5. AMP GuidelinesΒΆ

The top of the AMP Guidelines screen has a title bar that shows the tab navigation between the Patient, Mutation Profile, Variants, Biomarker, and Report tabs, as well as the sample name and Downloads button that brings up the VSClinical Dependencies dialog on the right side of the title bar. The AMP Guidelines initially opens on the Patient tab where the sample and collection data can be entered, and patient information can be added (this has already been done for this tutorial). This information will be used to automatically populate the report information.

amp guidelines patient info

Figure 5-1: The AMP Guidelines Patient tab sample/patient section.

Scrolling down the screen, the next section is the Current Diagnosis / Tumor Type. The tumor type can be selected by first narrowing down the tissue type on the left side of the selection menu, by searching for the tumor type directly in the Search Tumor Type search bar, or by using the tumor type acronym (for example (NSCLC) for Non-Small Cell Lung Cancer). It is important to select the tumor type at this stage as future analysis will use this to collect relevant data. This tutorial is examining a melanoma tissue sample.

amp guidelines tumor type

Figure 5-2: The AMP Guidelines Patient tab Current Diagnosis / Tumor Type section.

The right side of the screen also has a quick access list of common tumor types to select.

The next section below tumor type is the NGS Sequencing Summary showing the NGS statistics like the variant allele frequencies and the types of variants being analyzed.

amp guidelines sequencing summary

Figure 5-3: The AMP Guidelines Patient tab NGS Sequencing Summary section.

The final section at the bottom of the Patient tab is the NGS Coverage of Genes section that shows the gene panel coverage statistics summary and a coverage region plot.

amp guidelines coverage genes

Figure 5-4: The AMP Guidelines Patient tab NGS Coverage of Genes section.

The coverage region plot allows user to adjust the read depth and mapping quality thresholds, and also allows the switching between showing coverage on a per-gene or per-target region.

amp guidelines target region

Figure 5-5: The AMP Guidelines Patient tab target region section.

Since the patent, sample, and tumor type data has been entered, we will move on to the Mutation Profile tab by selecting it on the title bar.