[BioC] Circular binary segmentation for allele-specific CN data

[J.Oosting at lumc.nl]

The problem with segmenting fracB data is that it does not behave as a
certain value + noise in segments. This violates the assumption for any
segmentation algorithm. 
In normal samples neighboring SNPs can have fracB values of 0 (for AA
genotype), 0.5 (AB) or 1 (BB). 
In the ideal situation you can filter out the uninformative SNPs (AA,BB)
using a paired normal sample. Then you have to transform the fracB from
the informative heterozygous SNPs data so it changes in 1 direction when
genomic rearrangements occur, and after that you can apply the CBS to
the remaining data.
Corver et.al. Cancer Res 2008; 68: (24). December 15, 2008 describes a
method to transform fracB-like data so it can be segmented.


Jan

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-
> bounces at stat.math.ethz.ch] On Behalf Of Christine Ho
> Sent: donderdag 19 augustus 2010 21:55
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Circular binary segmentation for allele-specific CN
data
> 
> Good afternoon!
> 
> I hope this question is not redundant - I've tried searching the
> mailing list archives and doing a Google search.
> 
> I've just finished using aroma.affymetrix() to produce allele-specific
> copy number estimates. So, right now, I've got the allele frequency
> data, i.e. what the vignettes call "fracB" data. I would like to run
> circular binary segmentation on this to find breakpoints (so I can
> identify regions of LOH), but it seems that all of the related
> packages on Bioconductor just segment aCGH data.
> 
> So, I was wondering: are the segmentation algorithms in these packages
> (for ex., snapCGH) able to handle any dataset, or are they specific to
> aCGH data? If they are specific to aCGH data, would anyone happen to
> know where I can obtain code (or better yet, a package) for running
> CBS on any data set?
> 
> Thank you for your time! I really appreciate it.
> 
> Best,
> Christine Ho
> Graduate student in Statistics at UC Berkeley
> E-mail: cho at stat.berkeley.edu
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor