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DOE OSTI · 1831161

Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track

Kuo, Tsung-Ting·Bath, Tyler·Ma, Shuaicheng·Pattengale, Nicholas·Yang, Meng·Cao, Yang·Hudson, Corey M.·Kim, Jihoon·Post, Kai·Xiong, Li·Ohno-Machado, Lucila
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Abstract

Blockchain distributed ledger technology is just starting to be adopted in genomics and healthcare applications. Despite its increased prevalence in biomedical research applications, skepticism regarding the practicality of blockchain technology for real-world problems is still strong and there are few implementations beyond proof-of-concept. We focus on benchmarking blockchain strategies applied to distributed methods for sharing records of gene-drug interactions. We expect this type of sharing will expedite personalized medicine. We generated gene-drug interaction test datasets using the Clinical Pharmacogenetics Implementation Consortium (CPIC) resource. We developed three blockchain-based methods to share patient records on gene-drug interactions: Query Index, Index Everything, and Dual-Scenario Indexing. We achieved a runtime of about 60 s for importing 4,000 gene-drug interaction records from four sites, and about 0.5 s for a data retrieval query. Our results demonstrated that it is feasible to leverage blockchain as a new platform to share data among institutions.

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60 APPLIED LIFE SCIENCESBlockchain Distributed Ledger TechnologyData SharingGene-Drug InteractionPharmacogeneticsSmart Contract

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Kuo, Tsung-Ting, Bath, Tyler, Ma, Shuaicheng, Pattengale, Nicholas, Yang, Meng, Cao, Yang, Hudson, Corey M., Kim, Jihoon, Post, Kai, Xiong, Li, Ohno-Machado, Lucila. 2021-08-18. Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track. https://doi.org/10.1016/j.ijmedinf.2021.104559

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