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

Research output: Contribution to journalJournal articleResearchpeer-review

Documents

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

Background: 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. Basic Procedures: 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. Main Findings: 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. Principal Conclusions: We show the benchmarking results of novel blockchain-based methods for institutions to share patient outcomes related to gene-drug interactions. Our findings support blockchain utilization in healthcare, genomic and biomedical applications. The source code is publicly available at https://github.com/tsungtingkuo/genedrug.

Original languageEnglish
Article number104559
JournalInternational Journal of Medical Informatics
Volume154
Number of pages8
ISSN1386-5056
DOIs
Publication statusPublished - 2021

Bibliographical note

Publisher Copyright:
© 2021

    Research areas

  • Blockchain Distributed Ledger Technology, Data Sharing, Gene-Drug Interaction, Pharmacogenetics, Smart Contract

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