• Genomics & Informatics
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• 제6권3호
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• pp.130-135
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• 2008

The haplotypes of a 200 kb region in the human chromosome X terminal band (q28) were analyzed using the International HapMap Project Phasell data, which had been collected for three analysis panels (YRI, CEU, and CHB＋JPT). When multiple linkage disequilibrium blocks were encountered for a panel, the neighboring haplotypes that had crossover rate of 5% or more in the panel were combined to generate 'haploid' configurations. This resulted in 8, 7, and 5 'haploid' configurations for the panels of YRI, CEU, and CHB＋JPT, respectively. The multiple sequence alignment of these 'haploids' was used for the calculation of allele-sharing distances and the subsequent principal coordinate analysis. Two 'haploids' in CEU and CHB＋JPT were hypothesized as 'parental' in light of the observations that the successive recombinants of these haploids can model two other haploids in CEU and CHB＋JPT, and that their configurations were consistent with those in YRI. This study demonstrates the utility of haplotype phylogeny in understanding population evolution.

• Asian Journal of Innovation and Policy
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• 제8권2호
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• pp.180-207
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• 2019

This article explores the historical evolutionary process of the biopharmaceutical industry of Korea, and how intentional and unintentional policy interventions have triggered the creation of the industry's system dynamics and paved the way for the generation of a few global leading products, including biosimilar, as well as next-generation therapeutics of gene and cell. The policies cover the simple technology transfer of API synthesis to overcome the endemic parasitic disease, new substance patent adoption and new drug development consortia, human resource development, various national initiatives influenced by the Human Genome Project, and venture promotion schemes. The scope and implementation tools under these policies have been aligned and refined to transform traditional fine chemical-based pharmaceuticals, to stimulate large companies' participation and to create technology-based venture companies in the biopharma business of Korea.

• Journal of Interdisciplinary Genomics
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• 제6권1호
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• pp.1-5
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• 2024

Chromosome 22 is an acrocentric chromosome containing 500-600 genes, representing 1.5%-2% of the total DNA in cells. It was the first human chromosome to be fully sequenced by the Human Genome Project. Several syndromes involving the partial deletion or duplication of chromosome 22 are well descibed, including 22q11.2 deletion syndrome, 22q11.2 duplication syndrome, 22q11.2 distal deletion syndrome, Phelan-McDermid syndrome caused by a 22q13 deletion or pathogenic variant in SHANK3, and cat-eye syndrome caused by a 22 pter-q11 duplication. This review aims to provide concise information on the clinical characteristics of these syndromes. In particular, the similarities in features among these syndromes, genetic basis, and standard detection techniques are described, providing guidance for diagnosis and genetic counselling.

• Journal of Gastric Cancer
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• 제22권4호
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• pp.273-305
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• 2022

Gastric cancer (GC) is one of the most common lethal malignant neoplasms worldwide, with limited treatment options for both locally advanced and/or metastatic conditions, resulting in a dismal prognosis. Although the widely used morphological classifications may be helpful for endoscopic or surgical treatment choices, they are still insufficient to guide precise and/or personalized therapy for individual patients. Recent advances in genomic technology and high-throughput analysis may improve the understanding of molecular pathways associated with GC pathogenesis and aid in the classification of GC at the molecular level. Advances in next-generation sequencing have enabled the identification of several genetic alterations through single experiments. Thus, understanding the driver alterations involved in gastric carcinogenesis has become increasingly important because it can aid in the discovery of potential biomarkers and therapeutic targets. In this article, we review the molecular classifications of GC, focusing on The Cancer Genome Atlas (TCGA) classification. We further describe the currently available biomarker-targeted therapies and potential biomarker-guided therapies. This review will help clinicians by providing an inclusive understanding of the molecular pathology of GC and may assist in selecting the best treatment approaches for patients with GC.

• Genomics & Informatics
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• 제14권4호
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• pp.196-204
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• 2016

Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine), MIG++ implemented in PLINK 1.9 and S-MIG++. We used several experimental datasets obtained by sampling subsets of single nucleotide polymorphism (SNP) markers of chromosome 22 region in the 1000 Genomes Project data and also the HapMap phase 3 data to compare the results of haplotype block partitions by five methods. With decreasing sampling ratio down to 20% of the original SNP markers, the total number of haplotype blocks decreases and the length of haplotype blocks increases for all algorithms. When we examined the marker-independence of the haplotype block locations constructed from the datasets of different density, the results using below 50% of the entire SNP markers were very different from the results using the entire SNP markers. We conclude that the haplotype block construction results should be used and interpreted carefully depending on the selection of markers and the purpose of the study.

• Genomics & Informatics
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• 제5권4호
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• pp.188-193
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• 2007

The Functional Element SNPs Database (FESD) categorizes functional elements in human genic regions and provides a set of single nucleotide polymorphisms (SNPs) located within each area. Users may select a set of SNPs in specific functional elements with haplotype information and obtain flanking sequences for genotyping. Our previous version of FESD has been improved in several ways. We regenerated all the data in FESD II from recently updated source data such as HapMap, UCSC GoldenPath, dbSNP, OMIM, and $TRANSFAC^{(R)}$. Users can obtain information about tagSNPs and simulate LD blocks for each gene from four ethnicities in the HapMap project on the fly. FESD II employs a Java/JSP web interface for better platform portability and higher speed than PHP in the previous version. As a result, FESD II provides its users with more powerful information about functional element SNPs of human ethnicities.

• Genomics & Informatics
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• 제6권2호
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• pp.57-63
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• 2008

The Korean HapMap Project has been carried out for the last 5 years since it started in June, 2003. The project generated data for a sum of 1,764,000 Korean SNPs and formally registered the data to the dbSNP of NCBI (The dbSNP website. 2008). We have developed a series of software programs for association studies as well as for the comparison and analysis of Korean HapMap data with four other populations (CEPH, Yoruba, Han Chinese, and Japanese populations). The KHapmap Browser was developed and integrated to provide haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (http://www.khapmap.org). On that basis, GBrowse was adopted in the KHapmap Browser for inherent Korean genetic data, and a provision of extended services was pledged with the distributed sequence annotation system (DAS). The dynamic linking service of the KHapmap Browser to other tools in our intranetwork environment provides many enhanced functions over GBrowse without DAS. KHapmap Browser is expected to be an invaluable tool for the study of Korean and international Hapmap data.

• 한국정보통신학회논문지
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• 제12권2호
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• pp.315-320
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• 2008

오늘날 인간 genome프로젝트와 같은 종합적인 연구의 궁극적 목적을 달성하기 위해서는 이들 연구로부터 획득한 대량의 관련 데이터에 대해 새로운 현실적 의미를 부여할 수 있어야 한다. 이러한 맥락에서 유전자 발현 분석 시스템과 염기 서열 분석 시스템의 구축이 포스트 genome 시대를 맞이하여 새롭게 주복을 받고 있다. 최근에는 종양의 특정 부 클래스가 특정 염색체와 관련되어 있다는 사실이 밝혀지면서, 마이크로어레이는 유전자 발현 정보를 기반으로 암의 분류와 예측을 통한 진단 분야에도 활용되기 시작했다. 본 논문에서는 암에 걸린 흰쥐 외피 기간 세포 분화 실험에서 얻어진 3840 유전자의 마이크로어레이 cDNA를 이용하여 데이터의 정규화를 거쳐 정보력 있는 유전자 목록을 별도로 추출할 수 있는 시스템을 고안하고 보다 정보력 있는 유전자를 선택하기 위해 조합 방법을 제안하였다. 그리고 제안한 시스템과 방법론의 가능성을 실험을 통해 검증하였다. 그 결과 PC-ED 조합이 98.74%의 정확도와 0.04%의 MSE를 보여 단일 유사성 척도를 사용하여 유전자 목록을 생성하고 실험을 수행한 경우보다 분류 성능이 향상되었다.

• 대한지역사회영양학회:학술대회논문집
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• 대한지역사회영양학회 2005년도 춘계학술대회
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• pp.9-13
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• 2005

많은 질병의 발생원인의 약 60%이상이 환경요인 때문이라는 것이 잘 알려져 있고 영양과 식이섭취의 중요도는 이중에서도 가장 중요한 것으로 알려져 있다. 특히 Human Genome Project의 완성 이후 Genomics시대에 발맞추어 여러 가지 high throughput 실험들이 가능해지고 Single Nucleotide Polymorphism (SNP)의 발굴이 진행되면서 영양소와 식이요인들의 유전자 발현과 유전학적 변이와의 상관관계가 질병의 예방차원에서 앞으로 연구되어야할 큰 과제로 대두되고 있으며 이를 통한 개개인에 적합한 영양섭취를 권장하는 새로운 방향의 영양관리에 가능성에 대해 많은 관심이 쏠리고 있다. 이에 본 발표에서는 Nutrinogenomics와 Nutrinogenetics의 연구방향과 연구 성과들을 소개하여 유전적 요인에 의한 식이요소의 섭취경향이 질병에 어떠한 관련이 있는지, 최근까지의 연구에서의 제한점은 어떠한 것이 있는지 살펴보고자 한다.

• 한국지능정보시스템학회:학술대회논문집
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• 한국지능정보시스템학회 2002년도 춘계학술대회 논문집
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• pp.273-283
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• 2002

2000년 7월 인간게놈프로젝트 (Human Genome Project)가 완성되면서 Biotechnology(BT)산업에 대하여 많은 관심이 집중되고 있다. BT산업은 기술집약적·지식집약적인 산업 특성을 가지고 있고 R&D 활동의 중요성이 두드러진다. 이에 따라 방대한 데이터와 지식에 대한 효율적인 관리 등 R&D 전 과정에 걸쳐 생성되는 지식들에 대한 체계적인 관리가 요구된다 본 연구에서는 BT산업의 기초 조직인 BT연구실의 효과적이며 효율적인 업무 수행을 지원하기 위하여 기존의 지식경영시스템(Knowledge Management System, KMS)에 실험실정보관리시스템(Laboratory Information Management System, LIMS)이 통합된 BT실험실의 지식경영시스템 모델을 제시하였다. 이를 위해 BT연구실에서 생성되는 지식들의 체계를 분류하고 지식경영시스템 구축에 있어서의 핵심성공요인을 분석하였으며, 분석 결과를 바탕으로 모델을 개발하여 대학교 유전자 연구실에 실제 적용하였다.