New York Genome Characterization Center: Somatic Mosaicism across Human Tissues

项目概要/摘要-纽约基因组表征中心 在过去的二十年里，大规模测序工作一直集中在生成DNA序列上。 来自容易获得的组织如血液或唾液的数据集，以鉴定与以下相关的种系变异： 疾病表型然而，在表征健康人的体细胞变异方面取得的进展有限。 组织及其在人类寿命过程中对健康和疾病的贡献。体细胞变异 历史上，在肿瘤生物学的背景下进行了研究;然而，有越来越多的证据表明，体细胞 变异在衰老过程中以及在心血管，神经变性， 免疫和神经发育疾病。因此，迫切需要描述躯体疾病的特征， 不同种族和民族的个体在整个人类寿命中健康人体组织中的变异景观。 跨人类组织的体细胞镶嵌（SMaHT）计划将通过建立一个 一个有凝聚力的网络，将共同努力，创造高质量的体细胞变异目录;一个目录， 可在科学界共享，使研究能够调查 细胞群体和组织中的体细胞嵌合现象，可以阐明克隆形成的机制。 发展，进化和扩展，并使研究体细胞突变在疾病中的作用成为可能 发病机制和进展。纽约基因组表征中心（NYGCC）将 与其他SMaHT网络中心合作，使用三个 核心高深度测序分析：双链体全基因组测序（WGS）、mRNA测序和长- 读牛津纳米孔WGS。这三个核心分析将提供一个前所未有的和全面的看法 各种健康组织中的体细胞突变。来自深层WGS的数据将能够发现 体细胞SNV、插入缺失、移动的元件、拷贝数变化和结构变体。RNA测序 数据将被用来确认那些落入表达基因中的变异的存在，并进一步评估 它们对剪接的影响长读段WGS测序将用作短读段WGS的推论，以确认 并增强对移动的元件、拷贝数变化和结构变体的发现。这些核心检测 我们建议增加使用直接文库制备Plus（DLP+）的单细胞WGS测序和 转录组（GoT）。DLP+是一种无需扩增的单细胞WGS检测试剂盒，可实现高灵敏度检测 拷贝数变化、杂合性丢失和结构变异。它进一步使复制的研究 定时、克隆扩增和适应度，并与合并的伪批量分析兼容， 深散装WGS。转录组的基因分型分析将使我们能够探索，对于表达的体细胞变体， 它们发生的细胞类型或谱系，并通过与单细胞表达数据（和细胞表面 标记检测和长读段转录测序）这些突变的功能效应。

PROJECT SUMMARY/ABSTRACT - NEW YORK GENOME CHARACTERIZATION CENTER Large-scale sequencing efforts over the last two decades have been focused on generating DNA sequence datasets from readily available tissues such as blood or saliva to identify germline variants associated with disease phenotypes. However, limited progress has been made in characterizing somatic variants in healthy tissues and their contribution to health and disease over the course of the human lifespan. Somatic variation has historically been studied in the context of tumor biology; however, there is mounting evidence that somatic variation plays an important role in the aging process, as well as in cardiovascular, neurodegenerative, immunologic, and neurodevelopmental diseases. There is therefore a critical need to characterize the somatic variant landscape in healthy human tissues in individuals of diverse race and ethnicity across the human lifespan. The Somatic Mosaicism across Human Tissues (SMaHT) program will address this gap by establishing a cohesive Network that will work together to create high-quality somatic variant catalog; a catalog that is broadly shareable across the scientific community and that enables studies investigating the rates and patterns of somatic mosaicism across cell populations and tissues, that can elucidate the mechanisms underlying clonal development, evolution, and expansion, and that enables studies of the role of somatic mutation in disease pathogenesis and progression. The New York Genome Characterization Center (NYGCC) will work collaboratively with other SMaHT Network Centers to generate a high-quality somatic variant catalog using three core high-depth sequencing assays: duplex whole genome sequencing (WGS), mRNA sequencing, and long- read Oxford Nanopore WGS. These three core assays will provide an unprecedented and comprehensive view of somatic mutations across a variety of healthy tissues. The data from deep WGS will enable discovery of somatic SNVs, indels, mobile elements, copy number changes, and structural variants. The RNA sequencing data will be used to confirm the presence of those variants that fall in expressed genes, and further evaluate their effect on splicing. The long read WGS sequencing will be used as a corollary to short read WGS to confirm and enhance discovery of mobile elements, copy number changes and structural variants. To these core assays we propose adding single cell WGS sequencing using Direct Library Preparation Plus (DLP+) and genotyping of transcriptomes (GoT). DLP+ is an amplification-free single cell WGS assay that allows high sensitivity detection of copy number changes, loss of heterozygosity, and structural variation. It further enables the study of replication timing, clonal expansion and fitness and is compatible with pooled pseudo-bulk analysis to compare against deep bulk WGS. The genotyping of transcriptomes assay will allow us to explore, for expressed somatic variants, the cell type or lineage in which they occurred and by pairing with single cell expression data (and cell surface marker detection and long read transcript sequencing) the functional effects of these mutations.