Embedded Computers for Next-Generation DNA Sequencing

In 2014 a handheld DNA measurement device, the “MinION”, was commercialized. It is 100X smaller by volume and 6X faster and 20X less expensive than the next smallest DNA measurement device on the market. But its measurements are of a lower quality, about 90% of measured DNA is accurately ‘detected’ compared to 99.9% for leading machines. Further, a tremendous amount of computing power is needed to carry out the detection function of the MinION. In fact, this is done by a standalone computer or GPU. This greatly compromises the portability and inherent advantage of the MinION and technologies of the like. We propose to address this problem by creating an embedded bioinformatics computing engine that can ultimately be embedded inside a portable DNA measurement device like (but not exclusively) the MinION. The engine will be a custom complementary-medal-oxide-semiconductor (CMOS) chip that includes an embedded processor (the open-source RISC-V ISA and associated 5-stage multiple-issue in-order pipelined architecture) and on-chip hardware acceleration for executing key detection and data analysis functions associated with DNA sequencing. We anticipate a device that will reduce energy consumption by 10,000X relative to CPU-only solutions.

Faculty Supervisor:

Sebastian Magierowski

Student:

Karim Hammad

Partner:

CMC Microsystems And Applied Nanotools

Discipline:

Engineering - computer / electrical

Sector:

Professional, scientific and technical services

University:

York University