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Hi, I am new to bioconductor. Is there a good package/work flow that
does copy
number/LOH analysis for Affy 100K chips, starting from CEL files? I
have 100K
data from ~ 30 tumor samples; and I plan to download 100K trios data
(90 healthy
individuals) as normal references from Affymetrix website. Do I really
need
normal references for copy number/LOH analysis? Cheng Li of dChip had
a paper in
PLoS Computational Biology 2006 describing that dChip can infer LOH
from
unpaired tumor samples without using normal references, is there a
package in
bioconductor that can do this?
Thank you.
John
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Hi John
For copy number and LOH analysis from Affymetrix 100K SNP arrays you can use aroma.affymetrix or CRLMM packages in Bioconductor.
aroma.affymetrix supports raw CEL files and can process paired or unpaired samples for CN and LOH estimation. It also allows the use of public reference datasets if you dont have matched normals.
CRLMM (part of the oligoClasses and oligo framework) can call genotypes and estimate copy number from CEL files.
If you want to infer LOH without matched normals aroma affymetrix is usually the best supported option. There is also PennCNV (outside Bioconductor standalone) that can process Affy data once you convert it to LRR/BAF format.
References:
Bengtsson et al. (2009) Bioinformatics aroma.affymetrix workflow
Scharpf et al. (2011) Bioinformatics CRLMM for CN estimation
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