Table 3. Quantitation of copy number aberrations and CNNLOH in samples with varying proportions of normal cells.

Sample	Segments with CN loss	Segments with CN gain	Segments with CNNLOH>0.5
13A, N = 0.26	264	590	900
13A micro, N = 0.11	1349	1502	1226
13A micro/13A	5.0	2.6	1.4
234A, N = 0.20	1568	988	831
234A micro, N = 0.14	1581	953	808
234A micro/234A	1.0	1.0	1.0
296, N = 0.36	16	226	302
296 micro, N = 0.02	1958	887	505
296 micro/296A	122	3.9	1.6
319, N = 0.23	1036	1823	1274
319 micro, N = 0.01	2221	2116	1269
319 micro/319A	2.1	1.2	1.0
367, N = 0.23	2446	1324	873
337 micro, N = 0.01	2649	2026	593
367 micro/367A	1.1	1.5	0.7

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).