Affymetrix Snp6 Cn/Loh Cnv

Question

[Astoulpho]

Hello,

It's my first time in thei site and I'm just getting started on SNP analyses and genotyping. I'm studyin some data using SNP6 from affymetrix and its possible to measure CNV and Copy Number/LOH analyses. Whats the difference between these two characters? Aren't they almost the same? Many thanks

Answer 1

[Irsan]

Copy number loss from ploidy 2 to either 1 or 0 results in LOH (Note that on a SNP-array, B Allele Frequencies look different for loss of 2 to 1 and loss of 2 to 0 ). However, it does not mean that when you see LOH, there is a copy number loss. For example, it can happen that the paternal allele is lost while the maternal allele is gained, resulting in LOH but no copy number alteration. This is called copy neutral LOH

[Astoulpho]

thanks for the clarification