Note: Replication efficiency refers to the fold of PCR amplification achieved per cycle.

A value of 1, no amplification, while a value of 2, the maximum possible amplification.

PCR mutation accumulation model

Polymerase Chain Reaction (PCR) is a fundamental technique in molecular biology used to amplify DNA. However, polymerase-induced errors during amplification can introduce mutations, affecting the accuracy of downstream applications such as sequencing, cloning, and diagnostics. The fidelity of a PCR reaction depends on the choice of DNA polymerase, as different enzymes exhibit varying error rates.

To address this, our model estimates the error-free fraction of a PCR reaction based on the selected polymerase. By incorporating known polymerase error rates, the model provides users with a quantitative measure of amplification accuracy, helping them make informed decisions when designing their experiments.

The model is illustrated schematically below. The expected number of mutations per cycle is evaluated using the law of iterated expectations, and this iterative equation is solved to determine the error-free fraction of the amplicon at the desired number of PCR cycles.

Derivation of the mean of the mutation-free fraction

Derivation of the variance of the mutation-free fraction