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Old 06-20-2012, 10:09 PM   #10
DaleYuzuki
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Location: Maryland USA

Join Date: Mar 2012
Posts: 12
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Hi Miroslav, well let's just assume then that the term intended was 'redundant' regions of the genome in terms of amplicon specificity, which could be repetitive regions, pseudo-genes, or paralogous genes.

With a hybridization-based method (i.e. Agilent's SureSelect or NimbleGen's EZ Cap) these regions are simply 'repeat-masked' and designs simply cannot be made to those regions.

With RainDance, one of the nice things about it is that it is regular PCR primer design; a program like Primer 3 can be (and often is) used for the design, so there is a measureable increase in the percentage of successful designs. That being said, if you talk with RainDance customers they will tell you that the first exon of any gene is often not amplified in their enrichment (or not amplified very well) and this is a problem.

Hope this helps, feel free to ask further questions if you need any clarification.

Dale
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