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Old 08-12-2011, 06:59 AM   #2
krobison
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Location: Boston area

Join Date: Nov 2007
Posts: 747
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Probably design PCR primers (which will require qualification) and amplify it.

First decision is whether to design long PCR amplicons which require fragmentation or short amplicons which might go directly on a sequencer with sufficient read length. Also, your platform choice may be driven by your turnaround time needs. Another key question is how many different samples are you going to try to sequence simultaneously, and for what purpose?

For example, suppose you expect to get samples infrequently but want to analyze them quickly. That is going to steer you towards a short amplicon strategy. Similarly, speed and many samples will probably put you in that neighborhood, as you can barcode the amplicons with fusion primers.

On the other hand, if you will have a large number of such samples and don't care about speed, then perhaps long PCR with fragmentation is the way to go.

You might also look at the Olink selector technology; it may not pay off though unless you have a lot of samples.

In all of these cases, you should be able to find a service provider or core lab that can either do the run on a "benchtop" sequencer (Ion Torrent or 454jr now; MiSeq in future) or run it as a lane mixed with other projects. This, of course, needs to be designed in from the start. In any case, you shouldn't be paying more than $5K per sample, and should be able to make it much less (depends on platform, strategy, etc).
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