Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts

Abstract

Background: As pharmacogenomics data becomes increasingly integral to clinical treatment decisions, appropriate data storage and sharing protocols need to be adopted. One promising option for secure, high-integrity storage and sharing is Ethereum smart contracts. Ethereum is a blockchain platform, and smart contracts are immutable pieces of code running on virtual machines in this platform that can be invoked by a user or another contract (in the blockchain network). The 2019 iDASH (Integrating Data for Analysis, Anonymization, and Sharing) competition for Secure Genome Analysis challenged participants to develop time-and space-efficient Ethereum smart contracts for gene-drug relationship data. Methods: Here we design a specific smart contract to store and query gene-drug interactions in Ethereum using an index-based, multi-mapping approach. Our contract stores each pharmacogenomics observation, a gene-variant-drug triplet with outcome, in a mapping searchable by a unique identifier, allowing for time and space efficient storage and query. This solution ranked in the top three at the 2019 IDASH competition. We further improve our "challenge solution" and develop an alternate "fastQuery" smart contract, which combines together identical gene-variant-drug combinations into a single storage entry, leading to significantly better scalability and query efficiency. Results: On a private, proof-of-authority network, both our challenge and fastQuery solutions exhibit approximately linear memory and time usage for inserting into and querying small databases (<1,000 entries). For larger databases (1000 to 10,000 entries), fastQuery maintains this scaling. Furthermore, both solutions can query by a single field ("0-AND") or a combination of fields ("1-or 2-AND"). Specifically, the challenge solution can complete a 2-AND query from a small database (100 entries) in 35ms using 0.1 MB of memory. For the same query, fastQuery has a 2-fold improvement in time and a 10-fold improvement in memory. Conclusion: We show that pharmacogenomics data can be stored and queried efficiently using Ethereum blockchain. Our solutions could potentially be used to store a range of clinical data and extended to other fields requiring high-integrity data storage and efficient access.

Using Ethereum Smart Contracts to Store and Share COVID-19 Patient Data

“…The matching ID is taken to collect the value of the struct from the corresponding database mapping. The framework was adapted from Gürsoy et al [ 11 ].…”

“…Solutions utilizing blockchain technology, such as smart contracts, could prevent centralized point-of-failure scenarios, create an immutable database, and allow decentralization, ultimately mitigating the probability of data corruption. Indeed, blockchain technology is being conceptualized in other fields as well [11][12][17][18][19][20].…”

“…These characteristics allow for the platform and its smart contracts to be molded to other use cases that require robust integrity and amenability, such as holding patient data. For example, Ethereum blockchain has been shown to handle pharmacogenomics data comprising gene-variant-drug combinations, as well as neuroimaging data [11][12]. No studies, however, have so far investigated the implementation of Ethereum blockchain using COVID-19 patient data.…”

A Review of Smart Contracts Applications in Various Industries: A Procurement Perspective

“…Healthcare [8,29,53,76,82,109,110,125,131,157,176,177,183,190] Improve data transparency in clinical trials [29,157] Secure automated remote patient monitoring [53,82,177] Improve the security and privacy of electronic medical records [76,110,131] Protect patient privacy [82,125,176,183] Improve data sharing [109,176,183] Simplify procedures, reduce transaction costs, reduce administrative burdens, and remove intermediaries [8] Reduce query pharmacogenomics data time [190] ICT [28,30,38,42,45,46,54,58,59,63,67,70,71,74,75,77,78,<...>…”

Storing and analyzing a genome on a blockchain

“…MultiChain does not permit on-chain computation as Ethereum does, but it has several features that make it especially suitable for data storage use cases. Both the MultiChain platform and Ethereum Smart Contracts have been previously used in medical genomics applications, but in limited settings Pattengale and Hudson 2020;Ozdayi et al 2020;Ma et al 2020;Gursoy and Brannon et al 2020).…”