Abstract 5278: NGS-SWIFT: A cloud-based variant analysis framework using control-accessed sequencing data from dbGaP/SRA

Abstract

Abstract Genetic variation analysis plays an important role in elucidating the causes of various human diseases. The drastically reduced costs of genome sequencing driven by next generation sequence technologies now make it possible to analyze genetic variations with hundreds or thousands of samples simultaneously, but with the cost of ever increasing local storage requirements. The tera- and peta-byte scale footprint for sequence data imposes significant technical challenges for data management and analysis, including the tasks of collection, storage, transfer, sharing, and privacy protection. Currently, each analysis group must download all the relevant sequence data into a local file system before variation analysis is initiated. This heavy-weight transaction not only slows down the pace of the analysis, but also creates financial burdens for researchers due to the cost of hardware and time required to transfer the data over typical academic internet connections. To overcome such limitations and explore the feasibility of analyzing control-accessed sequencing data in cloud environment while maintaining data privacy and security, here we introduce a cloud-based analysis framework that facilitates variation analysis using direct access to the NCBI Sequence Read Archive through NCBI SRA Toolkit, which allows the users to programmatically access data housed within SRA with encryption and decryption capabilities and converts it from the SRA format to the desired format for data analysis. A customized machine image (ngs-swift) with preconfigured tools, including NCBI SRA Toolkit and NGS Software Development Kit, and resources essential for variant analysis has been created for instantiating an EC2 instance or instance cluster on Amazon cloud. Performance of this framework has been evaluated using dbGaP study phs000710.v1.p1 (1000Genome Dataset in dbGaP, http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id = phs000710.v1.p1), and compared with that from traditional analysis pipeline, and security handling in cloud environment when dealing with control-accessed sequence data has been addressed. We demonstrate that with this framework, it is cost effective to make variant calls without first transferring the entire set of aligned sequence data into a local storage environment, thereby accelerating variant discovery using control-accessed sequencing data. Citation Format: Chunlin Xiao, Eugene Yaschenko, Stephen Sherry. NGS-SWIFT: A cloud-based variant analysis framework using control-accessed sequencing data from dbGaP/SRA. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5278.