4.3.1 Parameters settings

The minimal alterations or minimal regions of amplification correspond to the intersection for all tumors of the amplified regions. These regions are minimal in that no breakpoint evidence is available to narrow the region further. To compute the minimal amplified regions click on: Tools $\rightarrow$Genome Alteration $\rightarrow$Compute (see Figure 4.4).

Figure 4.4: Tools menu - Genome Alteration

Then set the Genome Alteration parameters as follows (see Figure 4.5):

1. for the Minimum support of alterations click on Percent and set the value to $5$ (we want that the alteration is present at least in 5% of the samples)
2. for the Type of alterations deselect Gain and Loss to search only for Amplicon

Figure 4.5: Genome alteration parameters