A web-based platform to support team-based genome diagnostics

摘要/摘要 基因组测序正在迅速成为诊断复杂诊断病例的标准工具，特别是在 危重新生儿和患有罕见疾病的患者。当前的计划侧重于解决 这些病例使用基于团队的方法来识别、解释和评估患者的基因变异。 这些不同的团队包括生物信息学家、医学遗传学家、遗传咨询师和医生 其他的，并包含广泛的专业知识、技能和计算机方法的识字能力。这个 评估基因变异在导致患者特定表型组中的作用的复杂性需要 团队所有成员的专业知识和独特知识，以及有效的沟通方法 支持对所有可能感兴趣的观察数据进行快速、异步分析。目前，团队成员 根据自己的专业知识执行分析，并依靠电子邮件通信和定期面对面交流 召开会议，整合团队的知识。这个过程非常耗时，效率也很低，尤其是 当审查以前未诊断的病例时，危急病例信息隐藏在无数电子邮件中 线程、演示文稿等。此建议结合了一个非常流行的工具，用于快速可视化分析 基因变异与商业数据管理解决方案一起提供工具集来支持基于团队的 基因组医学。我们的gene.iobio工具以一种简单易用的方式实时分析患者的基因组 基于Web的应用程序，确保所有团队成员可以高效地贡献他们在诊断方面的专业知识 进程。该工具将使用Critical功能进行扩展，并提高到商业标准 部署，以确保其能够以可靠和可重复的方式发挥其潜力。我们的马赛克工具 提供对分布式数据的HIPAA合规访问、基于角色的身份验证以及全面的 可视化和通信功能。该工具还将扩展功能，以支持 与gene.iobio的集成，以及旨在支持此社区的协作功能。通过改进 这两个工具的功能；提供分析版本控制；开发基于API的深度集成 并确保组合后的包是快速、可靠和强大的，我们将提供 目前市场上缺少的产品；它将改善案例协作，显著节省 所有团队成员的时间，并最终使用这些效率收益来确保基因组 医学可以扩大规模，以服务于更多不断进步的患者。我们将自行部署此程序包 快速NICU测序计划，以及UDN临床现场对产品进行评估和提炼。

Summary/Abstract Genomic sequencing is rapidly becoming a standard tool in diagnosing complex diagnostic cases, especially in critically ill newborns, and patients suffering from rare diseases. Current programs focused on addressing these cases utilise a team-based approach to identify, interpret and evaluate a patient’s genetic variants. These diverse teams include bioinformaticians, medical geneticists, genetic counselors, and physicians among others, and encompass a wide range of expertise, skills, and literacy with computational methods. The complexity of evaluating a genetic variant’s role in causing a patient’s specific set of phenotypes requires the expertise and unique knowledge of all members of the team, and efficient methods of communication to support rapid, asynchronous analysis of all potentially interesting observations. Currently, team members perform analyses based on their own expertise, and rely on email communication, and regular in-person meetings to integrate the knowledge of the team. This process is very time-intensive, and inefficient, especially when previously undiagnosed cases are reviewed, and critical case information is hidden in myriad email threads, presentations etc. This proposal brings together a highly popular tool for rapid visual analysis of genetic variants with a commercial data management solution to provide a tool set to support team-based genomic medicine. Our gene.iobio tool performs real-time analysis of a patient’s genome in an easy-to-use web-based application, ensuring all team members can efficiently contribute their expertise in the diagnostic process. This tool will be expanded with critica features, and brought up to a commercial standard of deployment to ensure it can deliver on its potential in a reliable and repeatable manner. Our Mosaic tool provides HIPAA-compliant access to distributed data, role-based authentication, as well as comprehensive visualization, and communication features. This tool will also be expanded with functionality to support integration with gene.iobio, as well as collaboration features designed to support this community. By improving the features of both of these tools; providing analysis versioning; developing a deep API based integration between them; and ensuring the combined package is fast, reliable and robust, we will deliver a software product that is currently absent in the market; one that will improve collaboration on cases, save significant amounts of time for all team members, and ultimately use these efficiency gains to ensure that genomic medicine can be scaled up to serve more patients moving forwards. We will deploy this package in our own rapid NICU sequencing program, and UDN clinical site to evaluate and refine the product.