Massively Parallel Phenotypic Characterization of Non-coding Genetic Variation

非编码遗传变异的大规模平行表型表征

• 批准号: 8976275
• 负责人: Ryan Tewhey
• 金额: $ 10.98万
• 依托单位: HARVARD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-12-01 至 2017-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8976275
• 关键词: Address; Adopted; Alleles; Automobile Driving; Base Pairing; Biochemical; Biological Assay; Cataloging; Catalogs; Chromosomes; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Communities; Complex; Controlled Environment; Data Set; Databases; Dependency; Development; Disease; Elements; Engineering; Environment; Etiology; Foundations; Gene Expression; Generations; Genetic Variation; Genome; Genome Scan; Genome engineering; Genomics; Health; Human; Human Genetics; Human Genome; Human Genome Project; Indium; Individual; Link; Linkage Disequilibrium; Maps; Methods; Modification; Molecular; National Human Genome Research Institute; Natural Selections; Patients; Physiological; Play; Proteins; Publishing; Quantitative Trait Loci; Regulatory Element; Reporter; Research; Resolution; Role; Running; Site; Surveys; System; Technology; Testing; Time; Untranslated RNA; Validation; Variant; Viral; Work; assay development; base; clinical care; computerized tools; cost; follow-up; genetic variant; genome sequencing; genome wide association study; genome-wide; improved; in vivo Model; individualized medicine; insight; next generation; novel; personalized medicine; research study; screening; stem; success; tool; tool development; trait; vector

DESCRIPTION (provided by applicant): Project Summary Recent technological advances in genome sequencing have enabled numerous large-scale association studies aimed at discovering genetic variants underlying a wide array of complex diseases. It has become increasingly evident that the majority of these associations stem from a perturbation of regulatory function. While the ENCODE project and related efforts have strengthened our ability to comprehensively identify regulatory elements, our ability to decipher the impact of individual variants within these elements has not kept step. To address this gap, I aim to develop and apply the massively parallel reporter assay (MPRA) to empirically test the regulatory potential of thousands of individual variant sites for a wide range of roles. My specific aims are to: (1) Demonstrate the utility of MPRA by applying the method to loci in the human genome with evidence of recent positive selection and those identified in published genome wide association studies; (2) Modify MPRA to capture a more comprehensive array of regulatory mechanisms; and (3) Transition the current MPRA episomal vector to a viral delivery platform, allowing for chromosomal integration. I anticipate that these methods will provide the broader research community with a catalog of biologically meaningful regulatory variants and a valuable toolkit for understanding the role that regulatory variation plays in human health and disease.

描述（由申请人提供）：项目概述基因组测序的最新技术进步使大量大规模关联研究成为可能，旨在发现一系列复杂疾病背后的遗传变异。越来越明显的是，大多数这些关联源于调节功能的扰动。虽然ENCODE项目和相关的努力加强了我们全面识别调控元素的能力，但我们破译这些元素中单个变异的影响的能力并没有跟上步伐。为了解决这一差距，我的目标是开发和应用大规模平行报告分析（MPRA），以经验性地测试数千个个体变异位点的广泛作用的调节潜力。我的具体目标是：(1)通过将该方法应用于具有最近正选择证据的人类基因组中的位点以及在已发表的基因组广泛关联研究中确定的位点，证明MPRA的实用性；(2)修改MPRA以获取更全面的监管机制；(3)将当前的MPRA episal载体转化为病毒传递平台，允许染色体整合。我预计，这些方法将为更广泛的研究界提供具有生物学意义的调控变异目录，并为理解调控变异在人类健康和疾病中所起的作用提供有价值的工具包。

项目成果

Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH.

• DOI: 10.1038/s41588-021-00900-4
• 发表时间: 2021-08
• 期刊: Nature genetics
• 影响因子: 30.8
• 作者: Reilly SK;Gosai SJ;Gutierrez A;Mackay-Smith A;Ulirsch JC;Kanai M;Mouri K;Berenzy D;Kales S;Butler GM;Gladden-Young A;Bhuiyan RM;Stitzel ML;Finucane HK;Sabeti PC;Tewhey R
• 通讯作者: Tewhey R