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A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side.

Sungjoon Park1, Minsu Kim2, Seokjun Seo3

  • 1Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea.

BMC Genomics
|April 11, 2019
PubMed
Summary

This study introduces a secure SNP panel scheme protecting both patient genome data and hospital panels using homomorphic encryption. The novel method ensures data privacy without compromising clinical SNP detection for targeted therapies.

Keywords:
Genomic privacyGenomic securityHomomorphic encryptionK-merSNP panel

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cryptography

Background:

  • Single Nucleotide Polymorphisms (SNPs) are vital for clinical applications like targeted cancer therapy.
  • Genome information exchange between patients and hospitals is increasing, raising privacy concerns.
  • Existing SNP panel schemes do not adequately protect both patient data and hospital panel information.

Purpose of the Study:

  • To propose a novel secure SNP panel scheme that protects both user genome data and hospital panel information.
  • To enable secure SNP detection for clinical use without revealing sensitive data to either party.

Main Methods:

  • Developed a secure SNP panel scheme utilizing homomorphically encrypted K-mers.
  • Implemented a computationally feasible equality test for encrypted K-mers, avoiding direct sequence alignment.
  • Introduced Point Deviation Tolerance (PDT) to manage population-level sequence variations and ensure accuracy.

Main Results:

  • Demonstrated a novel secure SNP panel scheme using homomorphic encryption and an equality test on encrypted K-mers.
  • Validated the scheme's effectiveness on the TCGA BRCA dataset, handling over 100,000 somatic mutations.
  • Provided guidelines for panel design, including K-mer size and SNP count, for practical implementation.

Conclusions:

  • The proposed method is the first to secure both user sequences and hospital panels via homomorphic encryption.
  • Feasibility demonstrated with simulated and real-world genomic data (TCGA BRCA).
  • Further development is needed to translate this scheme into clinical practice.