PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension.
Ontology highlight
ABSTRACT:
SUBMITTER: Chen F
PROVIDER: S-EPMC5547453 | biostudies-other | 2017 Jul
REPOSITORIES: biostudies-other
Similar Datasets
Project description:MotivationWe introduce PRINCESS, a privacy-preserving international collaboration framework for analyzing rare disease genetic data that are distributed across different continents. PRINCESS leverages Software Guard Extensions (SGX) and hardware for trustworthy computation. Unlike a traditional international collaboration model, where individual-level patient DNA are physically centralized at a single site, PRINCESS performs a secure and distributed computation over encrypted data, fulfilling institutional policies and regulations for protected health information.ResultsTo demonstrate PRINCESS' performance and feasibility, we conducted a family-based allelic association study for Kawasaki Disease, with data hosted in three different continents. The experimental results show that PRINCESS provides secure and accurate analyses much faster than alternative solutions, such as homomorphic encryption and garbled circuits (over 40 000× faster).Availability and implementationhttps://github.com/achenfengb/PRINCESS_opensource.Contactshw070@ucsd.edu.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC5860394 | biostudies-literature
Project description:Differential privacy allows quantifying privacy loss resulting from accession of sensitive personal data. Repeated accesses to underlying data incur increasing loss. Releasing data as privacy-preserving synthetic data would avoid this limitation but would leave open the problem of designing what kind of synthetic data. We propose formulating the problem of private data release through probabilistic modeling. This approach transforms the problem of designing the synthetic data into choosing a model for the data, allowing also the inclusion of prior knowledge, which improves the quality of the synthetic data. We demonstrate empirically, in an epidemiological study, that statistical discoveries can be reliably reproduced from the synthetic data. We expect the method to have broad use in creating high-quality anonymized data twins of key datasets for research.
| S-EPMC8276015 | biostudies-literature
Project description:Anonymous transmission is an interesting and crucial issue in computer communication area, which plays a supplementary role to data privacy. In this paper, we put forward a privacy preserving quantum anonymous transmission protocol based on entanglement relay, which constructs anonymous entanglement from EPR pairs instead of multi-particle entangled state, e.g. GHZ state. Our protocol achieves both sender anonymity and receiver anonymity against an active adversary and tolerates any number of corrupt participants. Meanwhile, our protocol obtains an improvement in efficiency compared to quantum schemes in previous literature.
| S-EPMC4887793 | biostudies-other
Project description:PurposeThe implementation of genomic-based medicine is hindered by unresolved questions regarding data privacy and delivery of interpreted results to health-care practitioners. We used DNA-based prediction of HIV-related outcomes as a model to explore critical issues in clinical genomics.MethodsWe genotyped 4,149 markers in HIV-positive individuals. Variants allowed for prediction of 17 traits relevant to HIV medical care, inference of patient ancestry, and imputation of human leukocyte antigen (HLA) types. Genetic data were processed under a privacy-preserving framework using homomorphic encryption, and clinical reports describing potentially actionable results were delivered to health-care providers.ResultsA total of 230 patients were included in the study. We demonstrated the feasibility of encrypting a large number of genetic markers, inferring patient ancestry, computing monogenic and polygenic trait risks, and reporting results under privacy-preserving conditions. The average execution time of a multimarker test on encrypted data was 865 ms on a standard computer. The proportion of tests returning potentially actionable genetic results ranged from 0 to 54%.ConclusionsThe model of implementation presented herein informs on strategies to deliver genomic test results for clinical care. Data encryption to ensure privacy helps to build patient trust, a key requirement on the road to genomic-based medicine.Genet Med 18 8, 814-822.
| S-EPMC4985613 | biostudies-literature
Project description:MotivationGenome-wide association studies (GWAS) benefit from the increasing availability of genomic data and cross-institution collaborations. However, sharing data across institutional boundaries jeopardizes medical data confidentiality and patient privacy. While modern cryptographic techniques provide formal secure guarantees, the substantial communication and computational overheads hinder the practical application of large-scale collaborative GWAS.ResultsThis work introduces an efficient framework for conducting collaborative GWAS on distributed datasets, maintaining data privacy without compromising the accuracy of the results. We propose a novel two-step strategy aimed at reducing communication and computational overheads, and we employ iterative and sampling techniques to ensure accurate results. We instantiate our approach using logistic regression, a commonly used statistical method for identifying associations between genetic markers and the phenotype of interest. We evaluate our proposed methods using two real genomic datasets and demonstrate their robustness in the presence of between-study heterogeneity and skewed phenotype distributions using a variety of experimental settings. The empirical results show the efficiency and applicability of the proposed method and the promise for its application for large-scale collaborative GWAS.Availability and implementationThe source code and data are available at https://github.com/amioamo/TDS.
| S-EPMC10612407 | biostudies-literature
Project description:Clinical trials capture high-quality data for millions of patients each year, yet these data are largely unavailable for research beyond the scope of any individual trial due to a combination of regulatory, intellectual property, and patient privacy barriers. Synthetic clinical trial data that captures the analytical properties of the source data, could provide significant value for research and drug development by making insights widely available while protecting the privacy of the participants. We present a method “Simulants” for generating research-grade synthetic clinical trial data from a real data source. We compared the fidelity and privacy preservation performance of Simulants to the state-of-the-art deep learning synthesizers and found that Simulants had superior performance when applied to clinical trial data as assessed both by established metrics and when considering critical clinical features. We also demonstrate how Simulants’ privacy settings may be configured to conform to specific privacy policies governing data sharing.
| S-EPMC10148292 | biostudies-literature
Project description:Process mining has been successfully applied in the healthcare domain and has helped touncover various insights for improving healthcare processes. While the benefits of process miningare widely acknowledged, many people rightfully have concerns about irresponsible uses of personaldata. Healthcare information systems contain highly sensitive information and healthcare regulationsoften require protection of data privacy. The need to comply with strict privacy requirements mayresult in a decreased data utility for analysis. Until recently, data privacy issues did not get muchattention in the process mining community; however, several privacy-preserving data transformationtechniques have been proposed in the data mining community. Many similarities between datamining and process mining exist, but there are key differences that make privacy-preserving datamining techniques unsuitable to anonymise process data (without adaptations). In this article, weanalyse data privacy and utility requirements for healthcare process data and assess the suitabilityof privacy-preserving data transformation methods to anonymise healthcare data. We demonstratehow some of these anonymisation methods affect various process mining results using three publiclyavailable healthcare event logs. We describe a framework for privacy-preserving process mining thatcan support healthcare process mining analyses. We also advocate the recording of privacy metadatato capture information about privacy-preserving transformations performed on an event log.
| S-EPMC7084661 | biostudies-literature
Project description:ObjectiveRecord linkage to integrate uncoordinated databases is critical in biomedical research using Big Data. Balancing privacy protection against the need for high quality record linkage requires a human-machine hybrid system to safely manage uncertainty in the ever changing streams of chaotic Big Data.MethodsIn the computer science literature, private record linkage is the most published area. It investigates how to apply a known linkage function safely when linking two tables. However, in practice, the linkage function is rarely known. Thus, there are many data linkage centers whose main role is to be the trusted third party to determine the linkage function manually and link data for research via a master population list for a designated region. Recently, a more flexible computerized third-party linkage platform, Secure Decoupled Linkage (SDLink), has been proposed based on: (1) decoupling data via encryption, (2) obfuscation via chaffing (adding fake data) and universe manipulation; and (3) minimum information disclosure via recoding.ResultsWe synthesize this literature to formalize a new framework for privacy preserving interactive record linkage (PPIRL) with tractable privacy and utility properties and then analyze the literature using this framework.ConclusionsHuman-based third-party linkage centers for privacy preserving record linkage are the accepted norm internationally. We find that a computer-based third-party platform that can precisely control the information disclosed at the micro level and allow frequent human interaction during the linkage process, is an effective human-machine hybrid system that significantly improves on the linkage center model both in terms of privacy and utility.
| S-EPMC3932473 | biostudies-literature
Project description:Introduction:Available and practical methods for privacy preserving linkage have shortcomings: methods utilising anonymous linkage codes provide limited accuracy while methods based on Bloom filters have proven vulnerable to frequency-based attacks. Objectives:In this paper, we present and evaluate a novel protocol that aims to meld both the accuracy of the Bloom filter method with the privacy achievable through the anonymous linkage code methodology. Methods:The protocol involves creating multiple match-keys for each record, with the composition of each match-key depending on attributes of the underlying datasets being compared. The protocol was evaluated through de-duplication of four administrative datasets and two synthetic datasets; the 'answers' outlining which records belonged to the same individual were known for each dataset. The results were compared against results achieved with un-encoded linkage and other privacy preserving techniques on the same datasets. Results:The multiple match-key protocol presented here achieved high quality across all datasets, performing better than record-level Bloom filters and the SLK, but worse than field-level Bloom filters. Conclusion:The presented method provides high linkage quality while avoiding the frequency based attacks that have been demonstrated against the Bloom filter approach. The method appears promising for real world use.
| S-EPMC7482515 | biostudies-literature
Project description:BackgroundSearching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the database and uses them in a closed network. However, a serious dilemma arises when the database holder also wants to output no information except for the search results, and such a dilemma prevents the use of many important data resources.ResultsIn order to overcome this dilemma, we developed a novel cryptographic protocol that enables database searching while keeping both the query holder's privacy and database holder's privacy. Generally, the application of cryptographic techniques to practical problems is difficult because versatile techniques are computationally expensive while computationally inexpensive techniques can perform only trivial computation tasks. In this study, our protocol is successfully built only from an additive-homomorphic cryptosystem, which allows only addition performed on encrypted values but is computationally efficient compared with versatile techniques such as general purpose multi-party computation. In an experiment searching ChEMBL, which consists of more than 1,200,000 compounds, the proposed method was 36,900 times faster in CPU time and 12,000 times as efficient in communication size compared with general purpose multi-party computation.ConclusionWe proposed a novel privacy-preserving protocol for searching chemical compound databases. The proposed method, easily scaling for large-scale databases, may help to accelerate drug discovery research by making full use of unused but valuable data that includes sensitive information.
| S-EPMC4704467 | biostudies-literature