Secure top most significant genome variants search: iDASH 2017 competition.
Secure top most significant genome variants search: iDASH 2017 competition.
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DOI：
10.1186/s12920-018-0399-x
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发表时间：
2018-10-11
影响因子：
2.7
通讯作者：
Tortech T
中科院分区：
文献类型：
--
作者：
Carpov S;Tortech T
iDASH隐私与安全研讨会2017竞赛的三个项目之一是在私人基因组数据上执行全基因组变异搜索。特别是，搜索应用程序是在标记为对照或病例的基因组记录数据库中找到最显著的snp（单核苷酸多态性）。在本文中，我们讨论了我们团队提交的解决方案。基因组数据的隐私和机密性必须使用英特尔SGX飞地来确保。该应用程序的典型用例是多方计算（每一方拥有一个或多个基因组记录）的snp，这些snp在统计上区分对照和病例基因组数据集。我们的解决方案包括两个应用程序：(i)压缩和加密基因组文件和（ii）执行基因组处理（最重要的snp搜索）。我们选择了基因组记录的水平处理和大量使用的并行处理。采用Rust编程语言对两个应用程序进行开发。处理应用程序的执行性能可很好地扩展，并获得了非常好的性能指标。比赛组织者从其他收到的参赛作品中选择了它作为最佳提交，我们的团队在这条赛道上获得了一等奖。
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.
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DOI：
10.1136/amiajnl-2013-002059
发表时间：
2014-03
期刊：
Journal of the American Medical Informatics Association : JAMIA
影响因子：
--
作者：
LeDuc R;Vaughn M;Fonner JM;Sullivan M;Williams JG;Blood PD;Taylor J;Barnett W
通讯作者：
Barnett W
影响因子：
56.9
作者：
Gymrek, Melissa;McGuire, Amy L.;Erlich, Yaniv
通讯作者：
Erlich, Yaniv
影响因子：
9.8
作者：
Stephens ZD;Lee SY;Faghri F;Campbell RH;Zhai C;Efron MJ;Iyer R;Schatz MC;Sinha S;Robinson GE
通讯作者：
Robinson GE
影响因子：
2.7
作者：
Chen F;Wang C;Dai W;Jiang X;Mohammed N;Al Aziz MM;Sadat MN;Sahinalp C;Lauter K;Wang S
通讯作者：
Wang S
影响因子：
5.8
作者：
Chen, Feng;Wang, Shuang;Ohno-Machado, Lucila
通讯作者：
Ohno-Machado, Lucila