Precision medicine has the potential to provide more accurate diagnosis, appropriate treatment and timely prevention strategies by considering patients’ biological makeup. However, this cannot be realized without integrating clinical and omics data in a data-sharing framework that achieves large sample sizes. Systems that integrate clinical and genetic data from multiple sources are scarce due to their distinct data types, interoperability, security and data ownership issues. Here we present a secure framework that allows immutable storage, querying and analysis of clinical and genetic data using blockchain technology. Our platform allows clinical and genetic data to be harmonized by combining them under a unified framework. It supports combined genotype–phenotype queries and analysis, gives institutions control of their data and provides immutable user access logs, improving transparency into how and when health information is used. We demonstrate the value of our framework for precision medicine by creating genotype–phenotype cohorts and examining relationships within them. We show that combining data across institutions using our secure platform increases statistical power for rare disease analysis. By offering an integrated, secure and decentralized framework, we aim to enhance reproducibility and encourage broader participation from communities and patients in data sharing.

通过考虑患者的生物构成，精准医疗有可能提供更准确的诊断、适当的治疗和及时的预防策略。然而，如果不将临床和组学数据整合到实现大样本量的数据共享框架中，就无法实现这一点。由于数据类型、互操作性、安全性和数据所有权问题，集成来自多个来源的临床和遗传数据的系统非常稀缺。在这里，我们提出了一个安全的框架，允许使用区块链技术对临床和遗传数据进行不可变存储、查询和分析。我们的平台通过将临床和遗传数据组合在一个统一的框架下来协调它们。它支持基因型-表型组合查询和分析，使机构能够控制其数据，并提供不可变的用户访问日志，从而提高健康信息使用方式和时间的透明度。我们通过创建基因型-表型队列并检查其中的关系来展示我们的精准医学框架的价值。我们表明，使用我们的安全平台组合跨机构的数据可以提高罕见病分析的统计能力。通过提供集成、安全和去中心化的框架，我们的目标是提高可重复性并鼓励社区和患者更广泛地参与数据共享。