Genomics & Informatics Vol. 6(2) 57-63, June 2008 *Corresponding author: E-mail yjkim8@kribb.re.kr Tel +82-42-879-8127, Fax +82-42-879-8119 Accepted 10 June 2008 Development of KHapmap Browser using DAS for Korean HapMap Research Hoon Jin 1 , Seung-Ho Kim 2 , Young Uk Kim 1 , Young-Kyu Park 1 , Mihyun Ji 1 and Young Joo Kim 1 * 1 Medical Genomics Research Center, 2 Instrumental Analysis Laboratory, KRIBB, Daejeon 305-806, Korea Abstract The Korean HapMap Project has been carried out for the last 5 years since it started in June, 2003. The proj- ect 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 ser- ies 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 hap- lotype retrieval and comparative study tools of human ethnicities for comprehensive disease association stud- ies (http://www.khapmap.org). On that basis, GBrowse was adopted in the KHapmap Browser for inherent Korean genetic data, and a provision of extended serv- ices was pledged with the distributed sequence annota- tion system (DAS). The dynamic linking service of the KHapmap Browser to other tools in our intranetwork en- vironment provides many enhanced functions over GBrowse without DAS. KHapmap Browser is expected to be an invaluable tool for the study of Korean and in- ternational Hapmap data. Keywords: Korean, SNP, browser, DAS, Hapmap, asso- ciation Introduction Single nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation and are a re- source for mapping complex genetic traits. A genome is covered by millions of these markers, and researchers are able to compare which SNPs predominate in people who have a certain disease. The International HapMap Project, launched in October, 2002, motivated us to start the Korean HapMap Project in order to support Korean HapMap infrastructure development and to ac- celerate the finding of genes that affect health, disease, and individual responses to medications and environ- mental factors (The International HapMap Consortium. 2007). In the International HapMap Project, various types of genetic data are being gathered and analyzed from four populations (CEPH, Yoruba, Han Chinese, and Japanese populations). The International HapMap Pro- ject developed haplotype maps that describe what these variants are, where they occur in the genome, and how they are distributed among the persons within. A Korean SNP and haplotype database system was developed through the Korean HapMap Project to provide Korean researchers with useful data-mining information about disease-associated biomarkers for studies of complex diseases, such as diabetes, cancer, and stroke. As a partial result of this project, we generated and regis- tered data for 1,764,000 Korean SNPs to the dbSNP of NCBI (dbSNP website. 2008). The KHapmap Browser that is based on the generic genome browser (GBrowse) provides haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (Stein et al., 2002). GBrowse is a combination of databases and in- teractive web pages for manipulating and displaying an- notations on genomes. In other words, GBrowse is a web-based application tool that is developed for navi- gating and visualizing the genomic features and annota- tions interactively for users. Through it, users can view a certain region of the desired genomes and search for genetic biomarkers. They may conduct a full-text search for most features of the genomes. They also can down- load SNP assay, genotype, and allele frequency in- formation and generate customized sets of tag-SNPs for their association studies (Thorisson et al., 2005). GBrowse utilizes a web-based display that can be used to show arbitrary features of a nucleotide or protein se- quence and can accommodate genome-scale se- quences that are megabases in length. The GBrowse system consists of various kinds of software modules and systems, such as web servers, database systems, and Perl libraries. At present, many biological websites that provide ge- nomic variants or portal services have been developed using GBrowse, including the following: the UCSC Genome Browser (Kuhn et al., 2007), the International HapMap Project (Thorisson et al., 2005), PlasmoDB (The