How to set the fold-change cutoff when the sample purity is not 100%

Given a sample purity of $ X$%, and a desired detection level (absolute value of fold-change in 100% pure sample) of $ T$, the following formula gives the required fold-change cutoff for an amplification:

cutoff$\displaystyle = \frac{X\text{\%}}{100\text{\%}} \times T + (1-\frac{X\text{\%}}{100\text{\%}}).$ (31.19)

For example, if the sample purity is 40%, and you want to detect 6-fold amplifications (e.g. 12 copies instead of 2), then the cutoff should be:

cutoff$\displaystyle = \frac{40\text{\%}}{100\text{\%}} \times 6 + (1-\frac{40\text{\%}}{100\text{\%}}) = 3.0.$ (31.20)

The following formula gives the required fold-change cutoff for a deletion:

cutoff$\displaystyle = \frac{1}{\frac{X\text{\%}}{100\text{\%}} \times \frac{1}{T} + (1-\frac{X\text{\%}}{100\text{\%}})}.$ (31.21)

For example, if the sample purity is 40%, and you want to detect a 2-fold deletions (e.g. 1 copy instead of 2), then the cutoff should be:

cutoff$\displaystyle = \frac{1}{\frac{40\text{\%}}{100\text{\%}} \times \frac{1}{T} + (1-\frac{40\text{\%}}{100\text{\%}})} = 1.25.$ (31.22)

Figure 31.25 and Figure 31.26 shows the required fold-change cutoffs in order to detect a particular degree of amplification or deletion respectively at different sample purities.

Image sample_purity_graph_amp
Figure 31.25: The required fold-change cutoff to detect amplifications of different magnitudes as a function of sample purity.

Image sample_purity_graph_del
Figure 31.26: The required fold-change cutoff to detect deletions of different magnitudes as a function of sample purity.

The Copy Number Variant Detection tool calls CNVs that are both global outliers on the target-level, and locally consistent on the region-level. The tool produces several outputs, which are described below.