Abstract: Candidate cancer antigens are identified using transposable elements. Differential expression levels are determined for proteins using baseline expression levels (using measurements of healthy tissue) and tumor expression levels (using measurements of tumor tissue). Protein(s) having a differential expression level greater than a threshold are selected. Cancer vaccine(s) are generated for the selected cancer antigens (s). Particular cancer vaccine(s) are selected for a patient based on differential expression levels for proteins using baseline expression levels of the patient and tumor expression levels of the patient. A vaccine for protein(s) having a differential expression level greater than a threshold can be selected. A microarray can be used for the measurements of the patient. A first array of probes can hybridize to RNA from transposable elements. A second array of probes can hybridize to RNA of different MHC haplotypes. A third array of probes can hybridize to RNA of different APOBEC genotypes.