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Old 04-16-2013, 01:49 PM   #5
Location: Maryland

Join Date: Apr 2010
Posts: 31

I have not personally used the Haloplex platform before. I've analyzed a lot of exome data but not Haloplex.

From briefly looking at the information on the Agilent site it seems that first the DNA is fragmented with restriction enzymes which will be exact cuts (as opposed to "random" shearing in typical exome experiments), second the probes are hybridized (the way its described this also seems very specific since its to the ends of restriction fragments), third the targets are purified and ligated, fourth there is a PCR step, and then fifth sequencing.

From my interpretation of this setup I would think it would be okay to retain the PCR duplicates (since there's PCR in the 4th step to enrich for your targets) but I would hope someone else who has used the Haloplex technology could comment on this as well.
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