Anonymization of electronic medical records for validating genome-wide association studies.
Genome-wide association studies (GWAS) facilitate the discovery of genotype-phenotype relations from population-based sequence databases, which is an integral facet of personalized medicine. The increasing adoption of electronic medical records allows large amounts of patients' standardized clinical features to be combined with the genomic sequences of these patients and shared to support validation of GWAS findings and to enable novel discoveries. However, disseminating these data "as is" may lead to patient reidentification when genomic sequences are linked to resources that contain the corresponding patients' identity information based on standardized clinical features. This work proposes an approach that provably prevents this type of data linkage and furnishes a result that helps support GWAS. Our approach automatically extracts potentially linkable clinical features and modifies them in a way that they can no longer be used to link a genomic sequence to a small number of patients, while preserving the associations between genomic sequences and specific sets of clinical features corresponding to GWAS-related diseases. Extensive experiments with real patient data derived from the Vanderbilt's University Medical Center verify that our approach generates data that eliminate the threat of individual reidentification, while supporting GWAS validation and clinical case analysis tasks.
Loukides
Grigorios
G
Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA. grigorios.loukides@vanderbilt.edu
Gkoulalas-Divanis
Aris
A
Malin
Bradley
B
D000465:Algorithms; D035041:Anonymous Testing / Q000379:methods*; D003625:Data Collection / Q000379:methods*; D057286:Electronic Health Records; D030661:Genetic Privacy; D055106:Genome-Wide Association Study / Q000379:methods*; D057285:Precision Medicine / Q000379:methods*
Nat Rev Drug Discov. 2006 Jan;5(1):23-6
16374513
Nat Genet. 2007 Oct;39(10):1181-6
17898773
Science. 2007 Jun 1;316(5829):1341-5
17463248
Methods Inf Med. 2006;45(3):267-74
16685334
Nature. 2008 Dec 11;456(7223):728-31
19079049
Clin Pharmacol Ther. 2008 Sep;84(3):362-9
18500243
J Clin Invest. 2008 May;118(5):1590-605
18451988
J Am Med Inform Assoc. 2010 May-Jun;17(3):322-7
20442151
Fed Regist. 2002 Aug 14;67(157):53181-273
12180470
PLoS Genet. 2008 Aug 29;4(8):e1000167
18769715