Fig 2

Determination of chromosome 2 copy number changes under different experimental conditions: comparison between formalin-fixed, paraffin-embedded (FFPE) or frozen, LCM and WGA treatment, WGA alone, and untreated samples. An example with chromosome 2 is provided, left to right: untreated reference DNA extracted from bulk cell culture, DNA (0.6 ng total) diluted from untreated bulk culture reference and amplified using WGA, 100 cells laser capture microdissection (LCM) isolated from FFPE samples and amplified using WGA, and 100 cells LCM isolated from frozen samples and amplified using WGA. Chromosomal location (Mb) and log₂ ratio are plotted along the x- and y-axes, respectively. Across all chromosomes and within individual chromosomes (chromosome 2 shown in this example), the data were highly correlative when treatments were compared (see Results), demonstrating that the archiving procedures, LCM, or WGA techniques did not introduce experimental artifact.