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联盟为人和小鼠创建了基础参考基因组注释 根据生物学证据，将所有特征均以高精度鉴定和分类的基因组，以及 然后自由释放生物医学研究和基因组解释。 Gencode寻求 创建注释，通过优先级来提高人和小鼠中基因组功能的理解 人类疾病基因并尊重小鼠作为主要的哺乳动物模型生物的作用。有效 注释基因组，Gencode创建了一套工具，并借鉴了其合作伙伴的深厚专业知识 在四个基本组成部分中：1）综合基因注释管道利用手册和 计算注释； 2）一组评估和增强基因注释的计算方法； 3） 针对表达序列的实验管道在标准方案中较少可检测到； 4）机器 学习能力，以改善项目的所有方面。 Gencode将保持对蛋白质编码的主要关注 和非编码基因座，包括它们的剪接同工型和假基因并将扩展专家 对小型非编码RNA（NCRNA）的手动审查和非多丙二基化转录本的注释。 Gencode还将将调节注释扩展到一组定义的基因相关特征 准确反映调节区域之间的互连，包括具有转录序列的区域 例如NCRNA和总体转录输出。 Gencode将利用成熟度的增加 基因组学技术，包括长阅读转录组测序，功能基因组学测定和图形 基于基因组表示，以识别基因，伪基因，外显子和剪接位点等特征 当前参考组装中根本不存在不正确，不完整或基因组区域中。更多的 具体而言，在接下来的四年中，Gencode计划到1）将其人类和小鼠基因设置为近乎 尽可能完成可用的数据和当前的实验技术； 2）利用新的高质量 人类基因组组件和针对性的转录组数据以扩展表示形式，以使更多人类 单倍型将具有高质量的注释3）注释基因相关的调节区域，包括增强子 - 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调节特征和参考笔录； 5）分发gencode 注释并参与社区注释工作，以确保准确性和一致性。基本的 Gencode数据将继续从Ensembl和UCSC基因组浏览器以及 Gencode网站。我们将开发新的机制，以进行有效的双向外展，培训和 与社区的沟通，其长期目的是建立Gencode作为标准注释 设置用于研究和临床基因组学应用。