The design of highly multiplex nucleic acid primers and probes to enrich and detect many different DNA sequences is increasing in biomedical importance as new mutations and pathogens are identified. One major challenge in the design of highly multiplex PCR primer sets is the large number of potential primer dimer species that grows quadratically with the number of primers to be designed. During my Ph.D., one of my main focuses is how to design highly multiplex PCR primer sets that minimize primer dimer formation. Here I present and experimentally validate Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE), a stochastic algorithm for the design of highly multiplex PCR primer sets that minimize primer dimer formation. I also worked on the design of multiplex probes for variants detection. Many diseases are related to multiple genetic alterations along a single gene. Probing for highly multiple (>10) variants in a single qPCR tube is impossible due to a limited number of fluorescence channels and one variant per channel, so many more tubes are needed. Here, I experimentally validate a novel color-mixing strategy that uses fluorescence combinations as digital color codes to probe multiple variants simultaneously.