SHF: Medium: Custom Computing for Genome Sequencing

Genomics has the potential to revolutionize precision health by enabling the early detection of cancer through simple blood tests, treating rare genetic diseases, identifying infectious pathogens, and more. Adoption of genome sequencing in clinical practice is critically dependent on our computational ability to analyze large volumes of data – significantly larger than data processed today in modern data-centers. But unfortunately, due to the impending end of Moore’s law, growth in general-purpose processor performance has stagnated, and therefore commodity systems are unlikely to meet the growing computational needs in genomics. To address this need, this project is developing custom hardware accelerators that are co-designed and integrated with bioinformatics sequencing software to enable pervasive use of genome sequencing. Software and hardware artifacts and benchmarks from this project can directly impact genomics practitioners, as well as spur systems research in this area. This project also supports a broad range of educational and outreach activities. The project has three specific aims. One, design domain-specific dynamic programming and in-memory accelerators for whole genome sequencing (WGS). Instead of kernel-specific accelerators, they will support a wide range of genomics kernels, including emerging long-read sequencing and pangenomics. Two, develop point-of-care pathogen detectors using Oxford Nanopore Technologies' (ONT) long-read real-time sequencers. The project will develop custom hardware solutions to analyze sequenced raw data (squiggles) in real-time to leverage ONT sequencer’s read-until feature and produce actionable diagnostics results at point-of-care. Three, real-time sequencing for intra-operative liquid and tissue biopsy that can produce results in minutes to hours, as opposed to today where it takes days to weeks. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.