Cross-species Microarray-based Genomic Selection: application to nonhuman primate

描述（由申请人提供）：非人类灵长类动物为研究人类生物学、疾病和进化提供了一个独特的模型。然而，95%的非人类灵长类动物缺乏现代遗传和疾病比较遗传研究所需的基本基因组序列资源，包括艾滋病。因此，有必要开发经济有效的方法，利用现有的非人类灵长类动物基因组资源作为跳板，在更大的物种多样性中进行基于种群的基因组测序。本R21提案的重点是测试和展示新开发的基因组技术，基于微阵列的基因组选择（MGS）的能力，作为这样一种方法。我们和其他人已经证明，微阵列可以用于从总基因组DNA中选择性地富集复杂基因组的目标区域，从而为基于群体的目标间隔重测序提供必要的模板。然而，如果MGS能够以跨物种的形式使用，它的效用将呈指数增长。尽管MGS的跨物种应用尚未经过测试，但使用基因表达微阵列进行非人类灵长类动物跨物种杂交的类似研究已经证明是成功的。因此，本提案的第一个目标是确定跨物种MGS在差异水平为1-10%的非人灵长类动物的同源靶向基因组区域中富集的能力（目的1）。本提案的第二个目标是直接证明跨物种MGS在非人灵长类动物和艾滋病研究中的效用。为此，我们将采用跨物种MGS方法对黑白眉猴（一种特殊的非人类灵长类动物模型，缺乏基因组资源，用于艾滋病研究）中良性SIV感染的125-250个候选基因进行测序（目标2）。总之，一种可以同时从多个物种的目标区域产生比较和基于种群的序列数据的方法将被测试并应用于确定抑制艾滋病进展的遗传因素。公共卫生相关性：作为人类的近亲，非人类灵长类动物是研究艾滋病疾病进展的独特遗传资源。该研究项目的目标是将一种新的DNA测序技术应用于非人类灵长类动物的基因测序，包括用于艾滋病研究的生物医学模型。

DESCRIPTION (provided by applicant): Nonhuman primates offer a unique model for studying human biology, disease, and evolution. Nevertheless, 95% of nonhuman primates lack the basic genomic sequence resources required for modern genetic and comparative genetic studies of disease, including AIDS. Thus, there is a need to develop affordable and efficient methods that use the available nonhuman primate genomic resources as a springboard for population- based genomic sequencing in a greater diversity of species. The focus of this R21 proposal is to test and to demonstrate the capability of a newly developed genomic technology, microarray-based genomic selection (MGS), as such a method. We and others have shown that microarrays can be used to selectively enrich for targeted regions of a complex genome from total genomic DNA, thereby providing the templates necessary for population-based resequencing of the targeted intervals. However, if MGS could be used in a cross-species format, its utility would increase exponentially. Though the cross-species application of MGS is untested, analogous studies of cross-species hybridization between nonhuman primates using gene expression microarrays have already proved successful. The first goal of this proposal is therefore to determine the capability of cross-species MGS to enrich for orthologous targeted genomic regions of nonhuman primates at divergence levels from 1-10% (Aim 1). The second goal of this proposal is to directly demonstrate the utility of cross-species MGS for nonhuman primate and AIDS research. To do so we will apply the cross-species MGS approach toward sequencing 125-250 candidate genes for the benign nature of SIV infection in the sooty mangabey, an exceptional nonhuman primate model for AIDS research that lacks genomic resources (Aim 2). In summary, a method that can simultaneously produce both comparative and population-based sequence data from targeted regions in multiple species will be tested and applied toward the identification of genetic factors that suppress progression to AIDS. PUBLIC HEALTH RELEVANCE: As our closest living relatives, nonhuman primates are a unique genetic resource for studying disease progression to AIDS. The goal of this research project is to apply a new DNA sequencing technology toward sequencing genes in nonhuman primates, including a biomedical model for AIDS research.