1,015 Hits in 5.0 sec

A privacy-preserving solution for compressed storage and selective retrieval of genomic data

Zhicong Huang, Erman Ayday, Huang Lin, Raeka S. Aiyar, Adam Molyneaux, Zhenyu Xu, Jacques Fellay, Lars M. Steinmetz, Jean-Pierre Hubaux
2016 Genome Research  
Our method thus offers a space-saving, privacy-preserving, and effective solution for the storage of clinical genomic data.  ...  Here we present a privacy-preserving solution named SECRAM (Selective retrieval on Encrypted and Compressed Reference-oriented Alignment Map) for the secure storage of compressed aligned genomic data.  ...  We should emphasize that with SECRAM, one can query for a small region of data, while standard encryption approaches necessitate downloading the entire genome, making SECRAM more efficient as well as privacy-preserving  ... 
doi:10.1101/gr.206870.116 pmid:27789525 pmcid:PMC5131820 fatcat:nqld6eau5rd7djg565ps6vkryu

Privacy preserving processing of genomic data: A survey

Mete Akgün, A. Osman Bayrak, Bugra Ozer, M. Şamil Sağıroğlu
2015 Journal of Biomedical Informatics  
Additionally, we have also included open privacy problems coming with each genomic data processing procedure.  ...  However, a serious privacy challenge is confronted with increasing number of genetic tests as genomic data is the ultimate source of identity for humans.  ...  As a result, whole genome information can easily be covered by several iterative queries.  ... 
doi:10.1016/j.jbi.2015.05.022 pmid:26056074 fatcat:bzmkcb5xnnhtboowhusyeqgl6m

Accelerating Genomic Data Generation and Facilitating Genomic Data Access Using Decentralization, Privacy-Preserving Technologies and Equitable Compensation

Dennis Grishin, Kamal Obbad, Preston Estep, Kevin Quinn, Sarah Wait Zaranek, Alexander Wait Zaranek, Ward Vandewege, Tom Clegg, Nico César, Mirza Cifric, George Church
2018 Blockchain in Healthcare Today  
The intention is to preserve data privacy by enabling investigators to query the whole database and discover their data of interest, without compromising the privacy of the queried data.  ...  The CGF representation is also very space efficient (~30 megabytes/ genome), which facilitates file transfers, and enables fast queries and efficient analysis. 60 Figure 7 - 7 Simplified representation  ...  Conflict of Interest All authors are employees, advisors, or collaborators of Nebula Genomics. Funding Statement Development of the Nebula platform is funded by Nebula Foundation.  ... 
doi:10.30953/bhty.v1.34 fatcat:bgjyvrf54vglljkwskkl5dvwfu

A community effort to protect genomic data sharing, collaboration and outsourcing

Shuang Wang, Xiaoqian Jiang, Haixu Tang, Xiaofeng Wang, Diyue Bu, Knox Carey, Stephanie OM Dyke, Dov Fox, Chao Jiang, Kristin Lauter, Bradley Malin, Heidi Sofia (+4 others)
2017 npj Genomic Medicine  
, and scholars in ethical, legal, and social implications (ELSI) to assess the latest advances on privacy-preserving techniques for protecting human genomic data.  ...  The outcomes suggest that applying highly optimized privacy-preserving and secure computation techniques to safeguard genomic data sharing and analysis is useful.  ...  data analysis at the whole genome scale.  ... 
doi:10.1038/s41525-017-0036-1 pmid:29263842 pmcid:PMC5677972 fatcat:ews5hez3sndsfbas3ool3bl25a

PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension

Feng Chen, Chenghong Wang, Wenrui Dai, Xiaoqian Jiang, Noman Mohammed, Md Momin Al Aziz, Md Nazmus Sadat, Cenk Sahinalp, Kristin Lauter, Shuang Wang
2017 BMC Medical Genomics  
However, privacy and security concerns have emerged as a challenge for utilizing cloud computing to handle sensitive genomic data.  ...  Conclusions: The proposed PRESAGE provides an alternative solution for secure and efficient genomic data outsourcing in an untrusted cloud by using a hybrid framework that combines secure hardware and  ...  Genomic records in the VCF file is sparse, which only contains a few million variants in comparison to the whole genome with 3 billion base pairs.  ... 
doi:10.1186/s12920-017-0281-2 pmid:28786365 pmcid:PMC5547453 fatcat:qvfk5n5oijhjvn53m3ibhzcegu

Protecting Privacy and Security of Genomic Data in i2b2 With Homomorphic Encryption and Differential Privacy

Jean Louis Raisaro, Gwangbae Choi, Sylvain Pradervand, Raphael Colsenet, Nathalie Jacquemont, Nicolas Rosat, Vincent Mooser, Jean-Pierre Hubaux
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
In this paper, we address the challenge of designing and deploying in a real operational setting an efficient privacy-preserving explorer for genetic cohorts.  ...  Yet, when researchers need to access sensitive/identifying data, such as genomic data, in order to compile cohorts of well-characterized patients for specific studies, privacy and security concerns represent  ...  CONCLUSION In this paper, we have described how we designed, implemented and deployed, for the first time, a secure and efficient privacy-preserving solution for exploring genomic cohorts in a real operational  ... 
doi:10.1109/tcbb.2018.2854782 pmid:30004884 fatcat:d4lqtuzdbrhq5gsqkqzciqbyki

EPISODE: Efficient Privacy-PreservIng Similar Sequence Queries on Outsourced Genomic DatabasEs

Thomas Schneider, Oleksandr Tkachenko
2019 Proceedings of the 2019 ACM Asia Conference on Computer and Communications Security - Asia CCS '19  
CCS CONCEPTS • Security and privacyPrivacy-preserving protocols; Management and querying of encrypted data; Privacy protections; * A summary of preliminary results of this paper has been published as  ...  In addition, we show that our algorithm scales for practical database sizes by querying a database that contains up to a million short sequences within a few minutes, and a database with hundreds of whole-genome  ...  Whole-Genome Experiments.  ... 
doi:10.1145/3321705.3329800 dblp:conf/ccs/0003T19 fatcat:jgwib57iavdwvogwv3pa3u5mpa

Citizen-Centered, Auditable, and Privacy-Preserving Population Genomics [article]

Dennis Grishin, Jean Louis Raisaro, Juan Ramón Troncoso-Pastoriza, Kamal Obbad, Kevin Quinn, Mickaël Misbach, Jared Gollhardt, Joao Sa, Jacques Fellay, George M. Church, Jean-Pierre Hubaux
2019 bioRxiv   pre-print
Our work opens a path towards multi-functional, privacy-preserving genomic-data analysis.  ...  To enable a secure exploration of genomic datasets with controlled and transparent data access, we propose a novel approach that combines cryptographic privacy-preserving technologies, such as homomorphic  ...  The efficient, privacy-preserving, and auditable data-discovery functionality provided by the proposed platform can enable a number of common use cases for genomic data on millions of individuals with  ... 
doi:10.1101/799999 fatcat:hhwjh2t5ljh6zon5pd77eh6rhi

Privacy and Security in the Genomic Era

Erman Ayday, Jean-Pierre Hubaux
2016 Proceedings of the 2016 ACM SIGSAC Conference on Computer and Communications Security - CCS'16  
Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these  ...  The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy.  ...  In particular, differential privacy, a well-known technique for answering statistical queries in a privacy preserving manner [Dwork, 2006] , was recently adapted to compose privacy preserving query mechanisms  ... 
doi:10.1145/2976749.2976751 dblp:conf/ccs/AydayH16 fatcat:kpmg6s66ordppcl5blaqjv2blm

Privacy in the Genomic Era

Muhammad Naveed, Erman Ayday, Ellen W. Clayton, Jacques Fellay, Carl A. Gunter, Jean-Pierre Hubaux, Bradley A. Malin, Xiaofeng Wang
2015 ACM Computing Surveys  
Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these  ...  The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy.  ...  In particular, differential privacy, a well-known technique for answering statistical queries in a privacy-preserving manner [Dwork 2006 ], was recently adapted to compose privacy-preserving query mechanisms  ... 
doi:10.1145/2767007 pmid:26640318 pmcid:PMC4666540 fatcat:2s4nhu2d6vgrtiebdg5qeognbi

Identifying Disease-Causing Mutations with Privacy Protection

Mete Akgün, Ali Burak Ünal, Bekir Ergüner, Nico Pfeifer, Oliver Kohlbacher, Yann Ponty
2020 Bioinformatics  
Availability Supplementary information Supplementary data are available at Bioinformatics online.  ...  We present the first inheritance model (recessive, dominant, compound heterozygous) based privacy-preserving analyses of genomic data in order to find disease-causing mutations.  ...  Nurten Akarsu for providing us with the variant data of patients from the TMCO1 deficiency study.  ... 
doi:10.1093/bioinformatics/btaa641 pmid:32683440 pmcid:PMC7850099 fatcat:6u3meohq2rgaddnap64eat2l4q

Swarm: A federated cloud framework for large-scale variant analysis

Amir Bahmani, Kyle Ferriter, Vandhana Krishnan, Arash Alavi, Amir Alavi, Philip S. Tsao, Michael P. Snyder, Cuiping Pan, Mihaela Pertea
2021 PLoS Computational Biology  
We demonstrate its utility via common inquiries of genomic variants across BigQuery in the Google Cloud Platform (GCP), Athena in the Amazon Web Services (AWS), Apache Presto and MySQL.  ...  Compared to single-cloud platforms, the Swarm framework significantly reduced computational costs, run-time delays and risks of security breach and privacy violation.  ...  The main bottleneck of such computation-heavy privacy-preserving techniques is latency.  ... 
doi:10.1371/journal.pcbi.1008977 pmid:33979321 fatcat:s62adyyabffwzkoczg7j36mr4i

Inference Attacks against Kin Genomic Privacy

Erman Ayday, Mathias Humbert
2017 IEEE Security and Privacy  
Methods attackers use to infer genomic information, as well as recent proposals for enhancing genomic privacy, are discussed.  ...  Genomic data poses serious interdependent risks: your data might also leak information about your family members' data.  ...  However, differential privacy, a well-known technique for answering statistical queries in a privacy-preserving manner, 28 can be easily adapted to preserve kin genomic privacy at a lower cost for utility  ... 
doi:10.1109/msp.2017.3681052 fatcat:uz5tck3alzalbgmtrkfu4au3zm

Whole Genome Sequencing: Innovation Dream or Privacy Nightmare? [article]

Emiliano De Cristofaro
2015 arXiv   pre-print
Over the past several years, DNA sequencing has emerged as one of the driving forces in life-sciences, paving the way for affordable and accurate whole genome sequencing.  ...  Unfortunately, however, the proliferation of human genomes amplifies worrisome privacy concerns, since a genome represents a treasure trove of highly personal and sensitive information.  ...  In order for computational genetic tests on whole human genomes to become accepted and commonplace, efficient and (possibly) privacy-preserving versions of such tests need to be developed.  ... 
arXiv:1210.4820v6 fatcat:pgqu3uucjnf4poop4pkibt37yu

Systematizing Genome Privacy Research: A Privacy-Enhancing Technologies Perspective [article]

Alexandros Mittos and Bradley Malin and Emiliano De Cristofaro
2018 arXiv   pre-print
Rapid advances in human genomics are enabling researchers to gain a better understanding of the role of the genome in our health and well-being, stimulating hope for more effective and cost efficient healthcare  ...  However, this also prompts a number of security and privacy concerns stemming from the distinctive characteristics of genomic data.  ...  on "Enabling Progress in Genomic Research via Privacy-Preserving Data Sharing," and a grant from the National Institutes of Health (5RM1HG009034).  ... 
arXiv:1712.02193v2 fatcat:2pdqmdfv3nhfjbuyn3kwmudija
« Previous Showing results 1 — 15 out of 1,015 results