title: Privacy-preserving microbiome analysis using secure computation.
abstract: Developing targeted therapeutics and identifying biomarkers relies on large amounts of research participant data. Beyond human DNA, scientists now investigate the DNA of micro-organisms inhabiting the human body. Recent work shows that an individual's collection of microbial DNA consistently identifies that person and could be used to link a real-world identity to a sensitive attribute in a research dataset. Unfortunately, the current suite of DNA-specific privacy-preserving analysis tools does not meet the requirements for microbiome sequencing studies.
  
  
  
  To address privacy concerns around microbiome sequencing, we implement metagenomic analyses using secure computation. Our implementation allows comparative analysis over combined data without revealing the feature counts for any individual sample. We focus on three analyses and perform an evaluation on datasets currently used by the microbiome research community. We use our implementation to simulate sharing data between four policy-domains. Additionally, we describe an application of our implementation for patients to combine data that allows drug developers to query against and compensate patients for the analysis.
  
  
  
  The software is freely available for download at: http://cbcb.umd.edu/∼hcorrada/projects/secureseq.html
  
  
  
  Supplementary data are available at Bioinformatics online.
  
  
  
  hcorrada@umiacs.umd.edu.
authors.affiliation: Center for Bioinformatics and Computational Biologyand.
authors.forename: Justin
authors.initials: J
authors.lastname: Wagner
authors.affiliation: Center for Bioinformatics and Computational Biologyand.
authors.forename: Joseph N
authors.initials: JN
authors.lastname: Paulson
authors.affiliation: Maryland Cybersecurity Center, Department of Computer Science, University of Maryland, College Park, MD USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Wang
authors.affiliation: Maryland Cybersecurity Center, Department of Computer Science, University of Maryland, College Park, MD USA.
authors.forename: Bobby
authors.initials: B
authors.lastname: Bhattacharjee
authors.affiliation: Center for Bioinformatics and Computational Biologyand.
authors.forename: Héctor
authors.initials: H
authors.lastname: Corrada Bravo
mesh_terms: D004247:DNA; D006801:Humans; D056186:Metagenomics; D064307:Microbiota; D018907:Privacy; D012984:Software
chemical_list: D004247:DNA