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GPU-based real-time detection and analysis of biological targets using solid-state nanopores

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Abstract

The emergence of nanoscale devices has provided robust interfaces to biomolecules that faithfully transduce and define fundamental interactions of living systems. Measuring single-event behavior of important targets like DNA, and diseased cells has been achieved with a number of devices and systems. An important dimension to these systems, often discounted, is real-time computational decision-making from measured data. This paper describes an adaptive approach that can record single-molecule or single-cell events in real-time and automatically analyze patterns from the measured data. The automated analysis of measured data is done using a static threshold technique and two variations of a dynamic threshold technique: baseline-tracker and moving average filtering. Dynamic techniques for threshold detection enable noise suppression in the measured data and precise detection of patterns, but at the cost of more complex software as compared to static technique. To mitigate the computational overhead, a real-time system is implemented that uses advanced I/O techniques to minimize the execution stalls, thus enabling the system to process data significantly faster than the electrical measurement setup. Furthermore, the algorithms are implemented on programmable graphics processing units for parallel pattern detection. Our implementation provides five times faster data acquisition and pattern detection than the maximum sampling rate of the electrical measurement setup.

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Acknowledgments

This work is based upon projects supported by the National Science Foundation under Grants CNS-1119085, CNS-1119742, CNS-1016793, CNS-1016408, CCF-0746832 and ECCS-0845669. In addition, M. Mustafa Rafique is supported by a scholarship from the Fulbright Foreign Student Program, and W. Asghar was partially supported by a fellowship from the Consortium for Nanomaterials for Aerospace Commerce and Technology (CONTACT) program, Rice University, Houston, TX, USA.

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Authors and Affiliations

  1. Department of Computer Science, Virginia Tech, Blacksburg, VA, 24060, USA

    Abdul Hafeez, M. Mustafa Rafique & Ali R. Butt

  2. Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX, 76011, USA

    Waseem Asghar & Samir M. Iqbal

  3. Nanotechnology Research and Teaching Facility, University of Texas at Arlington, 500 S. Cooper Street, Room #217, Arlington, TX, 76019, USA

    Waseem Asghar & Samir M. Iqbal

  4. Joint Graduate Studies Committee of Bioengineering Program, University of Texas at Arlington and University of Texas Southwestern Medical Center at Dallas, Arlington, TX, 76010, USA

    Samir M. Iqbal

  5. Department of Bioengineering, University of Texas at Arlington and University of Texas Southwestern Medical Center at Dallas, Arlington, TX, 76010, USA

    Samir M. Iqbal

Authors
  1. Abdul Hafeez
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  2. Waseem Asghar
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  3. M. Mustafa Rafique
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  4. Samir M. Iqbal
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  5. Ali R. Butt
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Corresponding authors

Correspondence to Samir M. Iqbal or Ali R. Butt.

Additional information

A. Hafeez and W. Asghar contributed equally.

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Hafeez, A., Asghar, W., Rafique, M.M. et al. GPU-based real-time detection and analysis of biological targets using solid-state nanopores. Med Biol Eng Comput 50, 605–615 (2012). https://doi.org/10.1007/s11517-012-0893-9

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  • DOI: https://doi.org/10.1007/s11517-012-0893-9

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