GASP software method development in statistical genetics

统计遗传学中的 GASP 软件方法开发

• 批准号: 6556009
• 负责人: ALEXANDER F WILSON
• 金额: --
• 依托单位: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6556009
• 关键词: computer program /software; computer simulation; computer system design /evaluation; family genetics; genetic models; human data; quantitative trait loci; statistics /biometry

The Genometric Analysis Simulation Program (G.A.S.P.) is a software tool for generating samples of family data based on user-specified genetic models. Quantitative traits are defined in terms of a combination of user-defined components, including a major-locus (or loci), a polygenic component, common sibship environment, and/or other covariates. In addition, loci corresponding to discrete traits or markers can be generated. However, complications such as missing data, genotyping errors reduced penetrance, genetic heterogeneity, epistasis, and non-random ascertainment of samples are not handled directly by this software. G.A.S.P. is run in combination with a drevier which formats the generated data and can also be used to add layers of complexity to the model. Simple examples of driver-added traits modifications include: classification of a quantitative trait into a discrete trait using a specific threshold, suppressing (as unknown) genotyping data for older generations of a family and reduced penetrance for a qualitative trait. The software is being used extensively in the Inherited Disease Research Branch, and has been requested by over 40 investigators worldwide. During the past year, the software was used extensively in the development of a new method for testing association for quantitative traits (ROMP), comparing the statistical properties of tests of association (ROMP, ANOVA, Variance components), and comparing the statistical properties of linkage analysis.

基因计量分析模拟程序(G.A.S.P.)是一个软件工具，用于根据用户指定的遗传模型生成家庭数据样本。数量性状是根据用户定义的成分的组合来定义的，包括一个主基因座(或多个基因座)、一个多基因成分、共同的亲缘环境和/或其他协变量。此外，还可以产生与离散性状或标记相对应的基因座。然而，诸如数据缺失、基因分型错误降低外显率、遗传异质性、上位性以及样本的非随机确定等并发症不是由该软件直接处理的。G.A.S.P.与一个挖掘器一起运行，后者对生成的数据进行格式化，还可以用来增加模型的复杂程度。驱动因素增加的性状修改的简单例子包括：使用特定阈值将数量性状分类为离散性状，抑制(未知的)家族老一辈的基因分型数据，以及降低质量性状的外显率。该软件正在遗传病研究处广泛使用，全世界已有40多名研究人员要求使用该软件。在过去的一年里，该软件被广泛用于开发一种新的数量性状关联检验方法，比较关联检验(ROMP，ANOVA，Variance Components)的统计特性，并比较连锁分析的统计特性。