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Open Access Highly Accessed Software

GenePING: secure, scalable management of personal genomic data

Ben Adida1* and Isaac S Kohane2

Author affiliations

1 CSAIL, MIT, Cambridge, MA, USA

2 Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA

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Citation and License

BMC Genomics 2006, 7:93  doi:10.1186/1471-2164-7-93

Published: 26 April 2006

Abstract

Background

Patient genomic data are rapidly becoming part of clinical decision making. Within a few years, full genome expression profiling and genotyping will be affordable enough to perform on every individual. The management of such sizeable, yet fine-grained, data in compliance with privacy laws and best practices presents significant security and scalability challenges.

Results

We present the design and implementation of GenePING, an extension to the PING personal health record system that supports secure storage of large, genome-sized datasets, as well as efficient sharing and retrieval of individual datapoints (e.g. SNPs, rare mutations, gene expression levels). Even with full access to the raw GenePING storage, an attacker cannot discover any stored genomic datapoint on any single patient. Given a large-enough number of patient records, an attacker cannot discover which data corresponds to which patient, or even the size of a given patient's record. The computational overhead of GenePING's security features is a small constant, making the system usable, even in emergency care, on today's hardware.

Conclusion

GenePING is the first personal health record management system to support the efficient and secure storage and sharing of large genomic datasets. GenePING is available online at http://ping.chip.org/genepinghtml webcite, licensed under the LGPL.