Desktop Sequencing Using A Single-Use Cartridge-Based Consumable That Includes Target Enrichment, Amplification and Sequencing. T. Raz1, A. Gulamali1, F. Zhuang1, H. Ghandour1, J. Sram2, J. Healy1, J. Downer1, M. Griesbach1, N. Nerkizian1, P. Mary1, S. Haserlat1, V. Chellappa1, J. Boyce1 1) GnuBIO Inc., Cambridge, MA; 2) City of Hope, Duarte, CA.

   Several major challenges have impeded the widespread application of targeted sequencing assays in the clinical setting. Foremost among these challenges are the high cost and complexity of sample preparation for the next generation sequencing platforms. Current technologies for target enrichment require between two to four days of preparation before samples are ready for the sequencing run. Furthermore, in order for current solutions to approach cost effectiveness, many samples need to be batched in a single run, adding to the complexity, increased likelihood of error and increased turnaround time. The GnuBIO unique desktop sequencer uses a single-use cartridge-based consumable that incorporates all of the preparation steps that are typically performed separately including target enrichment, amplification and sequencing. This drastically simplifies clinical workflows and reduces the operator hands-on time to less than 5 minutes, an unprecedented total. Biochemical reactions take place in a cascading manner, with individual reactions contained inside minute emulsion droplets, which flow through microfluidic channels where they are injected with assay reagents, incubated at the required temperatures, and finally detected for sequencing. Each droplet results in a single DNA sequence read, with reads up to 1000nt long. GnuBIO is collaborating with the City of Hope to develop an oncology targeted gene panel for detection of actionable mutations on the GnuBIO platform. The system is designed to achieve the following: Starting material: genomic DNA from FFPE samples or other types of samples. Total run time of less than 4 hours Sample preparation requires only genomic DNA extraction (no DNA library preparation, enrichment or amplification required). Robust detection of low frequency alterations (~1%-5%). High accuracy - with average per base accuracy of 99.999% Ease of integration with existing analytic and sample tracking workflows Low per sample cost - $200 per sample Low instrument cost - $50,000 In addition, the cartridge consumable is a closed system, and can be readily adapted to new panels. The cartridge is a dry consumable, containing all reagents needed to run a single DNA sample, reducing the risk of contamination and error.

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