Sequencing a Genome by a Torrent of Ions: How an Old pH-Meter Got Its Groove Back

By Muhammad A. Alam

Electrical and Computer Engineering, Purdue University, West Lafayette, IN

Published on

Abstract

The ability to read the book of life, written in the genome of an organism, has been one of the most exciting development of our time. The first version of human genome was announced circa 2000 and it took a decade of industrial-scale collaboration and billions of dollars of funding. Today, we do the same for a few hundred dollars, and in a few hours time. In merely 10 years, the reactors that covered a football field has been reduced to the size of a postage-stamp. I will explain how a synthesis of electronics and biotechnology, especially the use of electronic biosensor made of i-phone scale transistors, has made this fantastic development possible.

Bio

Muhammad Asharaf Alam Professor Alam teaches Electrical Engineering at Purdue University, where his research focuses on the physics, simulation, characterization and technology of classical and novel semiconductor devices. From 1995 to 2001, he was with Bell Laboratories, Mrray Hill, NJ, as a Member of Technical Staff in the Silicon ULSI Research Department. From 2001 to 2003, he was a Distinguished Member of Technical Staff at Agere Systems, Murray Hill, NJ. He joined Purdue University in 2004. Dr. Alam has published over 200 papers in international journals and has presented many invited and contributed talks at international conferences. He is a fellow of IEEE, American Physical Society, and American Association for the Advancement of Science, and recipient of 2006 IEEE Kiyo Tomiyasu Award for contributions to device technology for communication systems.

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References

Cite this work

Researchers should cite this work as follows:

  • Muhammad A. Alam (2014), "Sequencing a Genome by a Torrent of Ions: How an Old pH-Meter Got Its Groove Back," https://nanohub.org/resources/20553.

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Time

Location

Physics, Room 203, Purdue University, West Lafayette, IN

Tags

Sequencing a Genome by a Torrent of Ions: How an Old pH-Meter Got Its Groove Back
  • Sequencing a Genome by a Torrent of Ions How a old pH-meter got its groove back Muhammad A. Alam alam@purdue.edu 1. Sequencing a Genome by a Torre… 0
    00:00/00:00
  • Grand Challenges of Engineering 2. Grand Challenges of Engineerin… 219.31931931931933
    00:00/00:00
  • Convergence of Disciplines 3. Convergence of Disciplines 282.11544878211544
    00:00/00:00
  • Back-story: A Century-long Convergence 4. Back-story: A Century-long Con… 452.61928595261929
    00:00/00:00
  • Outline 5. Outline 749.81648314981646
    00:00/00:00
  • The book of life written in the Genome 6. The book of life written in th… 761.1945278611945
    00:00/00:00
  • Lab on a chip: pH-based genome sequencer 7. Lab on a chip: pH-based genome… 928.89556222889564
    00:00/00:00
  • Conventional Sequence-by-Synthesis 8. Conventional Sequence-by-Synth… 1054.220887554221
    00:00/00:00
  • DNA Synthesis releases Proton 9. DNA Synthesis releases Proton 1371.237904571238
    00:00/00:00
  • ISFET: Theory of pH-sensing 10. ISFET: Theory of pH-sensing 1439.1725058391726
    00:00/00:00
  • Sequencing by Synthesis 11. Sequencing by Synthesis 1744.0774107440775
    00:00/00:00
  • pH-based Genome Sequencers 12. pH-based Genome Sequencers 1869.9032365699034
    00:00/00:00
  • Modeling Approaches (Go, JAP, 2013) 13. Modeling Approaches (Go, JAP, … 1989.155822489156
    00:00/00:00
  • Model Validation 14. Model Validation 2064.2642642642645
    00:00/00:00
  • Outline 15. Outline 2153.0530530530532
    00:00/00:00
  • Idealized Polymerase Chain Reaction (PCR) 16. Idealized Polymerase Chain Rea… 2180.3136469803139
    00:00/00:00
  • How PCR Doubles DNA Count 17. How PCR Doubles DNA Count 2265.4654654654655
    00:00/00:00
  • Emulsion PCR and Poisson Statistics 18. Emulsion PCR and Poisson Stati… 2377.610944277611
    00:00/00:00
  • Multiply Loaded Beads must be avoided 19. Multiply Loaded Beads must be … 2543.3433433433433
    00:00/00:00
  • How to avoid multiple loading 20. How to avoid multiple loading 2562.5625625625626
    00:00/00:00
  • Loading with Reference Wells 21. Loading with Reference Wells 2647.4140807474141
    00:00/00:00
  • Recall: Sequencing by synthesis 22. Recall: Sequencing by synthesi… 2726.7600934267602
    00:00/00:00
  • Homo-polymer Error (~3% for N=5) 23. Homo-polymer Error (~3% for N=… 2816.4831498164831
    00:00/00:00
  • Scaling challenges of Sequencing Chips 24. Scaling challenges of Sequenci… 2873.2065398732066
    00:00/00:00
  • Properties of Signal and Noise Scaling 25. Properties of Signal and Noise… 2918.0180180180182
    00:00/00:00
  • Putting together the pieces Computer is the bottleneck! 26. Putting together the pieces Co… 2985.051718385052
    00:00/00:00
  • Droplet PCR: Multifunctional Transistor 27. Droplet PCR: Multifunctional T… 3144.1107774441107
    00:00/00:00
  • Promise of nanobiotechnology 28. Promise of nanobiotechnology 3215.5822489155826
    00:00/00:00
  • Implanted Sensors: Heart 29. Implanted Sensors: Heart 3265.3653653653655
    00:00/00:00
  • Sensing and actuation: Optogenetics 30. Sensing and actuation: Optogen… 3303.5702369035703
    00:00/00:00
  • Conclusions 31. Conclusions 3385.2852852852852
    00:00/00:00