Next-generation DNA sequencing

Title:

Next-generation DNA sequencing

Author(s):

Jay Shendure Hanlee Ji

Publication:

Published in: Nature Biotechnology
Volume: 26, Issue: 10, Pages: 1135-1145
Published: 10//2008
DOI: 10.1038/nbt1486
Website: http://www.nature.com/doifinder/10.1038/nbt1486

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Our Discussion:

This article is an interesting review of how Next-Generation sequencing differs from traditional Sanger sequencing, along with the pros and cons of each approach.  Overall, the advantage of NextGen sequencing seems to be that it bypasses some of the traditional bottlenecks of Sanger sequencing, such E. Coli transformation and colony selection, and can be done more efficiently and significantly less expensively than Sanger sequencing.  The disadvantages include much larger datasets (processing, transfer and storage issues), smaller read lengths (processing issues), and quality of reads.  The article also covers how each Next Gen sequencing approach differs from its peers; for example, 454 sequencing tends to run high on the insertion-deletion error type due to limitations evaluating homopolymers, but it has the advantage of relatively long read lengths (~300bp), which might mitigate some of the processing and quality issues encountered with technologies that produce shorter reads.

A couple of points that were especially intriguing:

  • They remark that there will be cases where quality will have to override costs in order for accurate returns (ie, Sanger sequencing may continue to trump NextGen for awhile for certain applications);
  • That software may be key to bridging the quality gap between Sanger and NextGen sequencing (and, indeed, the authors highlight new developments in that arena);
  • The authors assume that the quality of NextGen sequencing will evolve with time, as Sanger sequencing has over the two decades that it has dominated, and one approach to this problem may lie in hybrid approaches that depend on more than one NextGen Sequencing technology.  The idea of a hybrid approach, especially one that carefully mitigates the specific shortcomings of the technologies in question, sounds promising, and one that may be approached using software first before any formal attempts to merge technologies occurs — if, indeed, formal attempts to merge the technologies are even required.

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