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Is Sanger better than Next-Gen for Anything?

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  • #16
    Originally posted by relaswar View Post
    I agree with most of the posts above. Additionally, I would like to emphasise that the main 'off-putting' aspect of NGS is still data analysis: both cost-wise and time-wise. While with Sanger sequencing data, even a biology graduate could grasp it very quickly and churn out the results very quickly, NGS demands specialist knowledge and trained bioinformaticians to analysis the mountains of data (and loads of computing power!). This incurs good amount of cost and time. So, unless the issue of data analysis is solved, NGS would still have applicability for high throughput projects only. The other issue is lack of proper standardization for data analysis methods. There is a need to develop robust QC metrics for data comparison between platforms and between various software outputs. I hope a day will come when we run a sequencer overnight and capture and analyse the data next morning, ready for presentation in the afternoon. Or am I being very naive?
    But this really isn't the fault of NGS, but rather the scale of the problem you are addressing. When Sanger sequencing was done at scale to sequence ESTs, BACs, genomes etc., the same issues you lament were present.

    New entrants such as GnuBio have emphasized that their boxes will spit out interpretable results, not raw data. But if the questions you are asking are complex, then expecting instant results->intelligent presentation still won't be realistic.

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    • #17
      I wonder what technology can displace Sanger, and if that technology could open more markets. For instance, if Illumina or Oxford or GnuBio came up with a sequencer that matches Sanger spec-for-spec (in readlength, error profile, and throughput), but provide real-time answers and be portable - Would this be disruptive, or only incremental over Sanger's stranglehold on low-plex applications? Reading the comments above, there doesn't seem much urgency to find a better version of Sanger in the markets it serves.

      Alternately, is there a market for a portable amplicon sequencer (1 to 96 amplicons) with similar price and performance specs as Sanger? What other attributes does it need to have to be considered disruptive or groundbreaking?

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      • #18
        Originally posted by bios90 View Post
        Alternately, is there a market for a portable amplicon sequencer (1 to 96 amplicons) with similar price and performance specs as Sanger? What other attributes does it need to have to be considered disruptive or groundbreaking?
        The only thing I can forsee displacing traditional Sanger sequencers (e.g. ABI 3730) is a small scale instrument that any lab could buy for perhaps <$15,000 and run perhaps 1-12 samples at a time and yield similar results. Pretty much anyone can send a DNA sample to their institution's core facility or a commercial company and have sequence back within 24-48 hours for <$10. The only thing that could make that better would be if you could do it in your own lab so you could have the data within a few hours for the same or less cost.

        It's already very cheap, so getting even cheaper wouldn't make much difference. There is room for improvement in time, but not much room.

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        • #19
          I feel like doing some vapourware calculations. What would it take for a MinION to get there? Taking ball-park figures, I think they can sequence 500 nanopores at something like 1 base per second for 6 hours at a cost of ~$1000. Say you need 10 copies for a sanger-accurate sequence:

          500 pores / 10 = 50 "good-quality" bases per second * 6 hours ~= 1Mbp of good-quality sequence per run, so ~$1 per kbp at $1000 per run

          That sounds reasonable. Of course, the cost-per-run is always a killer.

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          • #20
            Originally posted by gringer View Post
            500 pores / 10 = 50 "good-quality" bases per second * 6 hours ~= 1Mbp of good-quality sequence per run, so ~$1 per kbp at $1000 per run
            Updating this with genlyai's numbers. There are two significant differences from my original estimate:
            • high-quality sequencing speed (10bp/s vs 1bp/s)
            • run time (20h vs 6h)

            400 pores * 0.01 kbp/s = 4 kbp/s ~= 0.4 "good-quality" kbp/s
            0.4 kbp/s * 20h = 28800 kbp of good-quality sequence per run
            $1000 / 28800 kbp = $0.034 per kbp at $1000 per run

            ... which is quite a lot less.

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            • #21
              Hijacking the thread for a second. I have been researching diagnostic assays where single amplicon or low-plex sequencing will be useful, it seems a slim chance; PCR and RT-PCR seem to dominate the molecular diagnostics market.

              Are there specific, high value diagnostics areas that can only be addressed by sequening? My argument would be Sanger could be very useful in such applications (I couldn't identify many, want to put it out there to see if others might know more sequencing diagnostic assays)
              Last edited by bios90; 01-13-2014, 08:29 PM.

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