Secure top most significant genome variants search: iDASH 2017 competition

Federated Analysis for Privacy-Preserving Data Sharing: A Technical and Legal Primer

Continued advances in precision medicine rely on the widespread sharing of data that relate human genetic variation to disease. However, data sharing is severely limited by legal, regulatory, and ethical restrictions that safeguard patient privacy. Federated analysis addresses this problem by transferring the code to the data-providing the technical and legal capability to analyze the data within their secure home environment rather than transferring the data to another institution for analysis. This allows researchers to gain new insights from data that cannot be moved, while respecting patient privacy and the data stewards' legal obligations. Because federated analysis is a technical solution to the legal challenges inherent in data sharing, the technology and policy implications must be evaluated together. Here, we summarize the technical approaches to federated analysis and provide a legal analysis of their policy implications.

The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition

Concerns regarding inappropriate leakage of sensitive personal information as well as unauthorized data use are increasing with the growth of genomic data repositories. Therefore, privacy and security of genomic data have become increasingly important and need to be studied. With many proposed protection techniques, their applicability in support of biomedical research should be well understood. For this purpose, we have organized a community effort in the past 8 years through the integrating data for analysis, anonymization and sharing consortium to address this practical challenge. In this article, we summarize our experience from these competitions, report lessons learned from the events in 2020/2021 as examples, and discuss potential future research directions in this emerging field.

Functional genomics data: privacy risk assessment and technological mitigation

The generation of functional genomics data by next-generation sequencing has increased greatly in the past decade. Broad sharing of these data is essential for research advancement but poses notable privacy challenges, some of which are analogous to those that occur when sharing genetic variant data. However, there are also unique privacy challenges that arise from cryptic information leakage during the processing and summarization of functional genomics data from raw reads to derived quantities, such as gene expression values. Here, we review these challenges and present potential solutions for mitigating privacy risks while allowing broad data dissemination and analysis.

HySec-Flow: Privacy-Preserving Genomic Computing with SGX-based Big-Data Analytics Framework

Trusted execution environments (TEE) such as Intel's Software Guard Extension (SGX) have been widely studied to boost security and privacy protection for the computation of sensitive data such as human genomics. However, a performance hurdle is often generated by SGX, especially from the small enclave memory. In this paper, we propose a new Hybrid Secured Flow framework (called "HySec-Flow") for large-scale genomic data analysis using SGX platforms. Here, the data-intensive computing tasks can be partitioned into independent subtasks to be deployed into distinct secured and non-secured containers, therefore allowing for parallel execution while alleviating the limited size of Page Cache (EPC) memory in each enclave. We illustrate our contributions using a workflow supporting indexing, alignment, dispatching, and merging the execution of SGX- enabled containers. We provide details regarding the architecture of the trusted and untrusted components and the underlying Scorn and Graphene support as generic shielding execution frameworks to port legacy code. We thoroughly evaluate the performance of our privacy-preserving reads mapping algorithm using real human genome sequencing data. The results demonstrate that the performance is enhanced by partitioning the time-consuming genomic computation into subtasks compared to the conventional execution of the data-intensive reads mapping algorithm in an enclave. The proposed HySec-Flow framework is made available as an open-source and adapted to the data-parallel computation of other large-scale genomic tasks requiring security and scalable computational resources.

Privacy-preserving semi-parallel logistic regression training with fully homomorphic encryption

Background

Privacy-preserving computations on genomic data, and more generally on medical data, is a critical path technology for innovative, life-saving research to positively and equally impact the global population. It enables medical research algorithms to be securely deployed in the cloud because operations on encrypted genomic databases are conducted without revealing any individual genomes. Methods for secure computation have shown significant performance improvements over the last several years. However, it is still challenging to apply them on large biomedical datasets.

Methods

The HE Track of iDash 2018 competition focused on solving an important problem in practical machine learning scenarios, where a data analyst that has trained a regression model (both linear and logistic) with a certain set of features, attempts to find all features in an encrypted database that will improve the quality of the model. Our solution is based on the hybrid framework Chimera that allows for switching between different families of fully homomorphic schemes, namely TFHE and HEAAN.

Results

Our solution is one of the finalist of Track 2 of iDash 2018 competition. Among the submitted solutions, ours is the only bootstrapped approach that can be applied for different sets of parameters without re-encrypting the genomic database, making it practical for real-world applications.

Conclusions

This is the first step towards the more general feature selection problem across large encrypted databases.