Abstract
Demographic events such as migration, and evolutionary events like mutation and recombination, have contributed to the genetic variations that are found in the human genome. During the evolution and differentiation of human populations, different functional genes and pathways (a group of genes that act together to perform specific biological tasks) would have displayed different degrees of genetic diversity or evolutionary conservatism. To query the genetic differences of functional genes or pathways in populations, we have developed the human gene population genetic difference (HGPGD) database. Currently, 11 common population genetic features, 18,158 single human genes, 220 KEGG (Kyoto Encyclopedia of Genes and Genomes) human pathways and 4,639 Gene Ontology (GO) categories (3,269 in biological process; 862 in molecular function; and 508 in cellular component) are available in the HGPGD database. The 11 population genetic features are related mainly to three aspects: allele frequency, linkage disequilibrium pattern, and transferability of tagSNPs. By entering a list of Gene IDs, KEGG pathway IDs or GO category IDs and selecting a population genetic feature, users can search the genetic differences between pairwise HapMap populations. We hope that, when the researchers carry out gene-based, KEGG pathway-based or GO category-based research, they can take full account of the genetic differences between populations. The HGPGD database (V1.0) is available at http://www.bioapp.org/hgpgd.
Highlights
Any two unrelated individuals share about 99.9% of their genomic DNA sequence
Overview of the human gene population genetic difference (HGPGD) Database The HGPGD database is a freely available database that focuses on population genetic differences in human genes
For each of 18,158 single genes in the HGPGD database, by entering a list of Gene IDs, and selecting a population genetic feature, users can obtain the genetic differences between each pairwise HapMap population
Summary
Any two unrelated individuals share about 99.9% of their genomic DNA sequence. The approximately 0.1% that is different is important in explaining some human phenotypic differences, such as skin color [1], susceptibility to disease and response to pharmacological agents [2,3,4]. For example, drug-related gene regions [5], the neuregulin 1 gene [6] and the enzyme glucokinase (GCK) gene region [7], in different populations have been reported. These studies have been successful in understanding some population differences [8,9,10,11,12,13], they have focused on only one or several gene regions. With the development of high-throughput technologies, international projects, such as the HapMap project [14,15,16,17] and the 1000 genome project [18,19], have been developed The data from these projects allow genome-wide genetic differences to be investigated. We used the SNP genotype data from HapMap to measure population genetic differences in functional gene regions in the 11 HapMap populations
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