BMC Genomics BioMed Central Software GenePING: secure, scalable management of personal genomic data Ben Adida*1 and Isaac S Kohane2 Open Access Address: 1CSAIL, MIT, Cambridge, MA, USA and 2Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA Email: Ben Adida* - ben@mit.edu; Isaac S Kohane - isaac_kohane@hms.harvard.edu * Corresponding author Published: 26 April 2006 BMC Genomics 2006, 7:93 doi:10.1186/1471-2164-7-93 This article is available from: http://www.biomedcentral.com/1471-2164/7/93 Received: 27 January 2006 Accepted: 26 April 2006 © 2006 Adida and Kohane; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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, licensed under the LGPL. Background Genomic data for clinical decision making Genomic data are becoming a routine component of clin- ical diagnosis and treatment. Prospective parents with familial or ethnic history of genetic disease have long been encouraged to undergo genetic counseling, including gen- otyping for disease alleles such as Tay-Sachs and Cystic Fibrosis [1,2]. Recent research [3], demonstrating that sev- eral treatment responses are conditional on genomic pro- file, promises to usher in the long-awaited era of personalized medicine, all based on the patient's gene sequence or gene expression signature. Clinically pertinent genomic data extends far beyond the patient's somatic genome sequence. Advanced cancer treatment options include genetic testing of cancer cells for specific markers, e.g. estrogen receptors in breast can- cer or the Philadelphia chromosome in CML [4]. This type of diagnostic will likely expand into full genomic profil- ing of cancer cells to help determine appropriate treat- ment [5]. In addition, much recent literature has uncovered correlations between gene expression patterns and clinical diagnosis [6,7]. While genome sequence data changes rarely, gene expression data varies across cell types and time. The cost of both diagnostic tests is falling rapidly with high-throughput techniques [8]. It is likely Page 1 of 10 (page number not for citation purposes)