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Secure top most significant genome variants search: iDASH 2017 competition

机译：确保最重要的重要基因组变异搜索：iDASH 2017竞赛

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摘要

One of the 3 tracks of iDASH Privacy & Security Workshop 2017 competition was to execute a whole genome variants search on private genomic data. Particularly, the search application was to find the top most significant SNPs (Single-Nucleotide Polymorphisms) in a database of genome records labeled with control or case. In this paper we discuss the solution submitted by our team to this competition. Privacy and confidentiality of genome data had to be ensured using Intel SGX enclaves. The typical use-case of this application is the multi-party computation (each party possessing one or several genome records) of the SNPs which statistically differentiate control and case genome datasets. Our solution consists of two applications: (i) compress and encrypt genome files and (ii) perform genome processing (top most important SNPs search). We have opted for a horizontal treatment of genome records and heavily used parallel processing. Rust programming language was employed to develop both applications. Execution performance of the processing applications scales well and very good performance metrics are obtained. Contest organizers selected it as the best submission amongst other received competition entries and our team was awarded the first prize on this track.
机译：iDASH Privacy＆Security Workshop 2017竞赛的3条路线之一是对私人基因组数据执行全基因组变异搜索。特别是，该搜索应用程序是在标记有对照或病例的基因组记录数据库中找到最重要的SNP（单核苷酸多态性）。在本文中，我们讨论了我们的团队为此次比赛提交的解决方案。必须使用英特尔SGX安全区确保基因组数据的隐私性和机密性。此应用程序的典型用例是对SNP进行多方计算（每一方拥有一个或多个基因组记录），从而从统计学上区分对照和案例基因组数据集。我们的解决方案包含两个应用程序：（i）压缩和加密基因组文件，以及（ii）执行基因组处理（最重要的SNP搜索）。我们选择了对基因组记录的水平处理和大量使用的并行处理。使用Rust编程语言来开发这两个应用程序。处理应用程序的执行性能可以很好地扩展，并且可以获得非常好的性能指标。竞赛组织者将其选为最受好评的竞赛作品，我们的团队获得了该赛道的第一名。

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