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Old 11-04-2013, 11:34 PM   #1
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Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default Calling tumor CNVs without normal as control?

I noticed that the recently IPOed Foundation Medicine only used tumor sample to find mutations, CNVs and rearrangements by sequencing 200+ genes panel.

I think their approach is fine with mutations/indels but sequencing normal as well to differentiate the true somatic ones might be slightly better. For rearrangement/fusion genes, they are using some introns sequence for that. I think RNA-seq can cover more fusion cases than this approach, is that right?

The only thing that bugs me a lot is their claim about CNVs. Isn't that without the normal control, GC bias can't be removed?
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