The advancement of molecular profiling techniques
fuels biomedical research with a deluge of data. To facilitate
data sharing, the Global Alliance for Genomics and Health
established the Beacon system, a search engine designed to help
researchers find datasets of interest. While the current Beacon
system only supports genomic data, other types of biomedical
data, such as DNA methylation, are also essential for advancing
our understanding in the field. In this paper, we propose the first
Beacon system for DNA methylation data sharing: MBeacon. As
the current genomic Beacon is vulnerable to privacy attacks, such
as membership inference, and DNA methylation data is highly
sensitive, we take a privacy-by-design approach to construct
MBeacon.
First, we demonstrate the privacy threat, by proposing a
membership inference attack tailored specifically to unprotected
methylation Beacons. Our experimental results show that 100
queries are sufficient to achieve a successful attack with AUC
(area under the ROC curve) above 0.9. To remedy this situation,
we propose a novel differential privacy mechanism, namely SVT2
,
which is the core component of MBeacon. Extensive experiments
over multiple datasets show that SVT2
can successfully mitigate
membership privacy risks without significantly harming utility.
We further implement a fully functional prototype of MBeacon
which we make available to the research community
History
Preferred Citation
Inken Hagestedt, Yang Zhang, Mathias Humbert, Pascal Berrang, Tang Haixu, Wang XiaoFeng and Michael Backes. MBeacon: Privacy-Preserving Beacons for DNA Methylation Data. In: Network and Distributed System Security Symposium (NDSS). 2019.
Primary Research Area
Trustworthy Information Processing
Name of Conference
Network and Distributed System Security Symposium (NDSS)
Legacy Posted Date
2019-01-11
Open Access Type
Unknown
BibTeX
@inproceedings{cispa_all_2753,
title = "MBeacon: Privacy-Preserving Beacons for DNA Methylation Data",
author = "Hagestedt, Inken and Zhang, Yang and Humbert, Mathias and Berrang, Pascal and Haixu, Tang and XiaoFeng, Wang and Backes, Michael",
booktitle="{Network and Distributed System Security Symposium (NDSS)}",
year="2019",
}