Segment Calling Algorithm For Mixed Density Array Cgh

Question

[Ps376]

Hi all,

I have a mixed density array CGH (highly densed regions interspersed with low density regoins). Is there a segmentation algorithm out there that works best with this kind of array? That is optimized to call segments (and possibly assign copy number states) for a mixed probe density array?

Answer 1

[Sean Davis]

There are several, but I believe this was the first:

BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data

[Ps376]

Hi,

Thanks so much for the suggestion! I am looking into BioHMM, and it definitely seems useful. You mention there are several such algorithms...would you happen to know any others specifically? Since I am working on new data, I wanted to be able to try different algorithms to see what works best for our dataset. Thanks again!!