A comprehensive canine genetics resource including gene and variation annotation

全面的犬类遗传学资源，包括基因和变异注释

基本信息

批准号：
9238508
负责人：
Elinor Karlsson
金额：
$ 43.4万
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 2019-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9238508
关键词：
Adult Age Antibodies Area Behavioral Canis familiaris Cardiovascular Diseases Cardiovascular system 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 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 United States National Institutes of Health Untranslated RNA Variant Veterinary Schools base cell type cohesion comparative data hub dog genome epigenomics exhaustion 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 public health relevance sex trait transcriptome transcriptome sequencing transcriptomics translation to humans 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（由适用提供）：狗正在成为癌症，炎症，心血管疾病和行为疾病等人类疾病的越来越重要的生物医学模型。独特的品种结构使特征映射特别有效。虽然自2004年以来就可以使用基因组，基本注释和SNP目录，但改善的基因组资源将允许对疾病基因，途径和突变进行更有效的识别。在这个项目中，我们旨在通过创建更全面的基因组注释以及来自狗遗传界的广泛基因组数据来改善犬类基因组资源，作为UCSC基因组浏览器的轨道数据中心。出于其他医学原因而被安乐死的六只狗将分别捐赠30个组织，用于RNA测序和11个原代细胞培养物，用于RNA测序和芯片测序，用于五种组蛋白抗体。还将获得每只狗的整个基因组测序的样品。这将产生30次的广泛转录组资源，并产生狗中第一个全基因组的调节元素目录。还将获得胚胎狗组织，用于从已经牺牲的其他科学研究中牺牲的胚胎进行RNA测序。RNA传递数据将与以前的自定义注释管道中先前的人和狗基因注释相结合，从而导致改进的狗基因注释，这很大程度上基于特定于规范信息。上述所有数据，以及从狗仿制药社区收集的新基因注释和数据将托管在UCSC基因组浏览器上的广大研究所，从而使世界各地的狗科学家能够访问这些资源。这些基因组资源将大大增加狗作为生物医学模型的效用，并将加速狗的遗传学，并翻译由狗模型的研究引起的研究。这个重要项目的合作者包括塔夫茨兽医学校的兽医专家，狗胚胎开发专家Meyers-Wallen博士，Lander博士和Broad Institution Genomics平台，测序专家，Regev和Grabherr博士，转录组和基因组调节的专家Brouls and brors and bross and gres anders anders Lesors，