Discovering Splicing Defects in Human Genes

发现人类基因中的剪接缺陷

基本信息

批准号：
10753767
负责人：
William G Fairbrother
金额：
$ 70.15万
依托单位：
BROWN UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-08-23 至 2027-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10753767
关键词：
Affect Alleles Antisense Oligonucleotides Basic Science Biological Assay Cell Line Classification ClinVar Clinical Clustered Regularly Interspaced Short Palindromic Repeats Collaborations Contractor Data Defect Disease Elements Engineering Enhancers Exons Frequencies Funding Future Genes Genetic Genome Genomics Genotype-Tissue Expression Project Grant Healthcare Systems Hereditary Disease Human Individual Introns Large-Scale Sequencing Left Maps Measures Methods Missense Mutation Modeling Mutate Mutation Nonsense Mutation Organ Patients Phenotype Physician Executives Pilot Projects Population Predisposition Privatization Property RNA Splicing Reporter Research Research Personnel Role SARS-CoV-2 B.1.1.7 Signal Transduction Site Spliced Genes Symptoms Technology Testing Tissues Universities Untranslated RNA Variant Work autism spectrum disorder base biobank combinatorial de novo mutation design exome exon skipping functional genomics human disease improved mRNA Precursor mutant protein function repository

项目摘要

Project Summary/Abstract It is currently feasible for small research groups to sequence individual genomes and for larger groups to sequence tens of thousands of individuals. Unfortunately, our ability to identify variants that impact phenotype has not kept pace with our sequencing capacity. This is particularly true of non-coding variants. This proposal presents a pilot screen of more than 32K variants from myCode and ClinVar that suggest 1-2% of exonic mutations affect splicing. The pilot study also revealed that splicing mutations are not uniformly distributed across disease genes or even within genes. This proposal will continue this effort on variants from UK biobank, AllofUs, ClinVar and GTEx that localize to actionable genes. Splicing mutations do not occur uniformly across exons. The proposal seeks to map susceptibility to splicing mutations and identify hotspot exons (exons unusually susceptible to splicing mutations) in the genome. In addition to identifying loss of splicing variants, the little studied problem of gain of splicing variants (i.e. single base mutations that can activate pseudoexons) will also be explored. Preliminary studies locate many intronic regions in pre-mRNA that contain all-but-one of the numerous cis-elements necessary for splicing. In addition to mapping susceptibility to splicing mutations, these efforts will contribute to the basic science of combinatorial signal recognition with a high-level approach that will define mechanisms of splice site selection. Finally, we present a principled method of restoring splicing to mutated exons using antisense oligonucleotides (ASO) that weaken flanking splice sites.

项目摘要/摘要目前，对于小型研究小组，对于单个基因组和较大的小组进行测序是可行的序列成千上万个个体。不幸的是，我们识别影响表型的变体的能力尚未跟上我们的测序能力。非编码变体尤其如此。这个建议提出了来自MyCode和Clinvar的32K多种变体的试验屏幕，该屏幕表明1-2％突变会影响剪接。试点研究还表明，剪接突变不是均匀分布的跨疾病基因甚至基因内。该提案将继续对英国生物银行的变体进行这项工作，本地性基因的Allofus，Clinvar和GTEX。剪接突变在整个外显子。该提案旨在绘制易感性剪接突变和识别热点外显子（外显子在基因组中异常容易受到剪接突变的影响。除了确定剪接变体的丢失外，剪接变体获得的少量研究的问题（即可以激活伪exons的单基碱基突变）也将探索。初步研究将许多内含子区域定位在前MRNA中，其中包含全部但一种剪接所需的众多顺式元素。除了绘制对剪接突变的敏感性，这些努力将通过高级方法有助于组合信号识别的基础科学这将定义剪接站点选择的机制。最后，我们提出了一种恢复剪接的原则方法使用反义寡核苷酸（ASO）进行突变外显子，从而削弱了侧翼剪接位点。

项目成果

期刊论文数量（2）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans.

DOI：
10.1073/pnas.2218308120
发表时间：
2023-05-23
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
影响因子：
11.1
作者：
Rong, Stephen;Neil, Christopher R.;Welch, Anastasia;Duan, Chaorui;Maguire, Samantha;Meremikwu, Ijeoma C.;Meyerson, Malcolm;Evans, Ben J.;Fairbrother, William G.
通讯作者：
Fairbrother, William G.