Realtime visualization and analytics of epigenomic data using a serverless architecture

项目总结 表观遗传学描述了由于基因表达的改变而导致的表型结果的研究 编码DNA的变化。在过去的十年里，随着人们认识到表观遗传因素，这个领域出现了爆炸性的增长 (例如，组蛋白翻译后修饰、染色质相关蛋白、DNA甲基化)调节基因 表达和不同的下游细胞过程，包括人类疾病的发展。下一首 对这些表观遗传变化的世代测序(NGS)研究使更基本的 了解染色质结构如何影响人类健康，并揭示药物开发的新靶点。 这一领域的重要性推动了表观基因组图谱的显著进步；然而， 理解、比较和可视化这些大量表观遗传学数据的方法已经落后了。这个 目前这些第三级分析的框架速度很慢，对大多数用户来说太技术性了，并且无法处理 表观遗传学发现所需的日益复杂的查询。 Basepair®是简化NGS分析管道的行业领先者。这里，我们将利用这一点 在EpiBeacon™开发方面的专业知识，这是一个无服务器、用户友好的平台，用于快速第三级分析 表观遗传学数据。在目标1中，我们将使用Amazon Web Services(AWS)开发EpiBeacon平台 Lambda服务，可即时生成来自ENCODE的染色质图谱数据的热图。EpiBeacon 将与三次分析所需的多轮迭代采样唯一兼容，并且用户 将能够动态调整热图参数，并实时生成可供发布的数字。在AIM 2，我们将使EpiBeacon具有更复杂的比较分析能力，我们将应用于 回答该领域一个新出现的问题：来自染色质免疫沉淀的抗体和数据 其次是NGS(芯片序列)，适用于新的染色质分析技术Cut&Run。切割和运行 有可能取代芯片序列作为染色质分析的标准，因为它产生更高的分辨率。 与芯片顺序相比，读取更少、信元输入更少的数据。但是，每种方法的基础方法是 截然不同，在芯片序列中表现良好的抗体在Cut&Run中可能不会成功。我们会 与染色质技术开发领先者EpiCypher®合作，比较H3K4me3和H3K27me3 芯片和切割-运行实验中的抗体性能。这一目标的成功将验证EpiBeacon 用于比较染色质分析，并为科学家采用CUT&RUN提供必要的信息。在……里面 第二阶段，EpiBeacon将扩展到其他分析(例如，路径分析、基序发现)、其他 表观基因组分析(例如ATAC-SEQ)，推出整合多个数据集的新工具(例如CHIP-SEQ和RNA-SEQ SEQ)，并利用公共可用的数据集(例如，NCBI SRA)，这些数据集持有丰富的表观遗传学数据，这些数据具有 在现有软件中使用具有挑战性。因此，EpiBeacon将提供最快速和用户友好的 市场上的第三代NGS分析平台，推动先进生物医学应用的表观遗传学发现。

PROJECT SUMMARY Epigenetics describes the study of phenotypic outcomes due to alterations in gene expression without changes to the coding DNA. The field has exploded in the past decade with the recognition that epigenetic factors (e.g. histone post-translational modifications, chromatin-associated proteins, DNA methylation) regulate gene expression and diverse downstream cellular processes, including the development of human disease. Next Generation Sequencing (NGS) studies of these epigenetic changes have enabled a more fundamental understanding of how chromatin structure impacts human health and revealed new targets for drug development. The importance of this field has driven remarkable advances in epigenomic profiling; however, innovations in methods to intelligibly interpret, compare, and visualize this mass of epigenetic data have lagged behind. The current framework for these tertiary analyses is slow, too technical for most users, and unable to process the increasingly complex queries that are required for epigenetic discovery. Basepair® is an industry leader in streamlined NGS analysis pipelines. Here, we will leverage this expertise with the development of EpiBeacon™, a serverless, user-friendly platform for rapid tertiary analysis of epigenetic data. In Aim 1, we will develop the EpiBeacon platform using the Amazon Web Services (AWS) Lambda service to instantly generate heatmaps of chromatin profiling data sourced from ENCODE. EpiBeacon will be uniquely compatible with the multiple rounds of iterative sampling required for tertiary analysis, and users will be able to dynamically adjust heatmap parameters and produce publication-ready figures in real time. In Aim 2, we will enable EpiBeacon with more sophisticated comparative analysis capabilities, which we will apply to answer an emerging problem in the field: whether antibodies and data from Chromatin ImmunoPrecipitation followed by NGS (ChIP-seq) are applicable to the novel chromatin profiling technology, CUT&RUN. CUT&RUN has the potential to supersede ChIP-seq as the standard in chromatin profiling, as it produces higher resolution data with fewer reads and reduced cell input vs. ChIP-seq. However, the methods underlying each approach are strikingly different, and antibodies that perform well in ChIP-seq may not be successful in CUT&RUN. We will work with EpiCypher®, a leader in chromatin technology development, to compare H3K4me3 and H3K27me3 antibody performance across ChIP and CUT&RUN experiments. The success of this Aim will validate EpiBeacon for comparative chromatin analyses and provide essential information for scientists adopting CUT&RUN. In Phase II, EpiBeacon will be expanded to other analyses (e.g. pathway analysis, motif discovery), other epigenomic assays (e.g. ATAC-seq), launch new tools to integrate multiple data sets (e.g. ChIP-seq and RNA- seq), and leverage publicly available datasets (e.g. NCBI SRA), which hold a wealth of epigenetic data that have been challenging to utilize with existing software. EpiBeacon will thus deliver the most rapid and user-friendly tertiary NGS analysis platform on the market, driving epigenetic discovery for advanced biomedical applications.