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-   -   Calling tumor CNVs without normal as control? (http://seqanswers.com/forums/showthread.php?t=35070)

ymc 11-04-2013 10:34 PM

Calling tumor CNVs without normal as control?
 
http://www.foundationone.com/about-f..._Technical.pdf

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?:confused:

bw. 11-05-2013 01:11 AM

Also curious about this. Perhaps they are using pooled normals?
If library prep & sequencer are the same, and the pooled samples are copy-number neutral, it should be possible to get decent results using ExomeCNV.

ymc 11-06-2013 01:36 AM

Quote:

Originally Posted by bw. (Post 120780)
Also curious about this. Perhaps they are using pooled normals?
If library prep & sequencer are the same, and the pooled samples are copy-number neutral, it should be possible to get decent results using ExomeCNV.

If I understand correctly, pooled normal only helps for calling CNVs on normal samples in the context of ExomeCNV.

I presume they aren't very nosy about accuracy. As long as it works in their clinical trials, then it is ok. One error can bite their ass though....


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