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

基本信息

批准号：
10709568
负责人：
Ewan Birney
金额：
$ 296.77万
依托单位：
EUROPEAN MOLECULAR BIOLOGY LABORATORY
依托单位国家：
美国
项目类别：
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/10709568
关键词：
Algorithms Alternative Splicing Automated Annotation Biological Biological Assay Biological Models Biomedical Research Cells Classification Clinical Code Collaborations 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 Series Site Small RNA Specificity Technology Tissues Training Transcript Untranslated RNA Untranslated Regions Update Variant community engagement computational pipelines functional genomics genome annotation genome browser genome-wide human disease improved loss of function machine learning method machine learning model model organism mouse genome novel outreach promoter reference genome tool transcriptome transcriptome sequencing transcriptomics web site

项目摘要

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.

项目概要 GENCODE 联盟为人类和小鼠创建基础参考基因组注释基因组中的所有特征均根据生物学证据进行高精度识别和分类，以及然后免费发布以用于生物医学研究和基因组解释。 GENCODE 致力于创建注释，通过优先考虑来增加对人类和小鼠基因组功能的理解人类疾病基因并尊重小鼠作为主要哺乳动物模式生物的作用。为了有效地为了注释基因组，GENCODE 创建了一套工具并利用其合作伙伴的深厚专业知识跨越四个基本组成部分：1）利用手动和计算注释； 2）一套评估和增强基因注释的计算方法； 3）针对标准方案中不易检测到的表达序列的实验流程； 4) 一台机器提高项目各个方面的学习能力。 GENCODE 将继续重点关注蛋白质编码和非编码基因座，包括它们的选择性剪接亚型和假基因，并将扩展专家对小非编码 RNA (ncRNA) 的手动审查以及非聚腺苷酸化转录本的注释。 GENCODE 还将把监管注释扩展到一组已定义的基因相关特征，以获取更多信息。准确反映调节区域之间的互连，包括那些具有转录序列的区域例如 ncRNA 和总体转录输出。 GENCODE 将利用日益成熟的技术基因组学技术，包括长读长转录组测序、功能基因组学测定和图谱分析基于基因组表示来识别基因、假基因、外显子和剪接位点等特征不正确、不完整或基因组区域根本不存在于当前参考装配中。更多的具体来说，在未来四年中，GENCODE 计划 1) 将其人类和小鼠基因集扩展到尽可能接近考虑到现有数据和当前的实验技术，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，以便更多的人类单倍型将具有高质量的注释 3) 注释基因相关的调控区域，包括增强子- 启动子连接 4) 与其他资源合作，确保基因和基因的一致表达用于报告临床变异的监管特征和参考记录； 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。我们将建立有效的双向推广、培训和培训新机制与社区沟通，长期目标是建立 GENCODE 作为标准注释用于研究和临床基因组学应用。

项目成果

期刊论文数量（68）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

DOI：
10.1101/gr.222976.117
发表时间：
2018-03-01
期刊：
Genome research
影响因子：
7
作者：
Tardaguila M;de la Fuente L;Marti C;Pereira C;Pardo-Palacios FJ;Del Risco H;Ferrell M;Mellado M;Macchietto M;Verheggen K;Edelmann M;Ezkurdia I;Vazquez J;Tress M;Mortazavi A;Martens L;Rodriguez-Navarro S;Moreno-Manzano V;Conesa A
通讯作者：
Conesa A

Corrigendum: Loose ends: almost one in five human genes still have unresolved coding status.

DOI：
10.1093/nar/gky1146
发表时间：
2018-12-14
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Abascal F;Juan D;Jungreis I;Kellis M;Martinez L;Rigau M;Rodriguez JM;Vazquez J;Tress ML
通讯作者：
Tress ML

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.

一种用于翻译后修饰和变异的肽到基因组映射的快速定量方法。

DOI：
10.3791/57633
发表时间：
2018
期刊：
Journal of visualized experiments : JoVE
影响因子：
0
作者：
Schlaffner,ChristophN;Pirklbauer,GeorgJ;Bender,Andreas;Steen,JudithAJ;Choudhary,JyotiS
通讯作者：
Choudhary,JyotiS

The value of primary transcripts to the clinical and non-clinical genomics community: Survey results and roadmap for improvements.

DOI：
10.1002/mgg3.1786
发表时间：
2021-12
期刊：
Molecular genetics & genomic medicine
影响因子：
2
作者：
Morales J;McMahon AC;Loveland J;Perry E;Frankish A;Hunt S;Armean IM;Flicek P;Cunningham F
通讯作者：
Cunningham F

Alternative Splicing May Not Be the Key to Proteome Complexity.