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Abstract The rapid improvements in genomic sequencing technology have led to the proliferation of locally collected genomic datasets. Given the sensitivity of genomic data, it is crucial to conduct collaborative studies while preserving the privacy of the individuals. However, before starting any collaborative research effort, the quality of the data needs to be assessed. One of the essential steps of the quality control process is population stratification: identifying the presence of genetic difference in individuals due to subpopulations. One of the common methods used to group genomes of individuals based on ancestry is principal component analysis (PCA). In this article, we propose a privacy-preserving framework which utilizes PCA to assign individuals to populations across multiple collaborators as part of the population stratification step. In our proposed client-server-based scheme, we initially let the server train a global PCA model on a publicly available genomic dataset which contains individuals from multiple populations. The global PCA model is later used to reduce the dimensionality of the local data by each collaborator (client). After adding noise to achieve local differential privacy (LDP), the collaborators send metadata (in the form of their local PCA outputs) about their research datasets to the server, which then aligns the local PCA results to identify the genetic differences among collaborators’ datasets. Our results on real genomic data show that the proposed framework can perform population stratification analysis with high accuracy while preserving the privacy of the research participants.
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Locally Differentially Private Protocols for Frequency Estimation
Protocols satisfying Local Differential Privacy (LDP) enable parties to collect aggregate information about a population while protecting each user’s privacy, without relying on a trusted third party. LDP protocols (such as Google’s RAPPOR) have been deployed in real-world scenarios. In these protocols, a user encodes his private information and perturbs the encoded value locally before sending it to an aggregator, who combines values that users contribute to infer statistics about the population. In this paper, we introduce a framework that generalizes several LDP protocols proposed in the literature. Our framework yields a simple and fast aggregation algorithm, whose accuracy can be precisely analyzed. Our in-depth analysis enables us to choose optimal parameters, resulting in two new protocols (i.e., Optimized Unary Encoding and Optimized Local Hashing) that provide better utility than protocols previously proposed. We present precise conditions for when each proposed protocol should be used, and perform experiments that demonstrate the advantage of our proposed protocols.
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- Award ID(s):
- 1640374
- PAR ID:
- 10026346
- Date Published:
- Journal Name:
- Proceedings of the 26th USENIX Security Symposium
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
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