Context dependent polymerase errors [was Re: Sequence variations]
oberste at fcs260c.ncifcrf.gov
Mon Dec 14 10:58:17 EST 1992
In article <222 at sftwks.UUCP> bradbury at sftwks.UUCP (Robert Bradbury) writes:
>In article <Bz1w8o.ExA at ncifcrf.gov> oberste at fcs260c.ncifcrf.gov (Oberste) writes:
>>Since a PCR-induced base change is propagated through subsequent cycles,
>>it is important to collect and compare sequence from independent PCR
>>amplifications. It would be extremely unlikely to see the same artefact
>>in independent amplifications.
>I'm not sure that I agree with this. Polymerases will incorporate
>improper bases depending on the surrounding context. If a
>polymerase is inclined to make a mistake once, it might make the
>same mistake again.
Sure, but since the error frequency is fairly low to begin with, consecutive
amplifications will _most likely_ not have errors at the same place.
> A much better solution IMHO is to do the PCR
>with several different polymerases. The polymerases tend to show
>different misincorporation characteristics and it would be less
>likely that different polymerases would make the same context
>Another thing to consider is the error correction capabilities
>of the polymerase. Those without 3'-5' exonuclease activites
>have an error rate about 100x those with this exonuclease
Even more excellent point :-). You'll still want to look at multiple clones,
Steve Oberste Internet: oberste at ncifcrf.gov
LCMS, PRI, NCI-FCRDC
PO Box B "Never put off until tomorrow that which
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