Calypso: a web software system supporting team-based, longitudinal genomic diagnostic care

Calypso：支持基于团队的纵向基因组诊断护理的网络软件系统

基本信息

批准号：
10376642
负责人：
Gabor T Marth
金额：
$ 91.45万
依托单位：
UNIVERSITY OF UTAH
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-02-01 至 2027-01-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10376642
关键词：
Address Adopted Back Bioinformatics Caring Clinic Clinical Collaborations Communication Communities Complex Computer software Data Data Analyses Data Set Diagnosis Diagnostic Discipline Disease Ensure Environment Evaluation Felis catus Funding Genes Genetic Genetic Diseases Genome Genomics Genotype Goals Hand Individual Infrastructure Internet Intuition Joints Knowledge Literature Medical Medicine Modernization Molecular National Human Genome Research Institute Neonatal Intensive Care Units Pathogenicity Pathologist Patients Periodicity Phenotype Physicians Process Reporting Research Resources Secure Site Software Tools Support System System Testing Time United States National Institutes of Health Universities Update Utah Variant Visual adjudicate base clinical research site clinically relevant clinically significant cloud based cohort computational pipelines computer infrastructure critically ill newborn dashboard data access data infrastructure design diagnostic strategy genetic counselor genetic disorder diagnosis genetic variant genome sequencing genomic data implementation science improved insight longitudinal analysis member molecular diagnostics novel phenotypic data programs rapid diagnosis response software development software systems support tools tool whole genome

项目摘要

PROJECT SUMMARY/ABSTRACT Some of the most challenging diagnostic cases involve patients who present with complex phenotypes that evolve over time and intersect multiple medical disciplines. The two primary clinical settings for diagnosing such patients are undiagnosed disease clinics and neonatal intensive care unit rapid genome sequencing programs. These clinics have adopted an approach where diagnostic analysis is based on comprehensive genomic sequencing data; and analysis is carried out by a large, collaborative clinical team. This team-based approach leverages the treating physician’s detailed understanding of the patient’s phenotype, the medical geneticist’s deep knowledge of genetic diseases, the bioinformatic analyst’s expertise in adjudicating a variant’s quality and predicted pathogenicity, as well as the diagnostic pathologist’s ability to synthesize all relevant information and reach a conclusion regarding a given variant’s clinical significance. Diagnostic analysis of patients in both of these environments is a long-term process that often continues for months or even years, until new phenotypes in the patient are observed or novel gene-disease associations are reported in the literature that provide the necessary insight for case solution. However, existing software tools typically only cater to the bioinformatician expert or the diagnostic molecular pathologist, but not the treating physician or the genetic counselor; focus on making a genetic diagnosis at a single timepoint, rather than following the patient over time during a lengthy diagnostic process, and are therefore unable to adequately support team-based, longitudinal genomic diagnostic care. Addressing this pressing need, here we propose to develop a comprehensive software system, Calypso, to address this pressing need. Calypso will support team-based diagnostics via intuitive and visual iobio web tools tailored for each team member’s specialized contribution to diagnostic analysis; and facilitate long-term genomic care by keeping patient genomic data up-to-date via a systematic variant re- annotation infrastructure. We will put Calypso into the hands of the clinical teams in our undiagnosed disease clinic and our neonatal intensive care unit, ideal testing grounds for evaluating our tool’s impact on long-term genome diagnostic care in the context of team-based medicine. We will also centrally deploy and evaluate our tool in NHGRI’s Undiagnosed Disease Network to help realize the collaborative diagnostic opportunities presented by a large, clinically focused research consortium.

项目概要/摘要一些最具挑战性的诊断病例涉及具有复杂表型的患者，这些患者诊断此类疾病的两个主要临床环境随着时间的推移而发展并交叉多个医学学科。患者正在接受未确诊疾病诊所和新生儿重症监护室的快速基因组测序计划。这些诊所采用了一种基于综合基因组进行诊断分析的方法测序数据；并由一个大型协作临床团队进行分析。该方法利用了治疗医生对患者表型、医疗情况的详细了解遗传学家对遗传疾病的深入了解，生物信息分析师在判断变异的专业知识质量和预测的致病性，以及诊断病理学家综合所有相关信息的能力信息并就给定变异的临床意义得出结论。患者在这两种环境中的生存是一个长期的过程，通常会持续数月甚至数年，直到观察到患者的新表型或文献中报告新的基因-疾病关联为案例解决方案提供必要的洞察力。但是，现有的软件工具通常只能满足需求。生物信息学家或诊断分子病理学家，但不是治疗医生或遗传学家咨询师专注于在单个时间点进行基因诊断，而不是随着时间的推移跟踪患者在漫长的诊断过程中，因此无法充分支持基于团队的纵向为了满足这一迫切需求，我们建议开发一款综合软件。系统 Calypso 可以满足这一迫切需求，Calypso 将通过直观且支持基于团队的诊断。针对每个团队成员对诊断分析的专业贡献量身定制的视觉 iobio 网络工具；以及通过系统变异重新更新患者基因组数据，促进长期基因组护理我们将把 Calypso 交给临床团队来治疗我们未确诊的疾病。诊所和我们的新生儿重症监护室是评估我们的工具对长期影响的理想测试场我们还将集中部署和评估我们的团队医学背景下的基因组诊断护理。 NHGRI 未确诊疾病网络中的工具可帮助实现协作诊断机会由一个大型的、以临床为重点的研究联盟提出。