Storing and analyzing a genome on a blockchain

Gamze Gürsoy; Charlotte M Brannon; Eric Ni; Sarah Wagner; Amol Khanna; Mark Gerstein

doi:10.1186/s13059-022-02699-7

Storing and analyzing a genome on a blockchain

Genome Biol. 2022 Jun 29;23(1):134. doi: 10.1186/s13059-022-02699-7.

Authors

Gamze Gürsoy^{1

2

3

4}, Charlotte M Brannon^{1

2

5}, Eric Ni^{1

2}, Sarah Wagner⁶, Amol Khanna^{7

8}, Mark Gerstein^{9

10

11}

Affiliations

¹ Program in Computational Biology and Bioinformatics, Yale University, Whitney Avenue, New Haven, CT, 06520, USA.
² Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue, New Haven, CT, 06520, USA.
³ Current Address: Department of Biomedical Informatics, Columbia University, New York, NY, USA.
⁴ Current Address: New York Genome Center, New York, NY, USA.
⁵ Current Address: Stanford University, Stanford, CA, USA.
⁶ Department of Computer Science, Yale University, Prospect Street, New Haven, CT, 06520, USA.
⁷ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
⁸ Department of Applied Mathematics, Johns Hopkins University, Baltimore, MD, USA.
⁹ Program in Computational Biology and Bioinformatics, Yale University, Whitney Avenue, New Haven, CT, 06520, USA. mark@gersteinlab.org.
¹⁰ Department of Molecular Biophysics and Biochemistry, Yale University, Whitney Avenue, New Haven, CT, 06520, USA. mark@gersteinlab.org.
¹¹ Department of Computer Science, Yale University, Prospect Street, New Haven, CT, 06520, USA. mark@gersteinlab.org.

Abstract

There are major efforts underway to make genome sequencing a routine part of clinical practice. A critical barrier to these is achieving practical solutions for data ownership and integrity. Blockchain provides solutions to these challenges in other realms, such as finance. However, its use in genomics is stymied due to the difficulty in storing large-scale data on-chain, slow transaction speeds, and limitations on querying. To overcome these roadblocks, we developed a private blockchain network to store genomic variants and reference-aligned reads on-chain. It uses nested database indexing with an accompanying tool suite to rapidly access and analyze the data.

Keywords: Blockchain; Blockchain database; Multichain; Personal genome.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Blockchain*
Genome
Genomics

Abstract

Publication types

MeSH terms

Grants and funding