In the 26Q1 OmicsCNGeneWGS.csv release, what is the reported linear copy number ratio normalized against? Does a ratio of ~1.0 incorporate that specific cell line’s own ploidy (e.g. a value of ~1.0 for an unaltered gene in a tetraploid line, since 4 copies is ‘normal’ for that line, while a value of ~2.0 could mean 4 copies in a diploid line but 8 copies in a tetraploid line)? I want to use the data to define cell lines with loss or amplification of genes of interest and want to make sure I am interpreting the values correctly.
Hi,
OmicsCNGeneWGS contains copy number relative to the cell line’s ploidy, so you are correct that for an unaltered gene in a tetraploid line would be ~1.
Thanks,
Simone
