On Tumor Samples

Archived tumor samples are available as either frozen or formalin-fixed, paraffin-embedded (FFPE) tissue. FFPE samples are usually more readily available than are frozen samples.

Tumor samples are usually contaminated with normal stromal cells, resulting in a dilution effect, with chromosomal abnormalities of tumor cells masked by the presence of normal cells. As a result, the genotype's accuracy and sensitivity to copy number changes will be affected by the percentage of normal cells contaminating the tumor tissue. Laser capture microdissection circumvents this problem by allowing for visualization and thus procurement of a homogeneous population of tumor cells, increasing the assay's sensitivity to chromosomal abnormalities (51). On the other hand, a whole-genome copy number SNP array analysis using PPFE samples still need optimization.

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