One type of genetic mutation in enriched cancer stem cells is deletion.

Deletion of partial or the whole DNA sequence of a specific gene may alter the function of that gene partially or completely. If the deleted sequence were the red area in the diagram above, the DNA sequence after deletion would be shorter. Depending on the sequence deleted, there may be multiple consequences including but not limited to, protein encoding frame shift, malfunction of a gene and altered gene expression pattern. For example, the partial or complete deletion of tumor suppressor gene p53 and /or p73 can transform pre-cancer cells (with one to a few oncogenes expressed) into tumorigenic cancer cells.

Enriched cancer stem cells, CancerStemCell™, have all types of mutations, including deletions. It is not known what deleted DNA sequences are and how many deletions have occurred in any one cancer cell or the heterogeneous population. However, the degree of mutations and number of antigens in "solid tumors" grown from enriched cancer stem cells are comparable to that of metastasized tumor cells since the whole cell "giant liposome" cancer vaccines, CancerVaccine™, made out of in vitro solid tumors grown from enriched cancer stem cells and metastasized tumor cells have induced similar immune responses.