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Old 04-14-2011, 05:57 AM   #1
jlove
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Default Which DNA Pol is equivalent to TruSeq kit?

I've been trying to find a DNA polymerase to use as a substitute for the PCR master mix that comes with the Illumina TruSeq DNA prep kit, with some (but not great) success. So far I've tried Phusion HF and it didn't look quite the same as the library I made with Illumina's enzyme. I can't think of why, exactly, but I have just seen this empirically with a few samples.

I'd like to hear which DNA polymerase other folks have been using as a substitute. I know that Illumina acquired Epicentre and I've put in a request with them to find out if they provide the enzyme now, but haven't heard back yet.

Any advice on a 2X PCR master mix?
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Old 04-14-2011, 08:09 AM   #2
kthai
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Have you looked into the KAPA enzymes?
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Old 04-14-2011, 08:11 AM   #3
jlove
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Yeah, we just ordered that! Thanks!
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Old 04-18-2011, 03:07 PM   #4
epistatic
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Try using AccuPrime Taq High Fidelity (Invitrogen)

We started using it for GC-bias and the Broad published this paper comparing it with Phusion HF.

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Aird, MG et al. 2011. Genome Biology, 12:R18 doi:10.1186/gb-2011-12-2-r18
* Corresponding author: Andreas Gnirke gnirke@broadinstitute.org

http://genomebiology.com/2011/12/2/R18/abstract
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Old 04-29-2011, 10:42 AM   #5
daniellaw
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Our lab hasn't tried the TruSeq sample prep kits yet, but we have been using Stratagene Pfu Ultra II as a substitute for the Phusion in the old Genomic DNA sample prep kit. It works very well.
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