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Old 05-14-2010, 06:27 AM   #1
gantzgraf
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Location: UK

Join Date: May 2010
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Default Can Oragene-DNA be used for targeted capture and clonal sequencing?

Hi All,

I wondered if people could humour what might be a very naive question. We deal with a lot of samples that are collected from saliva using Oragene collection kits which we have found to provide good quality DNA for general PCR methods, SNP chipping etc. However, as we are starting to use clonal sequencing are these saliva samples of any use? Is the potential for bacterial contamination a serious problem and are there any other factors that would make these DNAs unsuitable? We have asked the manufacturers but are yet to hear anything back.

I am aware of colleagues who have used long-range PCR enrichment methods on saliva samples but for our uses we require targeted capture. So far we have only worked on samples extracted from blood.

We're using Agilent SureSelect reagent for our captures and the Illumina GA for our sequencing. I'd be very interested to hear if anyone has any experience with this or if it's just generally considered to be a bad idea.

Thanks

Dave
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Old 05-24-2010, 11:10 PM   #2
grace033
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Location: asia

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Default

TA clone may be use to test your sample, and bioinformatics analysis can also remove polluted reads. But target capture for Agilent or nimblegen, need much more DNA. does saliva contain much expressed DNA?
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