• Genomics & Informatics
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• 제16권3호
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• pp.71-74
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• 2018

Because castration-resistant prostate cancer (CRPC) does not respond to androgen deprivation therapy and has a very poor prognosis, it is critical to identify a prognostic indicator for predicting high-risk patients who will develop CRPC. Here, we report a dataset of whole genomes from four pairs of primary prostate cancer (PC) and CRPC samples. The analysis of the paired PC and CRPC samples in the whole-genome data showed that the average number of somatic mutations per patients was 7,927 in CRPC tissues compared with primary PC tissues (range, 1,691 to 21,705). Our whole-genome sequencing data of primary PC and CRPC may be useful for understanding the genomic changes and molecular mechanisms that occur during the progression from PC to CRPC.

• 생물정신의학
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• 제8권2호
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• pp.203-207
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• 2001

The genome sequencing project has generated and will continue to generate enormous amounts of sequence data including 5 eukaryotic and about 60 prokaryotic genomes. Given this ever-increasing amounts of sequence information, new strategies are necessary to efficiently pursue the next phase of the genome project-the elucidation of gene expression patterns and gene product function on a whole genome scale. In order to assign functional information to the genome sequence, DNA chip(or gene microarray) technology was developed to efficiently identify the differential expression pattern of independent biological samples. DNA chip provides a new tool for genome expression analysis that may revolutionize many aspects of biotechnology including new drug discovery and disease diagnostics.

• 정보처리학회논문지A
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• 제9A권3호
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• pp.387-398
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• 2002

최근 활발한 소단위 게놈 프로젝트의 수행으로 많은 생물체의 유전체 전체 서열이 밝혀짐에 따라서 전유전체(whole genome)를 기본 단위로 하여 개별 유전자나 그에 관련된 기능 연구가 매우 활발히 이루어지고 있다. 전유전체의 염기 서열은 수백만 bp(base pairs)에서 수백억 bp(base pairs) 정도의 대용량 텍스트 데이터이기 때문에 단순한 온라인 문자 일치(on-line string matching) 알고리즘으로 분석하는 것은 매우 비효율적이다. 본 논문에서는 대용량의 유전체 서열을 분석하는데 적합한 자료 구조인 스트링 B-트리를 사용하여 유전체 서열의 분석과 가시화를 위한 워크벤치를 개발한 과정을 소개한다. 본 연구에서 개발한 시스템은 크게 질의문 부분과 가시화 부분으로 나뉘어 진다. 질의문 부분에는 유전체 서열에 특정 서열이 나타나는 부분의 위치와 횟수를 알아보거나 k번 나타나는 서열을 조사하는 것과 같은 기본적인 패턴 검색 부분과 k-mer 분석을 위한 질의어가 다양하게 준비되어 있다. 가시화 부분은 전유전체 서열과 주석(annotation)을 보여주거나, 유전체 분석을 용이하도록 여러 가시화 방법, CGR(Chaos Game Representation), k-mer graph, RWP(Random Walk Plot) 등으로 생물학자들이 쉽게 전체 구조와 특성 파악할 수 있도록 도와준다. 본 논문이 제안하는 분석 시스템은 생물체의 진화적 관계를 밝히고, 염색체 내에 아직 알려지지 않은 새로운 유전자나 기능이 밝혀지지 않은 junk DNA들의 기능 등을 연구하는데 사용할 수 있다.

• Genomics & Informatics
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• 제21권1호
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• pp.11.1-11.5
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• 2023

Breast cancer is the most common cancer worldwide, and advanced breast cancer with metastases is incurable mainly with currently available therapies. Therefore, it is essential to understand molecular characteristics during the progression of breast carcinogenesis. Here, we report a dataset of whole genomes from the human mammary epithelial cell system derived from a reduction mammoplasty specimen. This system comprises pre-stasis 184D cells, considered normal, and seven cell lines along cancer progression series that are immortalized or additionally acquired anchorage-independent growth. Our analysis of the whole-genome sequencing (WGS) data indicates that those seven cancer progression series cells have somatic mutations whose number ranges from 8,393 to 39,564 (with an average of 30,591) compared to 184D cells. These WGS data and our mutation analysis will provide helpful information to identify driver mutations and elucidate molecular mechanisms for breast carcinogenesis.

• The Plant Pathology Journal
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• 제24권3호
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• pp.361-364
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• 2008

The complete nucleotide sequences of a Korean isolate of Potato virus X(PVX-Kr) has been determined. Full-length cDNA of PVX-Kr has been directly amplified by long template reverse transcription and polymerase chain reaction(RT-PCR) using virus specific 5'-end primer and 3'-end primer, and then constructed in a plasmid vector. Consecutive subclones of a full-length cDNA clone were constructed to identify whole genome sequence of the virus. Total nucleotide sequences of genome of PVX-Kr were 6,435 excluding one adenine at poly A tail, and genome organization was identical with that of typical PVX species. Comparison of whole genome sequence of PVX-Kr with those of European and South American isolates showed 95.4-96.8% and 77.4-77.9%, in nucleotide similarity, respectively. Sequenced PVX-Kr in this study and twelve isolates already reported could be divided into two subgroups in phylogeny based on their complete nucleotide sequences. Phylogenetic tree analysis demonstrated that PVX-Kr was clustered with European and Asian isolates(Taiwan, os, bs, Kr, S, X3, UK3, ROTH1, Tula) in the same subgroup and South American isolates(CP, CP2, CP4, HB) were clustered in the other subgroup.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2018년도 춘계학술대회 및 임시총회
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• pp.51-51
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• 2018

The application of recombinant DNA technology has been remarkable and nearly replaced commonly used traditional methods. Traditional industrial microbiology long depended on the discovery of valuable strains and mutagenesis of such strains to improve its secretion capacity of enzymes and secondary metabolites on the industrial scale. Commodities included industrial enzymes and biopharmaceuticals. The purpose of genome manipulation by the crossing of different strains or genetic recombination of naked DNA to the genome is of increased production of valuable metabolites. We optimized a transformation method to either for removal of innate genes, introduction of heterologous genes, or combination of both. We have been used selected whole or partial genes to manipulate target fungi toward the development of strains overproducing invaluable proteins. We have also used the whole genome sequence information of fungal genomes in public databases and functional genomics approach to select genes to manipulate and eventually contributing greatly to the development of overproducing industrial strains overproducing proteins or secondary metabolites. I will briefly review 1) filamentous fungi as a host for production of recombinant proteins and secondary metabolites, 2) markets of industrial metabolites, 3) a new approach to manipulate up to five genes at the same time in the system that ProxEnrem uses.

• 식품과학과 산업
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• 제50권1호
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• pp.11-15
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• 2017

Epigenomics is a study that analyzes and quantifies various epigenetic alterations that affect gene expressions in cells from the viewpoint of collective characteristics on biological molecular pools. DNA methylation and histone modification in cells can induce the epigenetic alterations. Especially, epigenetic alterations influenced by external factors as ingested foods and other environmental factors have been examined in the whole genome regions, which provide accumulated data of altered regions or patterns of global genome, Statistical analyses of these regions or patterns enables us to correlate epigenomic changes with human diseases in the whole genome region. Finding meaningful regulators is a major concern of epigenomic research in recent years, and these results will give the food industry an important clue to future food

• Genomics & Informatics
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• 제2권4호
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• pp.184-190
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• 2004

An approach for genome analysis based on assembly of fragments of DNA from the whole genome can be applied to obtain the complete nucleotide sequence of the genome of Zymomonas mobilis. However, the problem of fragment assembly raise thorny computational issues. Computer simulation studies of sequence assembly usually show some abnormal assemblage of artificial sequences containing repetitive or duplicated regions, and suggest methods to correct those abnormalities. In this paper, we describe five simulation studies which had been performed previous to the actual genome assembly process of Zymomonas mobilis ZM4.

• Molecular & Cellular Toxicology
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• 제4권3호
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• pp.246-252
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• 2008

Tumor tissue is usually contaminated by normal tissue components, which reduces the sensitivity of analysis for exploring genetic alterations. Although microdissection has been adopted to minimize the contamination of tumor DNA with normal cell components, there is a concern over the amount of microdissected DNA not enough to be applied to array-CGH reaction. To amplify the extracted DNA, several whole genome amplification (WGA) methods have been developed, but objective comparison of the array-CGH outputs using different types of WGA methods is still scarce. In this study, we compared the performance of non-amplified microdissected DNA and DNA amplified in 2 WGA methods such as degenerative oligonucleotide primed (DOP)-PCR, and multiple strand displacement amplification (MDA) using Phi 29 DNA polymerase. Genomic DNA was also used to make a comparison. We applied those 4 DNAs to whole genome BAC array to compare the false positive detection rate (FPDR) and sensitivity in detecting copy number alterations under the same hybridization condition. As a result microdissected DNA method showed the lowest FPDR and the highest sensitivity. Among WGA methods, DOP-PCR amplified DNA showed better sensitivity but similar FPDR to MDA-amplified method. These results demonstrate the advantage and applicability of microdissection for array-CGH analysis, and provide useful information for choosing amplification methods to study copy number alterations, especially based on precancerous and microscopically invaded lesions.

• International Journal of Oral Biology
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• 제45권2호
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• pp.70-75
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• 2020

The aim of this study was to identify strain KCOM 1265 isolated from subgingival plaque at the species level by comparing 16S ribosomal RNA gene (16S rDNA) and genome sequences. The whole genome of strain KCOM 1265 was extracted using the phenol-chloroform extraction method. 16S rDNA was amplified using polymerase chain reaction and sequenced using the dideoxy chain termination method. Pairwise genome comparison was performed using average nucleotide identity (ANI) and genome-to-genome distance (GGD) analyses. The data showed that the percent similarity of 16S rDNA sequence of strain KCOM 1265 was 99.6% as compared with those of Fusobacterium polymorphum ATCC 10953^T and Fusobacterium hwasookii KCOM 1249^T. The ANI values of strain KCOM 1265 with F. polymorphum ATCC 10953^T and F. hwasookii KCOM 1249^T were 95.8% and 93.0%, respectively. The GGD values of strain KCOM 1265 with F. polymorphum ATCC 10953^T and F. hwasookii KCOM 1249^T were 63.9% and 49.6%, respectively. These results indicate that strain KCOM 1265 belongs to F. polymorphum.