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Old 01-07-2010, 07:14 PM   #1
ECO
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Default Excellent NGS review: "Sequencing technologies - the next generation"

Great review article just out in Nature Reviews. Touches on every aspect of all the current technologies at a pretty detailed level (down to the chemistry of dyes/nucleotides).

Please check it out here. Abstract below:

Quote:
Sequencing technologies — the next generation

Michael L. Metzker

Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.
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Old 01-07-2010, 10:39 PM   #2
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The paper is good, however it should be noticed that the author has financial interests and conflicts in such matters...
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Old 01-08-2010, 06:34 AM   #3
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Originally Posted by francois.sabot View Post
The paper is good, however it should be noticed that the author has financial interests and conflicts in such matters...
Was there anything in particular that you felt showed that this author was not impartial?
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Old 01-08-2010, 06:38 AM   #4
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See here: http://www.nature.com/nrg/journal/v1...s/nrg2626.html

It is statued here that the author is itself the CEO from a company providing one of the described technology, LaserGen.
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Old 01-08-2010, 08:01 AM   #5
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Quote:
Originally Posted by francois.sabot View Post
See here: http://www.nature.com/nrg/journal/v1...s/nrg2626.html

It is statued here that the author is itself the CEO from a company providing one of the described technology, LaserGen.
I saw that. But is there anything in the review that is unbiased that you've found?
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Old 01-08-2010, 08:25 AM   #6
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Quote:
Originally Posted by francois.sabot View Post
The paper is good, however it should be noticed that the author has financial interests and conflicts in such matters...
Why? Like ECO, i am curious to know about any bias in the scientific content of this review.. If you find some, please let us know!
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Old 01-08-2010, 08:28 AM   #7
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On the technical side, no matter. On the limits and 'enthousism' on each method, I will be less prone to trust all the paper. I am a little reluctant when a 'partis-pris' author compares different techniques and gives some advices on which one is the best one... Whatever is the subject BTW. Just a łatter of deontology
Nevertheless the paper is a very good manual for all techniques described in.
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Old 01-08-2010, 10:54 AM   #8
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Another good recent review, though the conflict-paranoid should be forewarned that probably all the authors have financial interests in at least one company in the field.

http://dx.doi.org/10.1038/nbt.1585
Nat Biotechnol. 2009 Nov;27(11):1013-23. Epub 2009 Nov 6.
The challenges of sequencing by synthesis.
Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, Vezenov DV.


DNA sequencing-by-synthesis (SBS) technology, using a polymerase or ligase enzyme as its core biochemistry, has already been incorporated in several second-generation DNA sequencing systems with significant performance. Notwithstanding the substantial success of these SBS platforms, challenges continue to limit the ability to reduce the cost of sequencing a human genome to $100,000 or less. Achieving dramatically reduced cost with enhanced throughput and quality will require the seamless integration of scientific and technological effort across disciplines within biochemistry, chemistry, physics and engineering. The challenges include sample preparation, surface chemistry, fluorescent labels, optimizing the enzyme-substrate system, optics, instrumentation, understanding tradeoffs of throughput versus accuracy, and read-length/phasing limitations. By framing these challenges in a manner accessible to a broad community of scientists and engineers, we hope to solicit input from the broader research community on means of accelerating the advancement of genome sequencing technology.

PMID: 19898456
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Old 01-14-2010, 05:28 AM   #9
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Thanks Krobinson, the Fuller et al paper looks like an excellent review of the remaining difficulties in NGS. The authors are tops. And of course you are right, every knowledgeable person in this field almost certainly has connections with one or several firms - disclosure is the only safeguard. Don't know how I missed this article when it came out!
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