New York Genome Characterization Center: Somatic Mosaicism across Human Tissues

纽约基因组表征中心：人体组织的体细胞镶嵌

• 批准号: 10662878
• 负责人: Samuel Aparicio
• 金额: $ 150万
• 依托单位: NEW YORK GENOME CENTER
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-01 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10662878
• 关键词: Aging; Automation; Automobile Driving; Benchmarking; Biological Assay; Blood; Cardiovascular Diseases; Catalogs; Cell Lineage; Cell surface; Cells; Clonal Expansion; Collaborations; Communities; DNA Sequence; DNA Sequencing Facility; Data; Data Analyses; Data Files; Data Reporting; Data Set; Detection; Development; Disease; Elements; Ensure; Ethnic Origin; Evolution; Gene Expression; Genes; Genome; Genotype; Germ-Line Mutation; Goals; Grant; Health; Human; Human Resources; Immune System Diseases; Individual; Laboratories; Large-Scale Sequencing; Libraries; Longevity; Loss of Heterozygosity; Mediating; Metadata; Methods; Monitor; Mosaicism; Mutation; Neurodegenerative Disorders; Neurodevelopmental Disorder; New York; Pathogenesis; Patients; Pattern; Persons; Play; Population; Preparation; Procedures; Process; Production; Protocols documentation; Quality Control; RNA Splicing; Recurrence; Role; Running; Saliva; Sampling; Sensitivity and Specificity; Somatic Cell; Somatic Mutation; Staff Development; System; Technology; Tissue Procurements; Tissues; Transcript; Tumor Biology; Variant; Work; analysis pipeline; cell type; cohort; data exchange; data format; data quality; detection sensitivity; disease phenotype; experience; falls; file format; fitness; genome sequencing; genome wide association study; human tissue; improved; innovation; insertion/deletion mutation; laboratory development; laboratory experiment; mRNA sequencing; meetings; nanopore; new technology; organizational structure; process improvement; programs; racial diversity; task analysis; technology development; transcriptome; transcriptome sequencing; variant detection; whole genome

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.

项目摘要/摘要 - 纽约基因组表征中心 过去二十年的大规模测序工作一直集中在生成 DNA 序列 来自血液或唾液等容易获得的组织的数据集，用于识别与 疾病表型。然而，在表征健康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。体细胞变异有 历史上曾在肿瘤生物学背景下进行过研究；然而，越来越多的证据表明体细胞 变异在衰老过程以及心血管、神经退行性疾病、 免疫学和神经发育疾病。因此，迫切需要表征体细胞 在人类一生中，不同种族和民族的个体的健康人体组织中存在着不同的景观。 跨人体组织的体细胞镶嵌（SMaHT）计划将通过建立一个 凝聚力网络将共同创建高质量的体细胞变异目录；广泛的目录 可在整个科学界共享，使研究能够调查 跨细胞群和组织的体细胞嵌合体，可以阐明克隆背后的机制 发育、进化和扩展，从而能够研究体细胞突变在疾病中的作用 发病机制和进展。纽约基因组表征中心 (NYGCC) 将开展工作 与其他 SMaHT 网络中心合作，使用三个 核心高深度测序分析：双重全基因组测序 (WGS)、mRNA 测序和长链测序 阅读牛津纳米孔全基因组测序。这三个核心检测将提供前所未有的全面视图 各种健康组织的体细胞突变。来自深度全基因组测序的数据将有助于发现 体细胞 SNV、插入缺失、移动元件、拷贝数变化和结构变异。 RNA测序 数据将用于确认表达基因中的那些变异的存在，并进一步评估 它们对拼接的影响。长读长 WGS 测序将作为短读长 WGS 的推论来确认 并增强对移动元素、拷贝数变化和结构变异的发现。对于这些核心检测 我们建议使用 Direct Library Preparation Plus (DLP+) 添加单细胞 WGS 测序和基因分型 转录组（GoT）。 DLP+ 是一种无需扩增的单细胞 WGS 检测方法，可实现高灵敏度检测 拷贝数变化、杂合性丢失和结构变异。它进一步使得复制研究成为可能 计时、克隆扩增和适应度，并且与合并伪批量分析兼容以进行比较 深散装 WGS。转录组测定的基因分型将使我们能够探索表达的体细胞变异， 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 标记检测和长读转录本测序）这些突变的功能影响。