I'd like to do CNV analysis on tumor samples (frozen tissue) to detect large arm level CNV as well as focal LOH, amplification, homozygous deletion. Many studies have used the Affymetrix Human SNP 6.0, which now has been replaced by the CytoScan HD (~750k SNPs and ~2 million CNV probes). I also see Illumina has some options: the CytoSNP 850K (850K SNPs) and the Omni2.5 (>2 million SNPs). Surprisingly the Omni is less expensive than the CytoSNP despite having more probes (they overlap a great deal, ~100k difference in probes).
I'm wondering a few things if anyone has any experience with these platforms for tumor sample CNV analysis and has any input on these:
1) Recommend the Affy vs. the Illumina for this CNV analysis?
2) Any reason to choose CytoSNP over Omini2.5?
3) Any recommendations for good tools for analysis?
4) We're likely going to do exome sequencing on matched tumors and normals in this group. Software like Nexus can call CNV from this, has anyone done this and seen how it works compared to SNP arrays for CNV?
Any input would be appreciated!