Genomic Resources for the Collaborative Cross

协作型杂交的基因组资源 回应NIH FOA PAR-17-273 少年派：伦纳德·麦克米兰 我们建议为实验遗传学开发独特的、前所未有的基因组资源 支持合作十字(CC)的社区。CC是一种新兴的遗传学资源 由70多个新的同基因小鼠品系组成，其基因组来自8个创始人 这捕捉到了小鼠的大部分多样性。正如六月份的《遗传学》杂志所报道的那样，我们有 最近对每个CC菌株的样本进行了全基因组测序。这项提案的目的将是 是： 1.为每个可复制的CC菌株组装和注释独特的个体基因组。 2.提供辅助使用CC进行实验设计的工具。尤其是如何设计 重组近交系杂交，提供了一组足够大的平衡和 可重现的远缘繁殖样本。我们还将提供修复特定基因以进行测试的工具 在不同的遗传背景下。 3.我们建议开发定制组学分析管道，利用前所未有的 基因组学注释可用于CC，以支持探索等位基因的特定效应。 我们的主要目标是在医学研究社区内引导CC的使用， 希望经过五年的支持，这些资源将通过出售MICE来自给自足 北卡罗来纳大学系统的遗传学核心设施。 这项提案有两个首席调查员(PI)。联系人Pi是伦纳德·麦克米兰教授，来自 北卡罗来纳大学计算机科学系。与他一起工作的还有皮·费尔南多·帕尔多-曼努埃尔·德·维莱纳博士。Dr。 在过去的8年里，麦克米兰一直是CC的主要生物信息学专家和工具开发人员 几年来它的发展。帕尔多-曼努埃尔·德·维莱纳博士是一位遗传学家，他领导了 协作十字。我们一起带来了计算生物学、遗传学和 基因组学以确保CC是首要的哺乳动物遗传参考群体和 人类疾病的新小鼠模型。

Genomic Resources for the Collaborative Cross In response to NIH FOA PAR-17-273 PI: Leonard McMillan We propose to develop unique and unprecedented genomic resources for the experimental genetics community in support of the Collaborative Cross (CC). The CC is an emergent genetics resource consisting of more than seventy new isogenic mouse strains with genomes derived from eight founders that captures most of diversity in Mus musculus. As reported in June’s issue of Genetics, we have recently done full-genome sequencing for samples from each CC strain. The Aims of this proposal will be: 1. To assemble and annotate unique individual genomes for each reproducible CC strain. 2. To provide tools that aid in experimental designs using the CC. In particular, how to design recombinant inbred intercrosses, that provide a sufficiently sized set of balanced and reproducible outbred samples. We will also provide tools that fix particular genes for testing against variable genetic backgrounds. 3. We propose to develop custom -omics analysis pipelines that leverage the unprecedented genomics annotation available for the CC to support the exploration allele specific effects. Our primary goal is to bootstrap the use of the CC within the medical research community, with the hopes that after the five years of support these resources will be self-sustaining through selling mice by the UNC System’s Genetics Core facility. This proposal has two Principal Investigators (PIs). The contact PI is Professor Leonard McMillan from UNC’s department of Computer Science. He is joined by PI Fernando Pardo-Manuel de Villena, PhD. Dr. McMillan has been the primary bioinformatics expert and tool developer for the CC over the past 8+ years of its development. Dr. Pardo-Manuel de Villena is a geneticist who led the development of the Collaborative Cross. Together we bring extensive expertise in computational biology, genetics, and genomics to ensure that the CC is the premier mammalian genetic reference population and a source of new mouse models of human disease.