Individualized vaccines for cancer

A method for determining a false discovery rate based on next generation sequencing data, said method including:

• taking a first sample of genetic material from an animal or human;
• taking a second sample of genetic material from an animal or human;
• taking a first sample of genetic material from tumor cells;
• taking a second sample of genetic material from said tumor cells;
• determining a common coverage tumor comparison by counting all bases of the reference genome which is included in both the tumor and at least one of said first sample of genetic material from an animal or human and said second sample of genetic material from an animal or human;
• determining a common coverage same vs. same comparison by counting all bases of the reference genome which are covered by both said first sample of genetic material from an animal or human and said second sample of genetic material from an animal or human;
• dividing said common coverage tumor comparison by said common coverage same vs. same comparison to form a normalization;
• determining a false discovery rate by dividing 1) the number of single nucleotide variations with a quality score greater than Q in a comparison of said first sample of genetic material from an animal or human and said second sample of genetic material from an animal or human, by 2) the number of single nucleotide variations with a quality score greater than Q in a comparison of said first sample of genetic material from said tumor cells and said second sample of genetic material from said tumor cells and 3) multiplying the result by said normalization.

A method for determining an estimated receiver operating curve (ROC), said method including:

• receiving a dataset of mutations, each mutation associated with a false discovery rate (FDR);
• and
• for each mutation:
• determining a true positive rate (TPR) by subtracting said FDR from one;
• and
• determining a false positive rate (FPR) by setting said FPR equal to said FDR;
• and
• forming an estimated ROC by plotting., for each mutation, a point at the cumulative TPR and FPR values up to said mutation, divided by the sum of all TPR and FPR values.