Instrumenting the Delivery System for a Genomics Research Information Commons

检测基因组学研究信息共享的交付系统

基本信息

批准号：
10427386
负责人：
KENNETH D MANDL
金额：
$ 169.36万
依托单位：
BOSTON CHILDREN'S HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-07-31 至 2025-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10427386
关键词：
Address African ancestry Age Authorization documentation Big Data to Knowledge Biological Caring Childhood Clinical Collaborations Complex Confidence Intervals Consent Creativeness Data Data Aggregation Data Science Data Set Data Sources Databases Diagnosis Diagnostic Disease Electronic Health Record Enrollment Environment Fast Healthcare Interoperability Resources Fostering Frequencies Gender Genes Genetic Genetic Databases Genome Genomics Genotype Goals Heterogeneity Hospitals Hypertrophic Cardiomyopathy Individual Industry Collaboration Informatics Information Resources Information Systems Infrastructure Institution Institutional Review Boards Journals Laboratories Licensing Link Medicine National Health and Nutrition Examination Survey Nature New England Outcome Pathogenicity Patients Pediatric Hospitals Phenotype Policies Population Population Heterogeneity Process Prognosis Protocols documentation Publishing Recontacts Reference Values Reporting Research Research Personnel Resources Sampling Secure Site System Technology Testing Time United States National Institutes of Health Update Variant Vertebral column Work application programming interface authority biobank black patient cohort comorbidity data modeling data sharing ethnic diversity exome genetic pedigree genetic variant genomic data improved innovation instrument open source patient population phenotypic data population based programs self organization tool treatment response whole genome

项目摘要

Project Summary A patient’s genetic variant must be contextualized against a population-based reference and detailed phenotype to assess its pathogenicity and impact on prognosis, based on the care trajectories and outcomes of other patients with the variant, or similar variants of a particular gene. However, CTSA researchers do not have ready access to a definitive and representative reference dataset linking the genome to diagnosis, clinical progression, therapeutic response, and precision-adjusted laboratory reference ranges with the appropriate consents to recontact patients if needed. In preliminary work, three of the leading children’s hospitals in the CTSA program formed the Genomics Research and Innovation Network (GRIN) leveraging a combined, ethnically diverse population with unparalleled representation across the pediatric disease spectrum. GRIN sites broadly consent patients into compatible biobanking protocols. The next logical step is a truly federated CTSA-wide biobanking initiative, with the informatics supporting a Genomics Information Commons (GIC). With phenotype data produced as a byproduct of care, we develop the GIC technology, regulatory, and policy backbone, recognizing both heterogeneity of IT systems across CTSA hospitals and local control imperatives for a successful federated network. First, adhering to well-established common data models, each site exposes data to investigators across the secure PIC-SURE meta application programming interface (API), fostering incorporation of multiple heterogeneous clinical, omics, and environmental datasets. We demonstrate the self-scaling nature of the GIC as two additional CTSAs join in a modular fashion. Second, we develop two portals for researchers: (A) Prep-to- research portal. Investigators can execute genotype, phenotype, or combined genotype/phenotype queries, and receive aggregate results in real time; and (B) Study portal. With proper approvals, patient-level data are readily transferred to a cloud-hosted environment with data science tools (Jupyter Notebooks, R Studio), SMART on FHIR apps and resources, and API access to external data sources (e.g., gnomAD, NHANES). Third, we develop a GIC toolkit with policies for broadly consented biobank enrollment, investigator access, material transfer, and collaboration to enable new sites to participate and/or self-organize into collaboration networks. Finally, we leverage the GIC to build, and make publicly available, a knowledge resource of genetically-adjusted, precision laboratory reference ranges across demographically diverse populations.

项目摘要患者的遗传变异必须针对基于人群的参考和详细表型进行上下文化评估其致病性和对预后的影响，基于其他的护理轨迹和结果具有特定基因的变体或类似变异的患者。但是，CTSA研究人员尚未准备好访问将基因组与诊断，临床进展相关的确定性和代表性参考数据集，治疗反应和精确调整的实验室参考范围适当的同意如果需要，请重新连接患者。在初步工作中，CTSA计划中的三家领先儿童医院形成了基因组学研究与创新网络（笑）在小儿疾病谱系中具有无与伦比的代表性的人群。笑容广泛同意患者进入兼容的生物群体方案。下一个逻辑步骤是真正联合的CTSA范围内的生物库倡议，提供了支持基因组信息共享（GIC）的信息。使用表型数据作为护理的副产品，我们开发了GIC技术，监管和政策骨干，认可 CTSA医院的IT系统的异质性均和成功联邦的本地控制要求网络。首先，在遵守已建立的公共数据模型时，每个站点都向调查人员揭露数据安全的PIC-SUR-SURE元应用程序编程接口（API），促进了多个异质临床，OMIC和环境数据集。我们展示了GIC的自我缩放性质随着另外两个CTSA以模块化的方式加入。其次，我们为研究人员开发了两个门户：（a）准备工作研究门户。研究人员可以执行基因型，表型或组合基因型/表型查询，并且实时接收汇总结果；（b）学习门户。有了适当的批准，患者级数据很容易通过数据科学工具（Jupyter Notebooks，R Studio）转移到云托管的环境中，Smart On FHIR应用程序和资源，以及API访问外部数据源（例如，GNOMAD，NHANES）。第三，我们发展 GIC工具包，具有广泛同意的生物库的政策，调查员访问，材料转移和协作以使新站点能够参与和/或自我组织为协作网络。最后，我们利用GIC构建并公开可用，是一种普遍调整，精确度的知识资源实验室参考范围在人口统计学多样化的人群之间。

项目成果

期刊论文数量（16）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

ADGR: Admixture-Informed Differential Gene Regulation.

DOI：
10.3390/genes14010147
发表时间：
2023-01-05
期刊：
GENES
影响因子：
3.5
作者：
Lee, In-Hee;Kong, Sek Won
通讯作者：
Kong, Sek Won

Real world performance of the 21st Century Cures Act population-level application programming interface.

21 世纪治愈法案人口级应用程序编程接口的真实世界性能。

DOI：
10.1093/jamia/ocae040
发表时间：
2024
期刊：
Journal of the American Medical Informatics Association : JAMIA
影响因子：
0
作者：
Jones,JamesR;Gottlieb,Daniel;McMurry,AndrewJ;Atreja,Ashish;Desai,PankajaM;Dixon,BrianE;Payne,PhilipRO;Saldanha,AnilJ;Shankar,Prabhu;Solad,Yauheni;Wilcox,AdamB;Ali,MomeenaS;Kang,Eugene;Martin,AndrewM;Sprouse,Elizabeth
通讯作者：
Sprouse,Elizabeth

Real World Performance of the 21st Century Cures Act Population Level Application Programming Interface.

21 世纪治愈法案人口级应用程序编程接口的真实世界表现。

DOI：
10.1101/2023.10.05.23296560
发表时间：
2023
期刊：
medRxiv : the preprint server for health sciences
影响因子：
0
作者：
Jones,JamesR;Gottlieb,Daniel;McMurry,AndrewJ;Atreja,Ashish;Desai,PankajaM;Dixon,BrianE;Payne,PhilipRO;Saldanha,AnilJ;Shankar,Prabhu;Solad,Yauheni;Wilcox,AdamB;Ali,MomeenaS;Kang,Eugene;Martin,AndrewM;Sprouse,Elizabeth
通讯作者：
Sprouse,Elizabeth

Privacy protections to encourage use of health-relevant digital data in a learning health system.

DOI：
10.1038/s41746-020-00362-8
发表时间：
2021-01-04
期刊：
NPJ digital medicine
影响因子：
15.2
作者：
McGraw D;Mandl KD
通讯作者：
Mandl KD

Push Button Population Health: The SMART/HL7 FHIR Bulk Data Access Application Programming Interface.

DOI：
10.1038/s41746-020-00358-4
发表时间：
2020-11-19
期刊：
NPJ digital medicine
影响因子：
15.2
作者：
Mandl KD;Gottlieb D;Mandel JC;Ignatov V;Sayeed R;Grieve G;Jones J;Ellis A;Culbertson A
通讯作者：
Culbertson A