Gigagen, Inc. — Department of Health and Human Services SBIR Phase II: NHGRI

Description

<p>DESCRIPTION provided by applicant The Specific Aim of this Phase II SBIR grant application is to launch ClonoByteandquot a website and cloud based platform for the processing storage analysis comparison and visualization of immune signature data sets generated by deep sequencing of immune repertoires There is a rapidly growing demand for T cell receptor TCR and immunoglobulin Ig repertoire sequencing as a routine clinical and research practice but the lack of computational resources and tools is blocking widespread adoption There is thus a strong additional need for resources to translate immune repertoire data generated by NGS into a format useful to immunology researchers and clinicians The innovation of our product is to enable researchers with little or no bioinformatics expertise or resources to analyze and interpret immune repertoire sequencing data using a cloud based platform In Phase I we first built individual computational algorithms and components for processing analysis and visualization of immune repertoire data particularly i primary processing of sequencing data for V J gene identification and complementarity determining region CDR extraction ii calculation of sample oligoclonality and sample sample similarity iii visualization of comparisons of multiple data sets and iv statistical significnce testing of findings via a Monte Carlo method We tested the computational modules with actual immune repertoire data generated in house for internal research and for external customers We then integrated several of the key components into the alpha version of ClonoByteandquot In Phase II we will take the following steps to launch ClonoByteandquot i integrate remaining standalone computational modules into ClonoByteandquot for beta release ii perform software quality control QC and quality assurance QA and front end usability testing on ClonoByteandquot beta and iii refine ClonoByteandquot beta to launch version We will be successful if the website can achieve the following in the hands of end users i securely upload raw immune repertoire sequencing FASTQ files for automated primary processing ii track abundance and expansion of clonotype sequences across multiple annotated data sets and iii compare data sets on the basis of whole repertoire similarity sample diversity and behavior of specific clonotypes After Phase II the website will be fully available for commercial use by immune repertoire researchers worldwide GigaGenandapos s pricing plan will be to offer free use of ClonoByteandquot for the first samples and then charge a $ year subscription fee for users that upload more than samples Though ClonoByteandquot will enable analysis of immune repertoire sequencing data generated by most amplification kits or third party services GigaGen will use ClonoByteandquot andapos s best in class features and ease of use to promote its own GigaMune R lab services and amplification kits for immune repertoire sequencing PUBLIC HEALTH RELEVANCE New DNA sequencing methods have the potential to revolutionize how we monitor a patientandapos s immune system during disease progression and treatment We are building web based data processing and analysis tools that allow clinicians and researchers to use DNA sequencing data to better understand the immune system</p>