Quantitation of copy number aberrations and CNNLOH in samples with varying proportions of normal cells.

The number of genomic segments with predicted copy number gain or loss is indicated for each sample. The number of segments with CNNLOH larger than 0.5 and no copy aberrations detected in either analysis are also shown. The ratio of the number of aberrations in the microdissected and whole samples are indicated. For the samples with large differences in detection of segments with copy number differences, such as 13A, 296A and 319A, the corresponding detection of CNNLOH appears to be more robust. The proportion of normal cells for each sample is obtained either from manual counting (whole samples) or by the method presented here (microdissected samples).