GENCODE: comprehensive reference genome annotation for human and mouse

GENCODE：人类和小鼠的综合参考基因组注释

• 批准号: 10488576
• 负责人: Ewan Birney
• 金额: $ 292.17万
• 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 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10488576
• 关键词: Algorithms; Alternative Splicing; Animal Model; Automated Annotation; Biological; Biological Assay; Biological Models; Biomedical Research; Cells; Clinical; Code; Communication; Communities; Computing Methodologies; Data; Data Set; Databases; Development; Disease; Distal; Enhancers; Ensure; Excision; Exons; Feedback; Foundations; Future; Genes; Genetic Transcription; Genome; Genomics; Goals; Graph; Haplotypes; Health; Human; Human Genome; Knowledge; Lead; Machine Learning; Manuals; Methods; Modeling; Mouse Protein; Mus; Nucleic Acid Regulatory Sequences; Open Reading Frames; Output; Performance; Phenotype; Pilot Projects; Play; Population; Process; Protein Isoforms; Proteins; Protocols documentation; Pseudogenes; Public Health; RNA Splicing; Regulatory Element; Reporting; Research; Resources; Rest; Role; Seeds; Series; Site; Small RNA; Specificity; Supervision; Technology; Tissues; Training; Transcript; Untranslated RNA; Untranslated Regions; Update; Variant; base; community engagement; computational pipelines; functional genomics; genome annotation; genome browser; genome-wide; human disease; improved; loss of function; machine learning method; machine learning model; mouse genome; novel; outreach; promoter; reference genome; tool; transcriptome; transcriptome sequencing; transcriptomics; web site

Project Summary The GENCODE consortium creates foundational reference genome annotation for the human and mouse genomes in which all features are identified and classified with high accuracy based on biological evidence, and then freely released for the benefit of biomedical research and genome interpretation. GENCODE seeks to create annotation that increases the understanding of genome function in both human and mouse by prioritizing human disease genes and respecting the role of mouse as the major mammalian model organism. To effectively annotate genomes, GENCODE has created a suite of tools and draws on deep expertise across its partners across four fundamental components: 1) a comprehensive gene annotation pipeline leveraging manual and computational annotation; 2) a set of computational methods to evaluate and enhance gene annotation; 3) experimental pipelines targeted to expressed sequences less detectable in standard protocols; and 4) a machine learning capacity to improve all facets of the project. GENCODE will maintain a major focus on protein-coding and non-coding loci, including their alternatively spliced isoforms and pseudogenes and will extend expert manual review to small non-coding RNAs (ncRNA) and the annotation of non-polyadenylated transcripts. GENCODE will also expand regulatory annotation to a defined set of gene-associated features to more accurately reflect the interconnections between regulatory regions, including those with transcribed sequences such as ncRNA, and overall transcriptional output. GENCODE will take advantage of the increasing maturity of genomics technology including long-read transcriptome sequencing, functional genomics assays, and graph- based genome representations to identify features such as genes, pseudogenes, exons and splice sites that are incorrect, incomplete or in genome regions simply not present in the current reference assembly. More specifically, in the next four years GENCODE plans to 1) extend its human and mouse gene sets to as near completion as possible given available data and current experimental technology; 2) leverage new, high-quality human genome assemblies and targeted transcriptomic data to expand representation so that more human haplotypes will have high-quality annotation 3) annotate gene-associated regulatory regions including enhancer- promoter connections 4) collaborate with other resources to ensure a consistent representation of genic and regulatory features and reference transcripts for reporting clinical variation; and 5) distribute GENCODE annotations and engage with community annotation efforts to ensure accuracy and consistency. Primary GENCODE data will continue to be available from the Ensembl and UCSC Genome Browsers and the GENCODE web site. We will develop new mechanisms for effective two-way outreach, training and communication with the community with the long-term aim of establishing GENCODE as the standard annotation set for research and clinical genomics applications.

项目摘要 GENCODE联盟为人类和小鼠创建基础参考基因组注释 基因组，其中所有特征都基于生物学证据以高准确度被识别和分类，以及 然后为了生物医学研究和基因组解释的利益而自由释放。GENCODE旨在 创建注释，通过优先考虑 人类疾病基因和尊重小鼠作为主要哺乳动物模式生物的作用。有效 为了注释基因组，GENCODE创建了一套工具，并利用了其合作伙伴的深厚专业知识 跨越四个基本组件：1）利用手册和 计算注释; 2）一组用于评估和增强基因注释的计算方法; 3） 实验管道，其目标是在标准方案中较难检测到的表达序列;以及4）机器 学习能力，以改善项目的各个方面。GENCODE将主要关注蛋白质编码 和非编码基因座，包括其选择性剪接亚型和假基因，并将扩展专家 对小的非编码RNA（ncRNA）和非多聚腺苷酸化转录物的注释进行手动审查。 GENCODE还将把监管注释扩展到一组定义的基因相关特征， 准确反映调控区之间的相互联系，包括那些转录序列 如ncRNA和总转录输出。GENCODE将利用日益成熟的 基因组学技术，包括长读转录组测序、功能基因组学测定和图表 基于基因组表示，以确定特征，如基因，假基因，外显子和剪接位点， 不正确的、不完整的或在基因组区域中根本不存在于当前参考组装中。更 具体来说，在未来四年内，GENCODE计划1）将其人类和小鼠基因组扩展到尽可能接近 在现有数据和现有实验技术的情况下尽可能完成; 2）利用新的，高质量的 人类基因组组装和靶向转录组数据，以扩大代表性， 单倍型将具有高质量注释3）注释基因相关调节区， 启动子连接4）与其他资源合作，以确保基因和 用于报告临床变异的监管特征和参考转录本;以及5）分发GENCODE 注释和参与社区注释工作，以确保准确性和一致性。初级 GENCODE数据将继续从Ensembl和UCSC基因组浏览器和 GENCODE网站。我们将建立有效的双向外联、培训和 与社区沟通，长期目标是将GENCODE建立为标准注释 用于研究和临床基因组学应用。