Precision medicine and FPGA technology

Challenges and opportunities

Brian Hill, Jaclyn Smith, Gans Srinivasa, Mustafa (Kemal) Sonmez, Ashish Sirasao, Amit Gupta, Madhubanti Mukherjee

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

As genomic medicine becomes part of standard clinical care, Precision Medicine faces a daunting computational challenge in scaling up to support the genomic, image processing and analytics workloads required for millions of patients, especially in oncology clinics. Computational solutions based on heterogeneous hardware platforms like FPGAs have the potential to enable rollout of personalized care for large numbers of patients. We review several clinical use cases to shed light on how FPGA-based solutions can lead to large performance gains and tackle the computational bottlenecks in precision medicine. The biggest barrier to FPGA adoption is their accessibility and the steep learning curve for many bioinformatics and precision medicine codebase development groups. We describe new standard libraries and development environments that will facilitate FPGA-based development and show how they enable performance improvements with modest effort investment.

Original languageEnglish (US)
Title of host publication2017 IEEE 60th International Midwest Symposium on Circuits and Systems, MWSCAS 2017
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages655-658
Number of pages4
Volume2017-August
ISBN (Electronic)9781509063895
DOIs
StatePublished - Sep 27 2017
Event60th IEEE International Midwest Symposium on Circuits and Systems, MWSCAS 2017 - Boston, United States
Duration: Aug 6 2017Aug 9 2017

Other

Other60th IEEE International Midwest Symposium on Circuits and Systems, MWSCAS 2017
CountryUnited States
CityBoston
Period8/6/178/9/17

Fingerprint

Medicine
Field programmable gate arrays (FPGA)
Oncology
Bioinformatics
Image processing
Hardware

Keywords

  • FPGAs
  • Genomics
  • Precision Medicine

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Electrical and Electronic Engineering

Cite this

Hill, B., Smith, J., Srinivasa, G., Sonmez, M. K., Sirasao, A., Gupta, A., & Mukherjee, M. (2017). Precision medicine and FPGA technology: Challenges and opportunities. In 2017 IEEE 60th International Midwest Symposium on Circuits and Systems, MWSCAS 2017 (Vol. 2017-August, pp. 655-658). [8053008] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/MWSCAS.2017.8053008

Precision medicine and FPGA technology : Challenges and opportunities. / Hill, Brian; Smith, Jaclyn; Srinivasa, Gans; Sonmez, Mustafa (Kemal); Sirasao, Ashish; Gupta, Amit; Mukherjee, Madhubanti.

2017 IEEE 60th International Midwest Symposium on Circuits and Systems, MWSCAS 2017. Vol. 2017-August Institute of Electrical and Electronics Engineers Inc., 2017. p. 655-658 8053008.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hill, B, Smith, J, Srinivasa, G, Sonmez, MK, Sirasao, A, Gupta, A & Mukherjee, M 2017, Precision medicine and FPGA technology: Challenges and opportunities. in 2017 IEEE 60th International Midwest Symposium on Circuits and Systems, MWSCAS 2017. vol. 2017-August, 8053008, Institute of Electrical and Electronics Engineers Inc., pp. 655-658, 60th IEEE International Midwest Symposium on Circuits and Systems, MWSCAS 2017, Boston, United States, 8/6/17. https://doi.org/10.1109/MWSCAS.2017.8053008
Hill B, Smith J, Srinivasa G, Sonmez MK, Sirasao A, Gupta A et al. Precision medicine and FPGA technology: Challenges and opportunities. In 2017 IEEE 60th International Midwest Symposium on Circuits and Systems, MWSCAS 2017. Vol. 2017-August. Institute of Electrical and Electronics Engineers Inc. 2017. p. 655-658. 8053008 https://doi.org/10.1109/MWSCAS.2017.8053008
Hill, Brian ; Smith, Jaclyn ; Srinivasa, Gans ; Sonmez, Mustafa (Kemal) ; Sirasao, Ashish ; Gupta, Amit ; Mukherjee, Madhubanti. / Precision medicine and FPGA technology : Challenges and opportunities. 2017 IEEE 60th International Midwest Symposium on Circuits and Systems, MWSCAS 2017. Vol. 2017-August Institute of Electrical and Electronics Engineers Inc., 2017. pp. 655-658
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