Northwest Genomics Center for All of Us

西北基因组学中心

• 批准号: 10884599
• 负责人: Evan Eichler
• 金额: $ 208.48万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-25 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10884599
• 关键词: All of Us Genome Center; All of Us Research Program; Bioinformatics; CLIA certified; Clinical; DNA; Data; Data Analyses; Enrollment; Environment; Genes; Genome; Genomics; Genotype; Goals; Human Genome; Human Resources; Individual; Infrastructure; International; Laboratories; Logistics; Management Information Systems; Metadata; Methods; National Center for Advancing Translational Sciences; Patients; Process; Publications; Quality Control; Reporting; Research; Research Personnel; Sampling; Secure; Training; United States National Institutes of Health; Variant; Work; biobank; data exchange; empowerment; experience; flexibility; genome sequencing; instrumentation; programs; whole genome

The goal of the Northwest Genomics Center for All of Us (NWGC) is to provide high-throughput genotyping and whole genome sequencing (WGS) for individuals enrolled in the All of Us Research Program using a highly successful pipeline that has produced genotyping on nearly two hundred thousand samples and tens of thousands of high quality human genomes. The Northwest Genomics Center brings together three internationally recognized PIs (Nickerson (Contact), Eichler, and Jarvik), with decades of expertise in high-throughput clinical genomics and, together with their Co-Investigators, have returned tens of thousands of variant interpretations to patients. As we have done in the past with other NIH programs, we will coordinate our efforts with the All of Us program team in the National Center for Advancing Translational Sciences (NCATS), the other centers in the program such as the Data and Research Center (DRC) and the Biobank, and other Genome Centers if selected. To advance the goals and objectives of the All of Us Research Program we will produce and interpret variants from genotyping arrays for up to 100,000 samples in year 1 and up to 200,000 samples in years 2 - 5. We will also produce and interpret variants on more than 10,000 samples by WGS in year 1; up to 100,000 samples in year 2; and up to 200,000 samples in years 3-5 using the Illumina NovaSeq platform. To accomplish this, we will: 1- Work with the All of Us program, the DRC, the Biobank, and other groups to deliver an efficient and effective process for evaluating and completing high-throughput genotyping and WGS, call variants, and interpret the impact of variants in the ACMG 59 genes and other genes as indicated by the program in a CLIA-certified environment. 2- Interact directly with the Biobank to carefully develop the logistics and methods for preparing and receiving samples. 3- Track all samples and data transfers for all samples at every stage of the process (from project initiation to data delivery using our secure, completely interactive, and integrated laboratory information management system (LIMS)) and provide reports to the program, the DRC, and other groups as required. 4- Provide genotype and WGS data of the highest quality, in formats required by the program such as IDAT files for genotyping and CRAMs and VCFs for WGS. 5- Provide a team of specialized personnel and staff versed in the workflow of a well-established highthroughput CLIA-certified genome center. These include individuals specifically trained in DNA sample receipt, quality control, and large-scale bioinformatics analysis and variant interpretation. 6- Assist as needed with additional data interpretation (beyond the ACMG genes), with publications (i.e., materials and methods), and other activities as required for the program. 7- Provide secure backup of raw sequence data from the samples and all metadata associated with the project (i.e., sample tracking, storage, and QC information). The NWGC has worked successfully for more than 20 years with the NIH on a number of impactful, large-scale projects, and has a highly experienced team with a proven track record that is empowered by a robust administrative, computational, and instrumentation infrastructure that is state-of-the-art and can rapidly facilitate the goals of the All of Us Research Program. Depending on the needs of All of Us, the NWGC is flexible to handle the minimum number of samples proposed in all years while also being able to quickly scale to accommodate the maximum throughput needed by the All of Us Research Program (Table 1). The NWGC has extensive experience scaling in a short timeframe and has always met project goals and deadlines. The NWGC has a complete understanding of the requirements needed to be a full partner for the All of Us program and is fully capable and prepared.

西北基因组学中心 (NWGC) 的目标是提供高通量基因分型和 使用高度测序技术对参与“我们所有人研究计划”的个人进行全基因组测序 (WGS) 成功的管道已对近二十万个样本和数十个样本进行了基因分型 数以千计的高质量人类基因组。西北基因组中心汇集了三个国际 公认的 PI（Nickerson（联系人）、Eichler 和 Jarvik），在高通量临床领域拥有数十年的专业知识 基因组学并与他们的合作研究人员一起，返回了数以万计的变异解释 患者。正如我们过去对其他 NIH 项目所做的那样，我们将与我们所有人协调我们的努力 国家转化科学促进中心 (NCATS) 的项目团队，其他中心 数据和研究中心 (DRC) 和生物银行等计划，以及其他基因组中心（如果选择）。 为了推进“我们所有人研究计划”的目的和目标，我们将生产和解释变体 从第 1 年最多 100,000 个样本的基因分型阵列和第 2 - 5 年最多 200,000 个样本的基因分型阵列中。我们将 还在第一年通过 WGS 对 10,000 多个样本生成并解释变异；多达 100,000 个样本 第二年；使用 Illumina NovaSeq 平台在第 3-5 年内收集多达 200,000 个样本。为了实现这一目标，我们 将要： 1- 与“我们所有人”计划、DRC、生物银行和其他团体合作，提供高效且 评估和完成高通量基因分型和全基因组测序、检测变异的有效流程 解释 ACMG 59 基因和其他基因中变异的影响，如程序中所示 CLIA 认证的环境。 2- 直接与生物样本库互动，仔细开发准备和使用的物流和方法 接收样品。 3- 跟踪流程每个阶段的所有样品和所有样品的数据传输（从项目启动 使用我们安全、完全交互式和集成的实验室信息进行数据传输 管理系统（LIMS））并根据需要向项目、DRC 和其他团体提供报告。 4- 以项目所需的格式（例如 IDAT）提供最高质量的基因型和 WGS 数据 用于基因分型的文件以及用于 WGS 的 CRAM 和 VCF。 5- 提供一支由专业人员和精通完善高通量工作流程的员工组成的团队 CLIA 认证的基因组中心。其中包括接受过 DNA 样本专门培训的人员 收据、质量控制以及大规模生物信息学分析和变异解释。 6- 根据需要协助额外的数据解释（ACMG 基因之外）和出版物（即， 材料和方法），以及该计划所需的其他活动。 7- 提供样本中原始序列数据以及与样本相关的所有元数据的安全备份 项目（即样品跟踪、存储和 QC 信息）。 NWGC 已与 NIH 成功合作 20 多年 完成了许多有影响力的大型项目，并拥有经验丰富的 团队拥有良好的业绩记录，并由强大的管理人员授权， 最先进的计算和仪器基础设施 可以迅速促进“我们所有人研究计划”的目标的实现。 根据我们所有人的需求，NWGC 可以灵活地处理 在所有年份中提出的最小样本数量，同时也能够 快速扩展以适应所有所需的最大吞吐量 美国研究计划（表 1）。 NWGC拥有丰富的经验 在短时间内扩展并始终满足项目目标和最后期限。 NWGC 完全了解所需的要求 “我们所有人”计划的正式合作伙伴，并且完全有能力并做好准备。