The Baylor-Hopkins Clinical Genomics Center for All of Us

贝勒-霍普金斯大学临床基因组学中心

• 批准号: 10003441
• 负责人: ERIC A. BOERWINKLE
• 金额: $ 1385.5万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 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 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10003441
• 关键词: Awareness; Biological Assay; CLIA certified; Clinical; Collaborations; Communication; Communities; Cost efficiency; Data; Environment; Genetic; Genome; Genomics; Genotype; Hereditary Disease; Individual; Medicine; Metadata; Methods; Participant; Pathogenicity; Phase; Population; Process; Protocols documentation; Public Health Schools; Reporting; Research; Sampling; Secure; Texas; United States National Institutes of Health; Universities; Validation; Variant; Work; cloud based; college; cost; experience; frontier; genomic data; human genome sequencing; innovation; member; programs; software development; tool; whole genome

The Baylor-Hopkins Clinical Genomics Center (BHCGC), incorporating the Baylor College of Medicine (BCM) Human Genome Sequencing Center (HGSC) and the Johns Hopkins University Center for Inherited Disease Research (CIDR) will perform at least 900,000 whole genome array genotype assays and 700,000 whole genome sequences with a minimum of 35-fold coverage, over five years, for the National Institutes of Health’s All of Us Program (AoU). The work will all be carried out in CAP/CLIA certified environments and will favor Illumina platforms, with a projected average cost of less than $31 per genotype and $647 per WGS, respectively. Sequencing and analyses will be performed with NIH compliant pipelines and population-aware methods applied for phasing and ancestry determination. Automated methods will identify and rank putative pathogenic or likely pathogenic variants for every participant, and make available the results in both ‘pre-reports’ and in a searchable environment, assisting selection of a subset of individuals for Clinical Validation. Signed, Clinical Reports will be generated for up to six thousand participants per year, leveraging BCM’s deep experience in genetic interpretation. The partnership will maintain a secure cloud Baylor-Hopkins AoU Portal (BHAoU Portal) to manage sample tracking and to distribute all data, with symmetric access to BHCGC and AoU DCR and GRC members. Data flow and population level analyses will be overseen by partners at the University of Texas School of Public Health (UTSPH), DNAnexus will facilitate the cloud-based data communication and a collaboration with Microsoft Research will innovate in optimized computing. A new ‘Frontiers of Interpretation’ group will work locally, and with Microsoft, for application of AI methods for variant interpretation. Approximately 300 genomes will be ‘upgraded’ in quality with a battery of with other sequencing methods, in the first year, to determine the impact on Clinical Reporting and guide program adjustments. Pursuit of innovation for enhanced analytical value or cost efficiencies will be a priority. Direct deliverables to the AoU DRC will include sample metadata, raw and processed genomic data, variant interpretations, and preliminary and signed Clinical Reports. In addition, all protocols, tools, and software developed for the All of Us program will be made available to the program and to the broader scientific community.

贝勒-霍普金斯临床基因组学中心(BHCGC)，包括贝勒医学院(BCM) 人类基因组测序中心(HGSC)和约翰霍普金斯大学遗传病中心 研究(CIDR)将进行至少900,000次全基因组阵列基因分析和700,000次全基因组阵列基因分析 美国国立卫生研究院的基因组序列，在五年内至少覆盖35倍 我们所有人计划(AOU)。所有工作都将在CAP/CLIA认证环境中进行，并将有利于 Illumina平台，预计每个基因型的平均成本不到31美元，每个WGS的平均成本不到647美元。 测序和分析将使用符合NIH标准的管道和应用种群感知方法进行 用于分期和血统确定。自动化方法将识别和排序推定的致病或可能 每个参与者的致病变异体，并将结果同时显示在预先报告和可搜索的 环境，协助选择临床验证的个体子集。签字，临床报告将被 利用BCM在遗传方面的丰富经验，每年为多达6000名参与者生成 释义。合作伙伴关系将维护一个安全的云贝勒-霍普金斯AoU门户(BHAoU门户)，以 管理样本跟踪并分发所有数据，对称访问BHCGC和AOU DCR和GRC 会员。数据流和人口水平分析将由德克萨斯大学学院的合作伙伴监督 公共卫生部(UTSPH)的DNAnexus将促进基于云的数据通信，并与 微软研究院将在优化计算方面进行创新。将成立一个新的“口译前沿”小组 在当地，并与微软合作，应用人工智能方法进行变式解释。大约300个基因组 将在第一年用一组其他测序方法进行质量升级，以确定 对临床报告和指导计划调整的影响。追求创新，提高分析价值 否则，提高成本效率将是一个优先事项。直接交付给AOU DRC的内容将包括样本元数据、原始数据和 经过处理的基因组数据、不同的解释以及初步的和签署的临床报告。此外，所有 为我们所有人计划开发的协议、工具和软件将可供计划和 更广泛的科学界。