Novel methods for large-scale genomic interval comparison

大规模基因组区间比较的新方法

• 批准号: 10842040
• 负责人: Nathan Sheffield
• 金额: $ 31.47万
• 依托单位: UNIVERSITY OF VIRGINIA
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-10 至 2026-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10842040
• 关键词: Address; Administrative Supplement; Affect; Algorithms; Atlases; Automobile Driving; Award; Binding; Biological; Biomedical Research; Chromatin; Chromosome Territory; Communities; Confusion; Consensus; Consumption; CpG Islands; DNA; DNA Methylation; Data; Data Analyses; Data Reporting; Data Set; Data Sources; Databases; Dedications; Disease; Disease Outcome; Epigenetic Process; Exons; Friends; Gene Expression Regulation; Genes; Genetic; Genetic Variation; Genome; Genomic Segment; Genomics; Goals; Grant; Health; Individual; Introns; Knowledge; Learning; Location; Machine Learning; Measures; Metadata; Methods; Modeling; National Human Genome Research Institute; Outcome; Parents; Procedures; Process; Property; Research Personnel; Resources; Series; Site; Source; Standardization; System; Time; Training; Variant; Work; cell type; cloud based; data sharing; design; epigenome; epigenomics; experimental study; genome analysis; genome resource; histone modification; improved; innovation; machine learning model; novel; parent grant; promoter; transcription factor; user-friendly; vector

ABSTRACT This administrative supplement creates AI/ML-ready resources for epigenome genomic interval data. Epigenome data summarized as sets of genomic intervals are now available for thousands of variations of cell type, disease, condition, etc. This data holds tremendous promise to understand gene regulation and disease be- cause many health outcomes are affected by genetic variation or epigenetic perturbation in regulatory DNA. The parent R01 develops novel, scalable algorithms and measures of similarity between genomic interval datasets. These advances will improve both the efficiency and accuracy of existing biomedical research approaches that rely on analyzing genomic region data. They will open the door to new ways of exploring the vast and growing corpus of genome interval data. In this administrative supplement, we seek to take this rich data source and produce AI/ML-ready resources for the community. While there has been some effort to create uniformly processed databases of genomic interval data, there are few high-quality genomic interval currently available that are designed for machine learning applications. One of the first steps to integrating epigenome data across data sources is defining consensus regions that fit the original data well. Many downstream analyses, particularly learning tasks, rely on such a consensus region set. However, choosing a good consensus can be a time-consuming and confusing process, and also has potential to lose substantial information and introduce errors into results. To help alleviate this challenge, this proposal will take several datasets through a principled approach to generate AI/ML-ready resources. This process will include 1) defining consensus regions; 2) projecting raw data into the consensus to standardize it; and 3) standardizing annotation. Finally, we will make these available to the community with user-friendly and well-documented interfaces. The outcome will be a series of datasets that are ready for use for the community to build ML models.

摘要 该管理补充为表观基因组基因组间隔数据创建AI/ML就绪资源。 表观基因组数据总结为基因组间隔集，现在可用于数千种细胞变异。 类型，疾病，条件等。这些数据为了解基因调控和疾病提供了巨大的希望- 因为许多健康结果受到基因变异或调控DNA中的表观遗传干扰的影响。的 亲本R 01开发了新的、可扩展的算法和基因组间隔数据集之间的相似性度量。 这些进展将提高现有生物医学研究方法的效率和准确性， 依赖于分析基因组区域数据。他们将打开大门，以新的方式探索广阔的和不断增长的 基因组间隔数据库。 在这份行政补充中，我们试图利用这一丰富的数据源，为 社区虽然已经做出了一些努力来创建基因组间隔数据的统一处理的数据库， 目前几乎没有为机器学习应用设计的高质量基因组间隔。 跨数据源整合表观基因组数据的第一步是定义一致区域， 把原始数据做好。许多下游分析，特别是学习任务，依赖于这样的共识 区域设置。然而，选择一个好的共识可能是一个耗时和混乱的过程， 有可能丢失大量信息并在结果中引入错误。为了帮助缓解这一挑战， 该提案将通过一种原则性的方法来获取多个数据集，以生成AI/ML就绪的资源。这 过程将包括1）定义共识区域; 2）将原始数据投影到共识中以使其标准化; （3）规范注释。最后，我们会以简单易用的方式， 良好记录的接口。结果将是一系列数据集，可供社区使用， 构建ML模型。