A comprehensive canine genetics resource including gene and variation annotation

全面的犬类遗传资源，包括基因和变异注释

基本信息

批准号：
9128056
负责人：
Elinor Karlsson
金额：
$ 64.79万
依托单位：
BROAD INSTITUTE, INC.
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-08-17 至 2018-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9128056
关键词：
Adult Age Antibodies Area Behavioral Breeding Canis familiaris Cardiovascular Diseases Cardiovascular system Cataloging Catalogs Cell Line Cells ChIP-seq Chromosome Mapping Clinical Trials Code Communities Complex Coupling Custom Data Data Display Data Set Disease Dog Diseases Drug or chemical Tissue Distribution Embryo Embryonic Development Enhancers Gene Expression Regulation Genes Genetic Genetic Research Genetic Transcription Genome Genomics Goals Health Hereditary Disease Histones Human Human Genetics Human Genome Inflammatory Institutes Lifting Linkage Disequilibrium Longevity Malignant Neoplasms Maps Medical Modeling Mutation National Heart, Lung, and Blood Institute National Institute of Allergy and Infectious Disease National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institute of Diabetes and Digestive and Kidney Diseases National Institute of Mental Health Neurologic Organ Pathway interactions Primary Cell Cultures Production Protein Isoforms Proteins Protocols documentation Publishing Regulation Regulatory Element Research Resources Sampling Scientist Signal Transduction Specialist Structure Tissues Transcript Translating Translational Research Translations United States National Institutes of Health Untranslated RNA Variant Veterinary Schools base cell type comparative dog genome epigenomics genetic association genetic resource genetic risk factor genome annotation genome browser genome sequencing genome wide association study genome-wide genomic data genomic platform genomic variation human disease improved member novel promoter sex trait transcriptome transcriptome sequencing transcriptomics treatment strategy whole genome

项目摘要

DESCRIPTION (provided by applicant): The dog is becoming an increasingly important biomedical model for human diseases such as cancer, inflammatory, cardiovascular and behavioural diseases. The unique breed structure makes trait mapping particularly efficient. While a genome, basic annotation and SNP catalog have been available since 2004, improved genomic resources would allow a more efficient identification of disease genes, pathways and mutations. In this project we aim to improve the canine genomic resources by creating a more comprehensive genome annotation along with extensive genomic data from the dog genetic community as a track data hub on the UCSC Genome Browser. Six dogs, euthanized for other medical reasons, will donate 30 tissues each for RNA- sequencing and 11 primary cell cultures for both RNA-sequencing and ChIP-sequencing for five histone antibodies. A sample will also be obtained for whole genome sequencing of each dog. This will yield an extensive transcriptome resource for 30 tissues and the first genome-wide catalog of regulatory elements in the dog. Embryonic dog tissue will also be obtained for RNA- sequencing from embryos already sacrificed for other scientific studies.The RNA-sequencing data will be combined with previous human and dog gene annotations in a custom annotation pipeline, to result in an improved dog gene annotation, based largely on species-specific information. All of the above data, along with the new gene annotation and data gathered from the dog genetics community will be hosted at the Broad Institute on the UCSC Genome Browser, enabling access to these resources by dog scientists around the world. These genomic resources will vastly increase the utility of the dog as a biomedical model and will accelerate dog genetics, and translational research arising from the study of the dog model. Collaborators for this important project include Drs Sharp and Ferrer, veterinary specialists at Tufts Veterinary School, Dr. Meyers-Wallen, an expert in dog embryonic development, Dr Lander and the Broad Institute Genomics Platform, experts in sequencing, Drs Regev and Grabherr, experts at transcriptomics and genome regulation and Drs Haussler and Kent, leaders of the UCSC genome browser.

描述（由申请人提供）：狗正在成为人类疾病（如癌症、炎症、心血管和行为疾病）日益重要的生物医学模型，其独特的品种结构使得性状图谱特别有效，同时具有基因组、基本注释和 SNP 目录。自 2004 年以来，改进的基因组资源将能够更有效地识别疾病基因、途径和突变。在该项目中，我们的目标是通过创建更全面的基因组注释以及来自狗遗传的广泛基因组数据来改进犬类基因组资源。社区作为 UCSC 基因组浏览器的跟踪数据中心。六只因其他医疗原因而被安乐死的狗将捐赠 30 个组织用于 RNA 测序，以及 11 个原代细胞培养物用于 RNA 测序和 ChIP 测序，用于五种组蛋白 A 的测序。还将获得样本用于每只狗的全基因组测序，这将产生 30 个组织的广泛转录组资源，并且还将获得狗胚胎组织的第一个全基因组调控元件目录。对已经为其他科学研究牺牲的胚胎进行 RNA 测序。RNA 测序数据将与自定义注释管道中先前的人类和狗基因注释相结合，以主要基于物种特定信息改进狗基因注释。所有上述数据，以及从狗遗传学界收集的新基因注释和数据将托管在 UCSC 基因组浏览器上的 Broad 研究所，使世界各地的狗科学家能够访问这些基因组资源。将大大增加狗作为生物医学模型的实用性，并将加速狗遗传学以及狗模型研究中产生的转化研究，这一重要项目的合作者包括塔夫茨兽医学院的兽医专家 Sharp 和 Ferrer 博士以及 Meyers-Wallen 博士。、狗胚胎发育专家、Lander 博士和 Broad Institute 基因组平台、测序专家 Regev 和 Grabherr 博士、转录组学和基因组调控专家以及 Haussler 博士Kent，UCSC 基因组浏览器的领导者。