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首页> 外文会议>Pacific Symposium on Biocomputing 2006 >A TOOL FOR SELECTING SNPS FOR ASSOCIATION STUDIES BASED ON OBSERVED LINKAGE DISEQUILIBRIUM PATTERNS
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A TOOL FOR SELECTING SNPS FOR ASSOCIATION STUDIES BASED ON OBSERVED LINKAGE DISEQUILIBRIUM PATTERNS

机译：基于观察到的连锁不平衡模式的用于关联研究的SNPS选择工具

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The design of genetic association studies using single-nucleotide polymorphisms (SNPs) requires the selection of subsets of the variants providing high statistical power at a reasonable cost. SNPs must be selected to maximize the probability that a causative mutation is in linkage disequilibrium (LD) with at least one marker gcnotypcd in the study. The HapMap project performed a genome-wide survey of genetic variation with about a million SNPs typed in four populations, providing a rich resource to inform the design of association studies. A number of strategies have been proposed for the selection of SNPs based on observed LD, including construction of metric LD maps and the selection of haplotype tagging SNPs. Power calculations are important at the study design stage to ensure successful results. Integrating these methods and annotations can be challenging: the algorithms required to implement these methods are complex to deploy, and all the necessary data and annotations are deposited in disparate databases. Here, we present the SNPbrowser~(TM) Software, a freely available tool to assist in the LD-based selection of markers for association studies. This stand-alone application provides fast query capabilities and swift visualization of SNPs, gene annotations, power, haplotype blocks, and LD map coordinates. Wizards implement several common SNP selection workflows including the selection of optimal subsets of SNPs (e.g. tagging SNPs). Selected SNPs are screened for their conversion potential to either TaqMan~R Genotyping Assays or the SNPlex~(TM) Genotyping System, two commercially available genotyping platforms, expediting the set-up of genetic studies with an increased probability of success.
机译：使用单核苷酸多态性（SNP）进行遗传关联研究的设计要求选择变异体的子集，以合理的成本提供较高的统计能力。必须选择SNP，以使在研究中与至少一种标记gcnotypcd发生连锁不平衡（LD）时引起致病突变的可能性最大化。 HapMap项目对全基因组变异进行了全基因组调查，其中有大约100万个SNP位于四个种群中，从而为关联研究的设计提供了丰富的资源。已经提出了许多基于观察到的LD来选择SNP的策略，包括构建度量LD图和选择单倍型标记SNP。功率计算在研究设计阶段很重要，以确保获得成功的结果。集成这些方法和注释可能具有挑战性：实现这些方法所需的算法部署起来很复杂，并且所有必要的数据和注释都存储在不同的数据库中。在这里，我们介绍了SNPbrowser〜（TM）软件，这是一个免费的工具，可以帮助基于LD的关联研究标记选择。这个独立的应用程序提供了快速查询功能，并且可以快速显示SNP，基因注释，功效，单倍型模块和LD图坐标。向导实现了几种常见的SNP选择工作流程，包括选择SNP的最佳子集（例如标记SNP）。筛选选定的SNP，以将其转化为TaqMan〜R基因分型测定法或SNPlexTM基因型分型系统（两个可商购的基因分型平台）的转换潜力，从而加快了基因研究的成功可能性。

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