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 - 纽约基因组特征中心 在过去的二十年中，大规模测序工作一直集中在产生DNA序列上 来自随时可用的组织（例如血液或唾液）的数据集，以识别与 疾病表型。但是，在表征健康的体细胞变体方面取得了有限的进展 组织及其对人类寿命过程中对健康和疾病的贡献。体细胞变异具有 从历史上看，在肿瘤生物学的背景下进行了研究；但是，有越来越多的证据表明躯体 变异在衰老过程以及心血管，神经退行性，在衰老过程中起重要作用 免疫学和神经发育疾病。因此，迫切需要表征躯体 人类健康组织中健康的人类组织中各种种族和种族的变异景观在整个人类寿命中。 人类组织（SMAHT）计划的躯体镶嵌物（SMAHT程序）将通过建立一个 有凝聚力网络将共同创建高质量的体细胞变体目录；广泛的目录 在整个科学界都可以共享，并能够研究研究的速度和模式 跨细胞种群和组织的体细胞镶嵌物，可以阐明克隆的机制 发展，进化和扩展，这可以研究疾病中体突变的作用 发病机理和进展。纽约基因组特征中心（NYGCC）将起作用 与其他SMAHT网络中心合作，使用三个 核心高深度测序测定：双工全基因组测序（WGS），mRNA测序和长期 阅读牛津纳米孔WGS。这三个核心测定将提供前所未有的全面观点 各种健康组织的体细胞突变。来自深WGS的数据将使能够发现 体细胞SNV，Indels，移动元素，复制号码更改和结构变体。 RNA测序 数据将用于确认出现在表达基因中的那些变体的存在，并进一步评估 它们对剪接的影响。长阅读WGS测序将用作简短读取WGS的推论以确认 并增强移动元素的发现，副本数字更改和结构变体。这些核心测定法 我们建议使用直接库制备加上（DLP+）和基因分型添加单细胞WGS测序 转录组（GOT）。 DLP+是一种无扩增的单细胞WGS测定法，允许高灵敏度检测 拷贝数的变化，杂合性的丧失和结构变化。它进一步可以研究复制 时机，克隆扩张和健身，与合并的伪块分析兼容，以比较 深批量的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体， 它们发生的细胞类型或谱系，并与单细胞表达数据配对（和细胞表面） 标记检测和长读取转录测序）这些突变的功能效应。