Core C - Sequencing and Analysis.

项目摘要/摘要 核心C的目标是提供AML基因组和表观基因组的高通量生产和分析 此PPG中所有四个项目的序列数据。这包括测序、体细胞和生殖系变异 检测和验证，以及多种数据类型的集成。这将通过生成高质量的 DNA和RNA测序数据，并使用尖端算法和技术进行分析。 特定目标/核心服务1：(顺序制作) 核心C中的样品将使用Illumina HiSeqX、4000和NovaSeq平台进行测序。 核心C中产生的数据将是全面的：全基因组、外显子组和DNA捕获验证， 以及纠错测序、单细胞rna-seq、总和小rna-seq、全基因组亚硫酸盐 测序和其他定制的表观遗传学分析。这些数据将通过最先进的技术进行处理 基因组管道，以产生初步结果，如序列比对和变体调用。 特定目标/核心服务2：(生物信息学分析) 这些管道为详细、新颖和迭代的分析提供了起点，将在 核心C和是每个项目的基础。项目1将要求对基因组和 表观基因组(转录组、scRNA-Seq、WGBS)数据以更好地定义驱动启动的事件， 在有和没有DNMT3A突变的样本中，进展和复发。在项目2中，我们将利用我们的 免疫基因组学确定介导同种异体移植的次要组织相容性抗原的经验 反应，并表征导致复发的遗传和表观遗传变化的小鼠模型 移植。在项目3和4中，我们将利用增强的WGS、纠错测序、批量RNA-SEQ、 ScRNA-seq和分阶段读取数据，以定义驱动亚克隆扩展和进展的机制 从MDS到SAML(项目3)，或TP53突变对非整倍体AML发展的特定影响 (项目4)。 回答这些项目中概述的问题需要深入的综合分析，远远超出 简单的突变计数是以前基因组研究的一个标志。这需要公共 紧密集成将提供的基础设施、全面的数据库和广泛的专业知识 项目领导和Core C中的科学家之间的关系。

PROJECT SUMMARY/ABSTRACT The goal of Core C is to provide high-throughput production and analysis of AML genomic and epigenomic sequence data for all four projects in this PPG. This includes sequencing, somatic and germline variant detection and validation, and integration of many data types. This will be achieved by generating high-quality DNA and RNA sequencing data and analyzing it using cutting-edge algorithms and techniques. Specific Aim/Core Service 1: (Sequence Production) Sequencing of samples in Core C will take place using the Illumina HiSeqX, 4000, and NovaSeq platforms. The data produced in Core C will be comprehensive: whole genome, exome, and capture validation for DNA, as well as error-corrected sequencing, single-cell RNA-seq, total and small RNA-seq, whole genome bisulfite sequencing, and other custom epigenetic analyses. These data will be processed through state-of-the-art genomic pipelines to produce primary results like sequence alignments and variant calls. Specific Aim/Core Service 2: (Bioinformatic Analysis) These pipelines provide a starting point for the detailed, novel, and iterative analyses which will take place in Core C and are foundational for each project. Project 1 will require integrative analysis of genomic and epigenomic (transcriptome, scRNA-Seq, WGBS) data to better define the events that drive initiation, progression, and relapse in samples with and without DNMT3A mutations. In Project 2, we will leverage our experience in immunogenomics to define minor histocompatibility antigens that mediate allo-transplant response, and characterize the genetic and epigenetic changes that drive relapse in a mouse model of transplantation. In Projects 3 and 4, we will utilize enhanced WGS, error-corrected sequencing, bulk RNA-seq, scRNA-seq, and phased-read data to define the mechanisms that drive subclonal expansion and progression from MDS to sAML (Project 3), or the specific effects of TP53 mutations on the development of aneuploid AML (Project 4). Answering the questions outlined in these projects requires deep integrative analysis that goes far beyond the simple mutation counting that was a hallmark of previous genomic studies. This requires common infrastructure, comprehensive databases, and extensive expertise that will be provided by tight integration between project leadership and the scientists in Core C.