When there is a high concentration of only A. niger DNA in a reaction the A. fumigatus primers can cross-react giving a weaker FAM signal.
Cross-reactivity between Aspergillus niger DNA and the Aspergillus fumigatus primer probe set has been observed. This cross-reactivity yields a reduced FAM signal when compared to the ROX signal when an abundance of A. niger DNA is present and does not invalidate results. Both A. niger and A. fumigatus are pathogenic and the presence of either will result in failure of the sample.
Figure 1: Example of the Aspergillus fumigatus primer probe (blue line) showing low-level cross-reactivity when there is an abundance Aspergillus niger DNA present.