Single nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation and are a resource 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 accelerate the finding of genes that affect health, disease, and individual responses to medications and environmental factors.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 on complex diseases, such as diabetes, cancer, and stroke.Also, we have developed a series of software programs for association studies as well as the comparison and analysis of Korean HapMap data with other populations, such as European, Chinese, Japanese, and African populations.The developed software includes HapMapSNPAnalyzer, SNPflank, HWE Test, FESD, D2GSNP, SNP@Domain, KMSD, KFOD, KFRG, and SNP@WEB.We developed a disease-related SNP retrieval system, in which OMIM, GeneCards, and MeSH information were integrated and analyzed for medical research scientists.The kHapMap Browser system that we developed and integrated provides haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (http://www.khapmap.org).It is expected that researchers may be able to retrieve useful information from the kHapMap Browser to find useful biomarkers and genes in complex disease association studies and use these biomarkers and genes to study and develop new drugs for personalized medicine.
Abstract Background Mitochondrial sequence variation provides critical information for studying human evolution and variation. Mitochondrial DNA provides information on the origin of humans, and plays a substantial role in forensics, degenerative diseases, cancers, and aging process. Typically, human mitochondrial DNA has various features such as HVSI, HVSII, single-nucleotide polymorphism (SNP), restriction enzyme sites, and short tandem repeat (STR). Results We present a variome database (MitoVariome) of human mitochondrial DNA sequences. Queries against MitoVariome can be made using accession numbers or haplogroup/continent. Query results are presented not only in text but also in HTML tables to report extensive mitochondrial sequence variation information. The variation information includes repeat pattern, restriction enzyme site polymorphism, short tandem repeat, disease information as well as single nucleotide polymorphism. It also provides a graphical interface as Gbrowse displaying all variations at a glance. The web interface also provides the tool for assigning haplogroup based on the haplogroup-diagnostic system with complete human mitochondrial SNP position list and for retrieving sequences that users query against by using accession numbers. Conclusion MitoVariome is a freely accessible web application and database that enables human mitochondrial genome researchers to study genetic variation in mitochondrial genome with textual and graphical views accompanied by assignment function of haplogrouping if users submit their own data. Hence, the MitoVariome containing many kinds of variation features in the human mitochondrial genome will be useful for understanding mitochondrial variations of each individual, haplogroup, or geographical location to elucidate the history of human evolution.
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.
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