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Old 02-25-2012, 06:27 AM   #35
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Originally Posted by larissa View Post
That's one of the reasons why 4% error rate is not acceptable in the clinic, for guiding treatment/dosing and inclusion/exclusion criteria. It will be acceptable for lots of other things, all R&D oriented, in academia and private sector.
Two things to note

1) "The clinic" is not monolithic. You seem to use this as a poor shorthand for "calling missense/nonsense and short indel mutations". There are a number of other applications with clinical value, such as detecting CNVs, chromosomal rearrangements, and transcription states, for which 4% base calling error would be quite tolerable.

2) The 4% error rate is dominated by indels in specific contexts; for assays looking for missense/nonsense mutations outside these contexts the system might be acceptable; simply toss any reads which show an indel in the neighborhood of what you are interested in. This is a strategy not unheard of in the 454/Ion Torrent world, due to their indel issues.
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