Using positive and negative controls during a PCR-based genotype screen helps provide integrity to the screen. Positive controls demonstrate that all of the correct reagents were added, and that a PCR product (amplicon) can be produced. A negative control is beneficial, ensuring that there is no contamination present in the reaction, and that false negatives are not being obtained.
By using these controls, the PCR success can be demonstrated, or troubleshooting can be undertaken to identify the causes of any issues.