Talk:DNA sequencer
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Untitled
[edit]Okay, not only is this too technical, but it also really needs to be expanded. At least a brief explaination of the process would be nice. Nathanww 20:37, 11 February 2007 (UTC)
I agree. I have some sources that may have something that could be used. I'll start looking. jim.amen 11:34, 13 April 2007 (UTC)
I added a little paragraph but there is a large amount left out. I wonder if heavy linking to the DNA Sequencing description would be useful since you really need to understand one to understand the other. jim.amen 21:39, 19 April 2007 (UTC)
needs to tell how long sequencing takes
[edit]around 2000, sequencing human DNA took years and was a big deal. How long does it take now? Please omit qualifiers like the ones in the present article ("it still needs to go through process X") -- Dr. Tony Roberts, but I don't remember my login name or pw — Preceding unsigned comment added by 98.197.163.72 (talk • contribs) 00:52, 3 November 2010 (UTC)
Suggestions
[edit]This article as it stands needs a lot of work. There are now several different sequencing technologies available and this article seems to be written as if we were still in the age of capillary sequencing. I think it would be useful to include some of the following sections:
- History of sequencing machines - which would cover the various companies and machines that they released with some indications of their underlying technologie and capacities (could be expressed as a table).
- Growth of sequencing capacity - includes some discussion of the growth in DNA sequence data enabled by sequencing machines
- Technologies in development - It would be useful to point to some of the upcoming technologies that do not yet have production machines available.
Alexbateman (talk) 15:53, 25 January 2012 (UTC)
- The article on DNA sequencing looks much more developed and covers similar ground to my suggestions above. Should we consider merging this article into that one? Perhaps by adding a historical perspective on the development of sequencing machines to that article. Alexbateman (talk) 15:58, 25 January 2012 (UTC)
- The two are obviously related subjects, though to me it would make more sense to discuss the science and reasoning behind DNA sequencing itself at DNA sequencing and to leave this article open for discussion of the actual machines performing it. So, as in the table above, I'd place the first item in DNA sequencer and the other two in DNA sequencing. §everal⇒|Times 19:38, 5 September 2012 (UTC)
Comparison Table
[edit]I suggest updating the comparison table. I am drafting the update here. --Hdash (talk) 03:02, 16 October 2013 (UTC) Reference: http://www.hindawi.com/journals/bmri/2012/251364/ Data that is probably out of date is in bold. --Hdash (talk) 04:36, 16 October 2013 (UTC)
| Sequencer | Ion Torrent PGM [1][2][3] | 454 GS FLX [4] | HiSeq 2000 [4][3] | SOLiDv4 [4] | PacBio [5][3] | Sanger 3730xl [4] |
|---|---|---|---|---|---|---|
| Manufacturer | Life Technologies | Roche | Illumina | Applied Biosystems | Pacific Biosciences | Applied Biosystems |
| Sequencing Chemistry | Ion semiconductor sequencing | Pyrosequencing | Polymerase-based sequence-by-synthesis | Ligation-based sequencing | Phospholinked fluorescent nucleotides | Dideoxy chain termination |
| Amplification approach | Emulsion PCR | Emulsion PCR | Bridge amplification | Emulsion PCR | Single-molecule; no amplification | PCR |
| Data output per run | 100-200 Mb | 0.7 Gb | 600 Gb | 120 Gb | 100-500 Mb | 1.9∼84 Kb |
| Accuracy | 99% | 99.9% | 99.9% | 99.94% | 90% | 99.999% |
| Time per run | 2 hours | 24 hours | 3-10 days | 7-14 days | 2 hours | 20 minutes - 3 hours |
| Read length | 200-400 bp | 700 bp | 100x100 bp paired end | 50x50 bp paired end? | 1,500-5,000 bp (avg) | 400-900 bp |
| Cost per run | $350 USD | $7,000 USD | $6,000 USD (30x human genome) | $4,000 USD | $300 USD | $4 USD (single read/reaction) |
| Cost per Mb | $1.00 USD | $10 USD | $0.07 USD | $0.13 USD | $2.00 USD | $2400 USD |
| Cost per instrument | $80,000 USD | $500,000 USD | $690,000 USD | $495,000 USD | $695,000 USD | $95,000 USD |
- ^ Karow, J. (2010) Ion Torrent Systems Presents $50,000 Electronic Sequencer at AGBT. In Sequence.
- ^ Ion PGM - Ion Torrent
- ^ a b c Michael A Quail, Miriam Smith, Paul Coupland, Thomas D Otto, Simon R Harris, Thomas R Connor, Anna Bertoni, Harold P Swerdlow and Yong Gu (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics.
- ^ a b c d Lin Liu, Yinhu Li, Siliang Li, Ni Hu, Yimin He, Ray Pong, Danni Lin, Lihua Lu, and Maggie Law (2012) Comparison of Next-Generation Sequencing Systems. Journal of Biomedicine and Biotechnology.
- ^ Pacific Biosciences
- Looks good - the costs are always a moving target so perhaps it's best to remove that part of the table entirely and provide the cost per Mb as a range. §everal⇒|Times 13:43, 16 October 2013 (UTC)
History needs a little expansion
[edit]The ABI 370A could not sequence 96 bases early on. It was 24 lanes at the beginning expanding to 36. It was the 377 that went to 96. And what about the Dupont Genesis? First box with dye terminator before ABI bought the patents from them. Licor is forgotten as well as that box that was attached to a NeXT Cube. I liked the computer, completely forget the name of the sequencer. I think it was luciferase one dye technology.
For time to sequence: 24 lane 370A with new dye terminator could get about 350 bases per lane on a good day. 24x350 in one day. (That's only if you washed your plates correctly.) MBCF (talk)