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To investigate the impact of single nucleotide polymorphisms (SNPs) of SHBG gene the neighboring genes on SHBG levels, bone mineral density (BMD) and osteoporosis in Chinese males. A group of Chinese men, aged ⩾ 45 years were included in the analysis. BMD was measured with dual-energy X-ray absorptiometry (DXA), SHBG and total testosterone (TT) was measured using chemiluminescent immunoassay, and free testosterone (FT) was calculated. SNPs of SHBG gene and the neighboring genes were studied by means of improved multiple ligase detection reaction (iMLDR). A total of 404 men were included in our study. In the single locus analysis, significant associations were found between SHBG levels and four polymorphisms (rs11078701, rs9901675, rs9898876 and rs2541012) in age- and BMI-adjusted models. In addition, statistically significant difference was found between osteoporosis patients and control subjects in genotype distributions of rs9898876, rs2541012, rs6259 and rs3853894. In the models with or without adjustment for confounders (age, BMI, SHBG and free testosterone (FT) levels), carriers of variant genotype of rs9898876, rs2541012 and rs6259 had lower BMD and were more likely to suffer from osteoporosis, as compare to carriers of common genotype. Subjects with variant genotype of rs3853894 had higher BMD and were less likely to suffer from osteoporosis, as compared to subjects with common genotype. In the haplotypes analysis, CCGGT (constituted by rs11078701C, rs1017163C, rs9898876G, rs62059836G and rs2541012T) and haplotype CGGT (constituted by rs858521C, rs858518G, rs6259G and rs727428T) was associated with a significant risk effect for osteoporosis. Polymorphisms of SHBG or the neighboring genes were associated with SHBG levels or BMD and osteoporosis, suggesting the involvement of genetic variation of SHBG in bone health.
Pubmed ID: 26657339
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Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.
View all literature mentionsA Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.
View all literature mentionsGenotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment.
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