호성의 문제를 해결하고, 대량 검체 처리가 가능한 NGS 기반 고해상도 HLA 형별 검사법을, 자체 기술로 개발하고자 본 연구를 실시하였다. 방법: HLA NGS를 위한 핵산 추출 조건, 라이브러리 제작 및 PCR 체계 확립, 그리고 생물정보학을 이용한 HLA 형별 분석법을 개발하였다. 본 기관에서 개발한 NGS 기반 HLA 형별 검사의 정확성을 알아보기 위해 SSOP법으로 HLA 형별을 알고 있는 192개 검체와 SBT법으로 HLA 형별을 알고 있는 28개 검체에 대해 NGS 기반으로 검사한 HLA-A, -B 그리고 -DR 형별 결과를 비교해 보았다. 결과: 두 단계의 PCR을 통한 DNA 라이브러리 제작과 MiSeq (Illumina Inc., San Diego, USA) 기기를 이용한 NGS 시퀸싱 그리고 데이터 분석 시스템을 구축하였다. 기존에 HLA 형별을 알고 있는 220개 혈액 검체에 대해 NGS 기반 HLA 형별검사 결과가 모두 일치함을 확인하였다. 결론: NSG 기반 HLA 형별 검사법은 많은 검체를 효율적인 시간 내에 처리가 가능하여 조혈모세포기증 희망자 HLA 검사 등에 유용할 것으로 기대된다.

• Genomics & Informatics
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• 제12권1호
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• pp.2-11
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• 2014

After the initial enthusiasm of the human genome project, it became clear that without additional data pertaining to the epigenome, i.e., how the genome is marked at specific developmental periods, in different tissues, as well as across individuals and species-the promise of the genome sequencing project in understanding biology cannot be fulfilled. This realization prompted several large-scale efforts to map the epigenome, most notably the Encyclopedia of DNA Elements (ENCODE) project. While there is essentially a single genome in an individual, there are hundreds of epigenomes, corresponding to various types of epigenomic marks at different developmental times and in multiple tissue types. Unprecedented advances in next-generation sequencing (NGS) technologies, by virtue of low cost and high speeds that continue to improve at a rate beyond what is anticipated by Moore's law for computer hardware technologies, have revolutionized molecular biology and genetics research, and have in turn prompted innovative ways to reduce the problem of measuring cellular events involving DNA or RNA into a sequencing problem. In this article, we provide a brief overview of the epigenome, the various types of epigenomic data afforded by NGS, and some of the novel discoveries yielded by the epigenomics projects. We also provide ample references for the reader to get in-depth information on these topics.

• 생명과학회지
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• 제31권4호
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• pp.410-417
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• 2021

NGS (Next-generation sequencing), 즉 차세대염기서열분석은 유전체 수준의 방대한 DNA를 작은 절편으로 만들어서 그 절편들의 염기서열들을 동시에 읽어내는 기법이다. 현재 다양한 생명체의 유전체 염기서열 분석부터 cDNA (complementary DNA)나 ChIPed DNA (chromatin immunoprecipitated DNA)를 분석하는데 이 NGS 기법을 사용하고 있으며, 이 때 얻어진 데이터를 적절히 처리하고 분석하는 일은 생물학적으로 유의미한 결과를 얻기 위하여 중요하다. 하지만 대용량 데이터의 저장 및 활용, 그리고 컴퓨터 프로그래밍 바탕의 데이터 분석은 실험을 수행하는 일반 생물학자들에게 어려운 일이다. Galaxy 플랫폼은 다양한 NGS 데이터 분석 tool을 무료로 제공하는 웹 서비스이며, 생물정보학이나 프로그래밍에 대한 전문지식이 없는 연구자들에게 웹 브라우저만을 이용하여 데이터를 분석할 수 있는 환경을 제공한다. 본 논문에서는 ChIP-seq (chromatin immunoprecipitation-sequencing) 수행을 위한 라이브러리 제작 과정 및 Galaxy 플랫폼을 이용한 ChIP-seq 데이터 분석 과정을 설명하고, K562 세포주에서 수행한 히스톤 H3K4me1 ChIP-seq 결과가 public 데이터와 일치함을 보여준다. 따라서 Galaxy 플랫폼을 활용한 NGS 데이터 분석은 생물정보학에 대한 손쉬운 접근 방법을 제공할 것으로 기대된다.

• Genomics & Informatics
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• 제18권1호
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• pp.5.1-5.5
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• 2020

Highly pathogenic avian influenza (HPAI) viruses have caused severe respiratory disease and death in poultry and human beings. Although most of the avian influenza viruses (AIVs) are of low pathogenicity and cause mild infections in birds, some subtypes including hemagglutinin H5 and H7 subtype cause HPAI. Therefore, sensitive and accurate subtyping of AIV is important to prepare and prevent for the spread of HPAI. Next-generation sequencing (NGS) can analyze the full-length sequence information of entire AIV genome at once, so this technology is becoming a more common in detecting AIVs and predicting subtypes. However, an analysis pipeline of NGS-based AIV sequencing data, including AIV subtyping, has not yet been established. Here, in order to support the pre-processing of NGS data and its interpretation, we developed a user-friendly tool, named prediction of avian influenza virus subtype (PAIVS). PAIVS has multiple functions that support the pre-processing of NGS data, reference-guided AIV subtyping, de novo assembly, variant calling and identifying the closest full-length sequences by BLAST, and provide the graphical summary to the end users.

• 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.

• The Plant Pathology Journal
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• 제37권6호
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• pp.521-532
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• 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.

• 생명과학회지
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• 제25권3호
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• pp.349-356
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• 2015

최근 차세대염기서열해독법(Next Generation Sequencing, NGS)의 급속한 발전에 힘입어, 다양한 가축 종에 대한 전장유전체 수준의 해독 및 분석 연구수행이 가능하게 되었다. 소의 경우 현재 한우, 칡소, 흑우, 제주흑우 4품종의 재래소가 국제연합식량농업기구 가축다양성 정보시스템에 등록돼 있는 상태이다. 이러한 재래유전자원은 최근 NGS 기술을 이용 전장유전체에 걸친 대용량의 단일염기다형성 정보를 얻는데 성공하였으며, 또한 한국 재래소품종이 유럽기원의 소 품종들과 유전학적으로 차이가 있다는 점이 밝혀졌다. 또한 소 유전체학 분야에서 이 NGS의 응용은 유전체의 구조적 변이 특히 종전 대용량으로 정확한 발굴이 어려웠던 전장유전체에 널리 퍼진 복제수변이의 발굴에 성공적으로 적용되었다. 이러한 일련의 성공에도 불구하고 최근 NGS를 이용한 연구는 내재적인 한계점이 있었는데, 이는 연구 당시 고가의 연구비용 및 분석의 난해함으로 인해 각 대표 소 품종의 단수 또는 소수 개체에 대해서만 적용되었다는 점이 그 대표적 예라 할 수 있을 것이다. 즉, NGS에서 파생된 데이터의 보다 정확한 생물학적 의의를 찾기 위해서는 추가 실험적 검증과 더불어 면밀한 해석이 필요하다는 점을 시사하는 것이다. 최근 차세대염기서열 해독 비용이 지속으로 하락하고 있으며, 이는 단수개체가 아닌 집단수준에서의 NGS 적용이 가능해 짐에 따라 다양한 집단유전체학적 이론이 접목된 연구가 가능해지고 있다. 현재 국내 재래소 품종에 대한 집단수준에서의 연구는 극히 미흡한 상태이나, 이러한 상황은 최근 고밀도 칩, 차세대염기서열 자료와 같은 대용량 유전정보를 생산, 분석 중에 있어 재래가축에 대한 집단수준에서의 연구가 일부 해소될 것으로 기대된다.