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Contrasting results have been reported concerning the association of a splice-site polymorphism (rs10774671) in OAS1 with multiple sclerosis (MS). We analysed two OAS1 regions encompassing alternatively spliced exons. While the region carrying the splice-site variant is neutrally evolving, a signature of long-standing balancing selection was observed across an alternative exon 7. Analysis of variants in this exon identified an insertion/deletion polymorphism (rs11352835, A/-) that originates predicted products with distinct C termini. This variant is located along the major branch of the haplotype genealogy, suggesting that it may represent the selection target. A case/control study for MS indicated that rs11352835 is associated with disease susceptibility (for an allelic model with the deleted allele predisposing to MS, OR 1.27, 95% CI 1.072-1.513, p = 0.010). No association was found between rs10774671 and MS. As the two SNPs are in linkage disequilibrium in Europeans, the previously reported association between rs10774671 and MS susceptibility might be driven by rs11352835, possibly explaining the contrasting results previously observed for the splice-site polymorphism. Thus, we describe a novel susceptibility variant for MS in OAS1 and show that population genetic analyses can be instrumental to the identification of selection targets and, consequently, of functional polymorphisms with an effect on phenotypic traits.
Pubmed ID: 21735172
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A 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 mentionsSoftware program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs. Quanto is a 32-bit Windows application requiring Windows 95, 98, NT, 2000, ME or XP to run. The graphical user interface allows th e user to easily change the model and view the results without having to edit an input file and rerun the program for every model. The results of a session are stored to a log file. This log can be printed or saved to a file for reviewing at a later date. An option is included to create a text file of the log that can be imported into other documents. (entry from Genetic Analysis Software)
View all literature mentionsSoftware program that implements a new statistical method for reconstructing haplotypes from population genotype data (entry from Genetic Analysis Software)
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