Genomic Resources for the Collaborative Cross

协作交叉的基因组资源

基本信息

批准号：
10133118
负责人：
Leonard McMillan
金额：
$ 34.82万
依托单位：
UNIV OF NORTH CAROLINA CHAPEL HILL
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-05-17 至 2023-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10133118
关键词：
Address Alleles Animal Model Base Pairing Bioinformatics Biological Assay Biomedical Research Communities Computational Biology Core Facility Custom Databases Development Disease model Doctor of Philosophy Ensure Exhibits Experimental Designs Experimental Genetics Foundations Founder Effect Genetic Genetic Variation Genome Genomic Segment Genomics Genotype Goals House mice Inbred Strain Inbred Strains Mice Inbreeding Individual Inherited Knowledge Laboratories Laboratory mice Mammalian Genetics Medical Research Methods Modeling Monitor Mouse Strains Mus Online Systems Phenotype Population Population Genetics Principal Investigator Probability RNA Recombinants Reporting Reproducibility Research Personnel Resolution Resource Informatics Resources Sampling Source System The Jackson Laboratory Transcript United States National Institutes of Health Update Validation Variant analysis pipeline computer science design experimental study functional genomics genetic approach genetic resource genetic testing genome browser genome sequencing genomic tools human disease human model mouse genome mouse model novel professor reference genome response structural genomics tool transcriptome web-based tool whole genome

项目摘要

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.

协作交叉的基因组资源响应 NIH FOA PAR-17-273 PI：伦纳德·麦克米伦我们建议为实验遗传学开发独特且前所未有的基因组资源支持协作交叉 (CC) 的社区 CC 是一种新兴的遗传资源。由七十多个新的同基因小鼠品系组成，其基因组源自八位创始人正如《遗传学》六月号所报道的那样，我们捕获了小家鼠的大部分多样性。最近对每个 CC 菌株的样本进行了全基因组测序。是： 1. 为每个可重复的 CC 菌株组装并注释独特的个体基因组。 2. 提供有助于使用 CC 进行实验设计的工具，特别是如何设计。重组自交杂交，提供足够大小的平衡和我们还将提供修复特定基因的工具以进行测试。针对可变的遗传背景。 3. 我们建议开发定制组学分析管道，利用前所未有的 CC 可用的基因组学注释支持探索等位基因的特异性效应。我们的主要目标是在医学研究界引导 CC 的使用，希望在五年的支持之后，这些资源能够通过出售老鼠来自我维持北卡罗来纳大学系统的遗传学核心设施。该提案有两名首席研究员（PI），联系人 PI 是来自英国的 Leonard McMillan 教授。北卡罗来纳大学计算机科学系的成员包括 PI Fernando Pardo-Manuel de Villena 博士。在过去 8 年多的时间里，McMillan 一直是 CC 的主要生物信息学专家和工具开发人员 Pardo-Manuel de Villena 博士是一位领导该技术发展的遗传学家。我们共同带来计算生物学、遗传学和遗传学方面的广泛专业知识。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。