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.

西北我们所有人基因组中心(NWGC)的目标是提供高通量的基因分型和 我们所有人研究计划中登记的个人的全基因组测序(WGS)使用高度 成功的管道已经对近20万个样本和数万个 数以千计的高质量人类基因组。西北基因组学中心汇集了国际上三个 公认的PI(Nickerson(Contact)、Eichler和Jarvik)，在高通量临床方面拥有数十年的专业知识 基因组学和他们的合作调查人员已经将数万种不同的解释返回到 病人。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努力 国家高级翻译科学中心(NCATS)的项目团队，其他中心在 计划，如数据和研究中心(DRC)和生物库，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标和目的，我们将制作和解释变体 第一年最多100,000个样本，第二年至第五年最多200,000个样本。我们将 在第一年，WGS还制作和解释了10,000多个样本的变体；在第一年，多达100,000个样本 第二年；使用Illumina NovaSeq平台在第三至第五年提供多达20万个样本。为了实现这一目标，我们 将： 1-与我们所有人计划、DRC、生物库和其他团体合作，提供高效和 评估和完成高通量基因分型和WGS、CALL变体和 解释ACMG 59基因和其他基因中变异的影响，如程序在 CLIA认证的环境。 2-与生物库直接互动，仔细开发准备和 正在接收样本。 3-在流程的每个阶段(从项目启动开始)跟踪所有样本和所有样本的数据传输 使用我们的安全、完全交互和集成的实验室信息进行数据交付 管理系统(LIMS))，并根据需要向项目、DRC和其他小组提供报告。 4-以程序要求的格式(如IDAT)提供最高质量的基因型和WGS数据 用于基因分型和WGS的CRAM和VCFs的文件。 5-提供一支专业人员团队和精通工作流程的高吞吐量团队 CLIA认证的基因组中心。这些人包括在DNA样本方面接受过专门培训的个人 接收、质量控制、大规模生物信息学分析和变体解释。 6-根据需要协助额外的数据解释(ACMG基因以外的)，出版出版物(即， 材料和方法)，以及项目所需的其他活动。 7-提供样本中原始序列数据的安全备份以及与 项目(即样品跟踪、存储和质量控制信息)。 NWGC已经成功地与NIH合作了20多年 一批有影响力的、大型的项目，并拥有经验丰富的 团队具有经过验证的记录，并由强大的管理、 一流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。 视乎我们所有人的需要，新界西议会可灵活处理 所有年份建议的最小样本数，同时也能够 快速扩展以满足以下所有需求的最大吞吐量 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截止日期。 NWGC完全了解需要满足的要求 作为我们所有人计划的完全合作伙伴，并且完全有能力和准备。