Wednesday, December 05, 2012

Progress in pH Imager-Based Genome Sequencing

Electrophoresis journal published "Progress in Ion Torrent semiconductor chip based sequencing" paper by Barry Merriman, Ion Torrent R&D Team, Jonathan M. Rothberg, where Ion Torrent team includes over 300 people. The paper represents the collective work of the Ion Torrent R&D Team over the past three years:

"In order for next-generation sequencing to become widely used as a diagnostic in the healthcare industry, sequencing instrumentation will need to be mass produced with a high degree of quality and economy. One way to achieve this is to recast DNA sequencing in a format that fully leverages the manufacturing base created for computer chips, complementary metal-oxide semiconductor chip fabrication, which is the current pinnacle of large scale, high quality, low-cost manufacturing of high technology. To achieve this, ideally the entire sensory apparatus of the sequencer would be embodied in a standard semiconductor chip, manufactured in the same fab facilities used for logic and memory chips. Recently, such a sequencing chip, and the associated sequencing platform, has been developed and commercialized by Ion Torrent, a division of Life Technologies, Inc. Here we provide an overview of this semiconductor chip based sequencing technology, and summarize the progress made since its commercial introduction. We described in detail the progress in chip scaling, sequencing throughput, read length, and accuracy. We also summarize the enhancements in the associated platform, including sample preparation, data processing, and engagement of the broader development community through open source and crowdsourcing initiatives."


The progress of pH sensors is quite similar to image sensors: the resolution has grown from 1.5MP to 165MP (!), while pixel pitch has shrunk from 5.1um to 1.68um leveraging process scaling from 0.35um to 0.11um. Everything looks familiar, except the price is much higher than that of image sensors, see the last comment to the previous post on Ion Torrent.

Thanks to VZ for the link!

5 comments:

  1. Why we need so small pixel pitch for pH sensing please ?

    -yang ni

    ReplyDelete
    Replies
    1. Why? To make more pH pixels on the same die, thus make genome analyzing process much faster and cheaper. They intend to hit the price target of $1000 per full genome, which is quite impressive, if achieved.

      Delete
  2. Thanks Vladimir ! But is it easy to fill the 1.6um micro pipe on the top of the pixel ?

    -yang ni

    ReplyDelete
    Replies
    1. I do not know if it's easy, but Ion Torrent's products prove that it's possible.

      Delete
  3. Surface can be made hydrophilic to facilitate the wetting.

    And the wells' aspect ratio isn't and can't be that severe. The wells just have to be deep enough to hold the emPCR beads, and during synthesis nucleotides needs to easily diffuse in and H+ ions need to diffuse out. Shouldn't think of these as "pipes", "divots" would be closer. Thus a bit of surface hydrophilicity will suck the water above in quite easily.

    ReplyDelete

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