Precision medicine is an approach to healthcare that tailors medical treatment and interventions to the individual characteristics of each patient, such as their genetic makeup, environment, and lifestyle. This requires combining different data types such as clinical and genetic data. Progress has been slowed by challenges like distinct data formats, strict privacy and security requirements and insufficient technology.
A new study suggests a solution called PrecisionChain, a data sharing and analysis platform built on blockchain technology. This system can securely store, harmonize, share, integrate, and analyze both genetic and clinical data. It uses a unified data model, an efficient indexing system and an end-to-end analysis pipeline to make data more accessible and usable.
“PrecisionChain is an immutable and secure system based on blockchain,” says corresponding author Gamze Gürsoy, the Herbert Irving Assistant Professor of Biomedical Informatics at Columbia University and a core faculty member at the New York Genome Center. “It keeps an immutable log of everything that is done on the data, including sharing, querying, and analyzing. This makes it easy to both track and audit, which gives institutions more confidence to share data because they can ensure it remains private and secure, and they can benefit from any discoveries made using the data.”
PrecisionChain was introduced in a Nature Medicine study published on Sept. 3, titled A framework for sharing of clinical and genetic data for precision medicine applications.
Harmonizing data for individual treatment
Both clinical and genetic data are often stored in different formats, making it difficult to combine information from various sources. PrecisionChain, in addition to providing blockchain-based decentralization, immutability, and data integrity, solves this issue by integrating well-established systems like the OMOP Common Data Model and the Variant Call Format (VCF) to harmonize the data. This allows for complex searches that combine clinical and genetic data, enabling the creation of specific patient groups based on both their genes and medical history.
“One of the big hurdles for researchers is learning how to work with many different data formats and tools,” says lead author Ahmed Elhussein, a PhD student in the Columbia University Department of Biomedical Informatics. “With PrecisionChain, researchers only need to interact with one framework. We hope this reduces some of the technical barriers for conducting precision medicine research.”
By securing this data together in a single pipeline, PrecisionChain creates more opportunities to provide personalized care for patients globally.
“Precision medicine tailors treatment to the individual characteristics of each patient, which leads to more effective and targeted healthcare,” Gürsoy says. “In order to comprehensively understand the characteristic of each patient, we need to look at both their clinical and genetic information, since many complex diseases are influenced by both environmental and genetic components. For collaborating institutions, it is important to increase the sample size to find connections between genetics and health outcomes.”
Ensuring privacy while also enabling research
Though blockchain technology is still new, it has demonstrated to provide both security and immutability to the data. However, it also comes with a series of challenges, especially when it is used to store large-scale datasets. PrecisionChain overcomes these challenges by introducing innovations in data indexing and compression to protect sensitive patient data around the world. It ensures that the data is tightly controlled, cannot be tampered with, and tracks every action on the network, making it easy to see who accessed what. This not only safeguards privacy but also supports important research by providing a clear and reliable way to manage and monitor data, while enabling multi-modal data analysis.
“PrecisionChain is designed to be easy to use, regardless of a researcher’s familiarity with blockchain technology,” Gürsoy says. “It has a simple, user-friendly interface that lets researchers access the network, search for data, and run analyses. By simplifying the complex parts and providing interactive tools like Jupyter Notebooks, PrecisionChain makes it easy for researchers to leverage blockchain’s benefits in their studies.”
Additional information
All authors (from Columbia unless noted): Ahmed Elhussein, Ulugbek Baymuradov (New York Genome Center), NYGC ALS Consortium New York Genome Center), Noémie Elhadad, Karthik Natarajann, and Gamze Gürsoy
A framework for sharing of clinical and genetic data for precision medicine applications was published Sept. 3, 2024 by Nature Medicine.
This work has been supported by the NIH grants R00HG010909 and R35GM147004.
