HIIT Kumpula Seminar: Secure genome sequence search based on homomorphic encryption

Speaker: Prof. Kana Shimizu

Affiliation: Department of computer science and engineering, Faculty of science and engineering, Waseda University, Japan

Short bio: Dr. Kana Shimizu is an associate professor of Waseda university. After receiving Dr.Eng. in computer science from Waseda University in 2006, she joined the National Institute of Advanced Industrial Science and Technology (AIST). She also worked at the Memorial Sloan-Kettering Cancer Center in 2013-2015 as Visiting Investigator. In April 2016, she started her lab at Waseda University. Her research interest mainly centers on algorithms for biological sequence analyses. Her recent interest also includes privacy-preserving datamining for biological/biomedical data analyses. URL: http://iskana.github.io/web/index.html

Title: Secure genome sequence search based on homomorphic encryption.

Abstract: The state-of-the-art DNA sequencer generates 160 Giga bases per day, which is hundreds of thousands times as large amount of data as the technology of 15 years ago can generate. The huge cost down in DNA sequencing has encouraged large-scale personal genome sequencing, which eventually spotlighted privacy issues in genomics. In our work, we assumed the frequent case such that the user wish to query the server while hiding the contents of the query, and developed a novel algorithm that enables searching on DNA sequences without leaking user’s query to the server. The proposed algorithm combines a searchable string data structure such as (positional) Burrows-Wheeler Transform and a cryptographic technique called oblivious transfer, and allows variable length substring match. In an experiment using the dataset created from 1000 Genome project, our algorithm was order of magnitude efficient both in run time and data transfer overhead compared to the base line exhaustive method.