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Register a new userPrivacy-Preserving and Efficient Verification of the Outcome in Genome-Wide Association Studies
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Added by
Anisa Halimi
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Providing provenance in scientific workflows is essential for reproducibility and auditability purposes. Workflow systems model and record provenance describing the steps performed to obtain the final results of a computation. In this work, we propose a framework that verifies the correctness of the statistical test results that are conducted by a researcher while protecting individuals privacy in the researchers dataset. The researcher publishes the workflow of the conducted study, its output, and associated metadata. They keep the research dataset private while providing, as part of the metadata, a partial noisy dataset (that achieves local differential privacy). To check the correctness of the workflow output, a verifier makes use of the workflow, its metadata, and results of another statistical study (using publicly available datasets) to distinguish between correct statistics and incorrect ones. We use case the proposed framework in the genome-wide association studies (GWAS), in which the goal is to identify highly associated point mutations (variants) with a given phenotype. For evaluation, we use real genomic data and show that the correctness of the workflow output can be verified with high accuracy even when the aggregate statistics of a small number of variants are provided. We also quantify the privacy leakage due to the provided workflow and its associated metadata in the GWAS use-case and show that the additional privacy risk due to the provided metadata does not increase the existing privacy risk due to sharing of the research results. Thus, our results show that the workflow output (i.e., research results) can be verified with high confidence in a privacy-preserving way. We believe that this work will be a valuable step towards providing provenance in a privacy-preserving way while providing guarantees to the users about the correctness of the results.
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In Genome-Wide Association Studies (GWAS) where multiple correlated traits have been measured on participants, a joint analysis strategy, whereby the traits are analyzed jointly, can improve statistical power over a single-trait analysis strategy. There are two questions of interest to be addressed when conducting a joint GWAS analysis with multiple traits. The first question examines whether a genetic loci is significantly associated with any of the traits being tested. The second question focuses on identifying the specific trait(s) that is associated with the genetic loci. Since existing methods primarily focus on the first question, this paper seeks to provide a complementary method that addresses the second question. We propose a novel method, Variational Inference for Multiple Correlated Outcomes (VIMCO), that focuses on identifying the specific trait that is associated with the genetic loci, when performing a joint GWAS analysis of multiple traits, while accounting for correlation among the multiple traits. We performed extensive numerical studies and also applied VIMCO to analyze two datasets. The numerical studies and real data analysis demonstrate that VIMCO improves statistical power over single-trait analysis strategies when the multiple traits are correlated and has comparable performance when the traits are not correlated.
Motivation: The rapid growth in genome-wide association studies (GWAS) in plants and animals has brought about the need for a central resource that facilitates i) performing GWAS, ii) accessing data and results of other GWAS, and iii) enabling all users regardless of their background to exploit the latest statistical techniques without having to manage complex software and computing resources. Results: We present easyGWAS, a web platform that provides methods, tools and dynamic visualizations to perform and analyze GWAS. In addition, easyGWAS makes it simple to reproduce results of others, validate findings, and access larger sample sizes through merging of public datasets. Availability: Detailed method and data descriptions as well as tutorials are available in the supplementary materials. easyGWAS is available at http://easygwas.tuebingen.mpg.de/. Contact: [email protected]
A trusted execution environment (TEE) such as Intel Software Guard Extension (SGX) runs a remote attestation to prove to a data owner the integrity of the initial state of an enclave, including the program to operate on her data. For this purpose, the data-processing program is supposed to be open to the owner, so its functionality can be evaluated before trust can be established. However, increasingly there are application scenarios in which the program itself needs to be protected. So its compliance with privacy policies as expected by the data owner should be verified without exposing its code. To this end, this paper presents CAT, a new model for TEE-based confidential attestation. Our model is inspired by Proof-Carrying Code, where a code generator produces proof together with the code and a code consumer verifies the proof against the code on its compliance with security policies. Given that the conventional solutions do not work well under the resource-limited and TCB-frugal TEE, we propose a new design that allows an untrusted out-enclave generator to analyze the source code of a program when compiling it into binary and a trusted in-enclave consumer efficiently verifies the correctness of the instrumentation and the presence of other protection before running the binary. Our design strategically moves most of the workload to the code generator, which is responsible for producing well-formatted and easy-to-check code, while keeping the consumer simple. Also, the whole consumer can be made public and verified through a conventional attestation. We implemented this model on Intel SGX and demonstrate that it introduces a very small part of TCB. We also thoroughly evaluated its performance on micro- and macro- benchmarks and real-world applications, showing that the new design only incurs a small overhead when enforcing several categories of security policies.
Federated learning has emerged as a promising approach for collaborative and privacy-preserving learning. Participants in a federated learning process cooperatively train a model by exchanging model parameters instead of the actual training data, which they might want to keep private. However, parameter interaction and the resulting model still might disclose information about the training data used. To address these privacy concerns, several approaches have been proposed based on differential privacy and secure multiparty computation (SMC), among others. They often result in large communication overhead and slow training time. In this paper, we propose HybridAlpha, an approach for privacy-preserving federated learning employing an SMC protocol based on functional encryption. This protocol is simple, efficient and resilient to participants dropping out. We evaluate our approach regarding the training time and data volume exchanged using a federated learning process to train a CNN on the MNIST data set. Evaluation against existing crypto-based SMC solutions shows that HybridAlpha can reduce the training time by 68% and data transfer volume by 92% on average while providing the same model performance and privacy guarantees as the existing solutions.
Combining data from several case-control genome-wide association (GWA) studies can yield greater efficiency for detecting associations of disease with single nucleotide polymorphisms (SNPs) than separate analyses of the component studies. We compared several procedures to combine GWA study data both in terms of the power to detect a disease-associated SNP while controlling the genome-wide significance level, and in terms of the detection probability ($mathit{DP}$). The $mathit{DP}$ is the probability that a particular disease-associated SNP will be among the $T$ most promising SNPs selected on the basis of low $p$-values. We studied both fixed effects and random effects models in which associations varied across studies. In settings of practical relevance, meta-analytic approaches that focus on a single degree of freedom had higher power and $mathit{DP}$ than global tests such as summing chi-square test-statistics across studies, Fishers combination of $p$-values, and forming a combined list of the best SNPs from within each study.
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