GENCODE: comprehensive genome annotation for human and mouse

GENCODE：人类和小鼠的全面基因组注释

• 批准号: 9980954
• 负责人: Paul Flicek
• 金额: $ 222.7万
• 依托单位: EUROPEAN MOLECULAR BIOLOGY LABORATORY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-04-01 至 2021-09-13
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9980954
• 关键词: Affect; Alternative Splicing; Biological; Biomedical Research; Classification; Clinical; Code; Communities; Complementary DNA; Computing Methodologies; Data; Data Set; Disease; Enhancers; Ensure; Expressed Sequence Tags; Foundations; Genes; Genetic Transcription; Genome; Genomic approach; Genomics; Genotype-Tissue Expression Project; Goals; Graph; Haplotypes; Health; Human; Human Genome; Individual; Informatics; Investigation; Knock-out; Knowledge; Length; Manuals; Mass Spectrum Analysis; Methods; Modeling; Mouse Strains; Mus; Nucleic Acid Regulatory Sequences; Pilot Projects; Polymerase; Population; Protein Isoforms; Proteins; Pseudogenes; Public Health; Quality Control; RNA; Research; Research Design; Series; Source; Technology; Tissues; Transcript; Transcription Initiation; Untranslated RNA; Validation; base; epigenome; evidence base; genome annotation; genome browser; mouse genome; new technology; novel; population based; recruit; reference genome; tool; transcriptome; transcriptome sequencing; transcriptomics; web site

OVERALL - PROJECT SUMMARY The objective of the GENCODE consortium is to create a foundational reference genome annotation, in which all gene features in the human and mouse genomes are identified and classified with high accuracy based on biological evidence, and then to release these annotations for the benefit of biomedical research and genome interpretation. GENCODE aims for a better understanding of a `normal' human genome; using genome sequences of the most commonly used mouse strains will facilitate the most effective use of these key models for large-scale knockout analysis and disease-specific research. To produce regular annotation releases of high accuracy, GENCODE will continue to follow its well-established and conservative research design, supplemented by targeted investigations into the value of new technologies, new data and new sources of evidence. GENCODE focuses on protein-coding and non-coding loci, including their alternatively spliced isoforms and pseudogenes. Over the course of this proposal GENCODE will follow major directions in genomics, including graph- based genome representations, long-read transcriptome sequencing, connecting genes and the associated regulatory regions that affect their transcription, and identifying genes that are not present on the current reference assembly. The GENCODE consortium has four fundamental components: (1) a comprehensive gene annotation pipeline leveraging manual annotation; (2) an integrated approach to pseudogene identification and classification; (3) a set of computational methods to evaluate and enhance gene annotation; and (4) complementary experimental pipelines for validation and functional annotation. More specifically, in the next four years GENCODE aims to (1) extend the human and mouse GENCODE gene sets to as near completion as possible given current experimental technology; (2) deploy population-based genome annotation to ensure that any transcript isoform expressed in an individual human will be present in the reference annotation set; (3) extend the gene annotation to include core regulatory regions and tissue-specific enhancers from selected datasets; (4) to distribute GENCODE annotations and engage with community annotation efforts. Current popular distribution channels for GENCODE data including the GENCODE web site, the Ensembl and UCSC Genome Browsers, will be maintained. Finally, new mechanisms for prioritizing genes for manual annotation with community input will be established, with the long-term aim of establishing GENCODE as the standard annotation set for research and clinical genomics efforts.

总体 - 项目概要 GENCODE 联盟的目标是创建一个基础参考基因组 注释，其中识别人类和小鼠基因组中的所有基因特征并 根据生物证据进行高精度分类，然后发布这些 注释有利于生物医学研究和基因组解释。 GENCODE 的目标 为了更好地理解“正常”人类基因组；使用最多的基因组序列 常用的小鼠品系将有助于最有效地利用这些关键模型 大规模敲除分析和疾病特异性研究。生成常规注释 高精度的发布，GENCODE 将继续遵循其完善的和 保守的研究设计，辅之以对新产品价值的有针对性的调查 技术、新数据和新证据来源。 GENCODE 专注于蛋白质编码 和非编码基因座，包括它们的选择性剪接异构体和假基因。超过 该提案的过程 GENCODE 将遵循基因组学的主要方向，包括图- 基于基因组表示、长读转录组测序、连接基因和 影响其转录的相关调控区域，并识别不影响其转录的基因 存在于当前参考装配体上。 GENCODE 联盟有四个基本原则 组件：（1）利用手动注释的综合基因注释管道； (2) 假基因识别和分类的综合方法； (3)一组 评估和增强基因注释的计算方法； (4) 互补 用于验证和功能注释的实验管道。更具体地说，在接下来的四 年 GENCODE 的目标是 (1) 将人类和小鼠 GENCODE 基因集扩展到尽可能接近 鉴于当前的实验技术，尽可能完成； （二）以人群为基础部署 基因组注释，以确保在人类个体中表达的任何转录亚型 出现在参考注释集中； (3) 扩展基因注释以包括核心 来自选定数据集的调控区域和组织特异性增强子； (4) 分发 GENCODE 注释并参与社区注释工作。目前流行 GENCODE 数据的分发渠道，包括 GENCODE 网站、Ensembl 和 UCSC 基因组浏览器将得到维护。最后，优先考虑基因的新机制 将建立带有社区意见的手动注释，长期目标是 建立 GENCODE 作为研究和临床基因组学的标准注释集 努力。