Realizing privacy preserving genome-wide association studies

Bioinformatics
Sean Simmons, Bonnie Berger

Abstract

As genomics moves into the clinic, there has been much interest in using this medical data for research. At the same time the use of such data raises many privacy concerns. These circumstances have led to the development of various methods to perform genome-wide association studies (GWAS) on patient records while ensuring privacy. In particular, there has been growing interest in applying differentially private techniques to this challenge. Unfortunately, up until now all methods for finding high scoring SNPs in a differentially private manner have had major drawbacks in terms of either accuracy or computational efficiency. Here we overcome these limitations with a substantially modified version of the neighbor distance method for performing differentially private GWAS, and thus are able to produce a more viable mechanism. Specifically, we use input perturbation and an adaptive boundary method to overcome accuracy issues. We also design and implement a convex analysis based algorithm to calculate the neighbor distance for each SNP in constant time, overcoming the major computational bottleneck in the neighbor distance method. It is our hope that methods such as ours will pave the way for more widespread use of patient data in b...Continue Reading

References

Sep 7, 2007·The New England Journal of Medicine·Robert M PlengePeter K Gregersen
Nov 19, 2008·Proceedings of the National Academy of Sciences of the United States of America·Shannon C WielandBonnie Berger
Jul 2, 2009·Journal of the American Medical Informatics Association : JAMIA·Griffin M WeberIsaac S Kohane
Feb 18, 2010·JAMA : the Journal of the American Medical Association·Thomas Lumley, Kenneth Rice
Oct 11, 2011·Journal of the American Medical Informatics Association : JAMIA·Shawn N MurphyIsaac Kohane
Apr 19, 2012·Journal of the American Medical Informatics Association : JAMIA·Staal A VinterboAziz A Boxwala
Dec 18, 2012·Journal of the American Medical Informatics Association : JAMIA·Cynthia Dwork, Rebecca Pottenger
Feb 11, 2014·Journal of Biomedical Informatics·Fei YuCaroline Uhler
May 9, 2014·Nature Reviews. Genetics·Yaniv Erlich, Arvind Narayanan
Dec 19, 2014·BMC Medical Informatics and Decision Making·Xiaoqian JiangHaixu Tang
Aug 1, 2013·KDD : Proceedings·Aaron Johnson, Vitaly Shmatikov

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Citations

Jul 28, 2016·Cell Systems·Sean SimmonsBonnie Berger
May 8, 2018·Nature Biotechnology·Hyunghoon ChoBonnie Berger
Jul 14, 2018·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jean Louis RaisaroJean-Pierre Hubaux
Feb 8, 2018·Biology Direct·Antti HonkelaSamuel Kaski
Feb 14, 2019·Briefings in Bioinformatics·Abukari Mohammed Yakubu, Yi-Ping Phoebe Chen
Aug 8, 2018·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·C-A Azencott
Dec 24, 2018·BMC Bioinformatics·Charlotte BonteFrederik Vercauteren
May 7, 2019·Annual Review of Biomedical Data Science·April Moreno ArellanoLucila Ohno-Machado
Jul 1, 2020·Nature Genetics·Luca BonomiLucila Ohno-Machado
Nov 10, 2017·Briefings in Bioinformatics·Md Momin Al AzizNoman Mohammed
Aug 2, 2021·Journal of the American Medical Informatics Association : JAMIA·Joseph FicekEllen Daley

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