6. Mutation Profile TabΒΆ

The Mutation Profile tab is made of 2 sections: Included Somatic Variants and Biomarkers and Genes with Significant Wild-Types. First, the Included Somatic Variants is the table that displays all of the variants to be analyzed. The top of the table lists the different variant types which include Small Variants, CNVs, Fusions, and Wild-Types. This tutorial has already been populated with 2 Small Variants, 1 CNV, and 1 Fusion. Keep in mind that any of these markers can be added from the project or they can be manually entered into the AMP Guidelines.

amp guidelines mutation profile variants

Figure 6-1: The AMP Guidelines Mutation Profile tab Included Somatic Variants section.

Looking closely at the Origin and Report columns of the Small Variants entry shows that the BRAF variant was added as a Somatic variant and selected to be reported as a Biomarker and the RAF1 variant was added with an Origin of Germline Suspected so will be placed in a Secondary Germline report. Clicking on the CNVs and Fusions entry in the table will also show the Report status for each of these entries to be Biomarker, so all three of these markers that will be analyzed in the Biomarker section of the report are listed in the Biomarkers and Genes with Significant Wild-Types section at the bottom of the Mutation Profile tab.

amp guidelines mutation profile biomarkers

Figure 6-2: The AMP Guidelines Mutation Profile tab biomarkers section.

Since we already have the marker of interest here, we will move on to the Variants tab to specifically look at the 2 Small Variants included by selecting the Variants tab in the title bar.