A cloud-based system for scalable, privacy-preserving, and interactive immune repertoire analysis in vaccination and infection

PROJECT SUMMARY We propose to build a cloud based integrated solution for scalablecustomizableprivacy preservingand interactive antibody repertoire analysisImmune repertoire sequencingIR seqhas become a useful tool in both basic research and clinical settingsAs the heart of the adaptive immunity to infection and many vaccinesthe abundance and diversity composition of the B cell receptorBCRand its dynamic changes in health and diseases bear information of how to evaluate immune healthperform disease diagnosis and prognosisand measure vaccination effectHoweverthere is a computational bottleneck for large scale antibody lineage constructiona lack of decomposable pipeline modules that preserve privacy and ownershipand a missing gap for interactive linage analysis and visualizationIn this Phase I grantwe willbreak the bottlenecks of pipeline processing and scale up the core algorithms to handle large sequence data setsprotect private data and proprietary processing algorithms with modularized pipelineintegrated cloud local processingand data perturbation methodsdevelop end to end web services for pipeline composition and interactive analysis visualization in a cloud based deployment solutionExisting commercial efforts are mostly focusing on cancer related IR seq analysis aiming to trace the disappearing of cancer cells after therapywhich solely focus on cataloging sequence species and abundanceThis kind of analysis is much simpler and easiercompared to analyzing IR seq data in infection and vaccinationProviding insights on host immune responses is a much more challenging but much needed taskOnce the pipeline is builtit can be readily adapted to analyze cancer IR seq dataAlsoexisting algorithms and optimizations that have been developed for other big data analysis can be further developed and applied to the IR seq data analysisWe will use a publically available BCR repertoire data on an influenza vaccination cohort and a TCR repertoire data on an aging cohort to test the feasibility of the projectThe long term goal of this proposal is to build cloud based accessible and customizable services for experts as well as non specialistsWe aim to provide an integrated solution for the ingestionprocessinganalysisexploration and visualizationinterpretation and sharing of data generated by deep sequencing of full length antibody and TCR repertoireThe success of this Phase I SBIR will provide a solid foundation for the product launch of a commercial cloud based solution in Phase IIduring which we will continue our investigation on big data security and privacy to facilitate compliance with institutional policies and design and develop programmable APIs and tools to facilitate integrations with more third party modules and services PROJECT NARRATIVE Fueled by the exponential decline in sequencing costsnext generation sequencingNGSof the immune repertoire is increasingly being applied to gain insights into the adaptive immune response in healthy individuals and in those with a wide range of diseasessuch as autoimmune diseaseallergyHIV and cancerWe are building cloud based data processing and analysis tools with service oriented architecture that can easily integrate existing and future analysis components developed by us or other teams as well as data sources and services distributed over the web and the cloud