9. Example 2 SNV BRAF V600E

This BRAF V600E variant represents the first somatic marker to analyze in this project. The variant tab is arranged very similarly as to the other small variant, but due to the somatic nature, the ACMG Criteria section is replaced with an Oncogenicity Scoring Recommendations section. Also, the pathogenicity color scale in the slide bar has been replaced with an Oncogenicity Scale color bar.

amp scoring summary

Figure 9-1: The AMP Criteria Recommendations for Example 2.

Scrolling down to the Oncogenicity Scoring Recommendations section shows that this variant has been scored with an oncogenicity score of +10 by all of the criteria listed on the left, but we will go through each of these separately.

First, scroll down to the Report Variant as Biomarker section of this page.

amp variant biomarker

Figure 9-2: The AMP Guidelines Variant tab Report Variant as Biomarker section.

Like with the previous variant analysis, this section shows the information that will be used in the final report, but this somatic variant has a related tumor type which in this example is, melanoma.

As an example of how to populate this interpretation section, click on the plus sign at the end of the first Oncogenicity Evidence entry on the right and select, Copy Text.

amp variant biomarker add interpretation

Figure 9-3: The AMP Guidelines Variant tab Report Variant as Biomarker section add to Interpretation.

Then click within the interpretation text box on the left, hit Enter on your keyboard to reach a new line, and paste. Since the entry was adjusted, the option to Review & Save Now… becomes available so select it. If there was already an interpretation for this variant saved, the dialog that appears would show the differences and allow the user to select which interpretation to save.

amp variant interpretaion review and save

Figure 9-4: The AMP Guidelines Variant tab Biomarker Summary Review and Save.

The other important feature in this dialog is the blue checkbox in the lower left-hand corner. If this is checked, the interpretation will be shared with the Golden Helix Curation Team to improve the CancerKB database. For this example, though, Close out of this dialog.

Scrolling down to the next section gets us to the start of our somatic variant classification.

The Somatic Catalogs section asks if this variant appears in COSMIC, and if it does, how often. Since this variant appears in almost 30,000 sample, the highest value, SC+3 is selected. The card on the right shows the tumor type frequency for different catalogs like COSMIC and ICGC.

somatic catalogs

Figure 9-5: The AMP Guidelines Variant tab Somatic Catalogs section.

The next section looks at the frequency of the variant in different Germline Population Catalogs. This variant shows up rarely in gnomAD (only in the South Asian group) and not at all in 1000 Genomes, so PF+0 is selected for this category and the oncogenicity score is not adjusted.

population catalogs

Figure 9-6: The AMP Guidelines Variant tab Population Catalogs section.

The next section, Relevant Clinical Assessments results in the CE+3 criteria being selected since this variant has been previously classified as pathogenic in ClinVar as well as previously classified as oncogenic in CiVIC.

The following sections analyze the impact of the variant on the gene level and since there are multiple pathogenic variants nearby, the NP+1 criteria can be selected.

relevant clinical assessments

Figure 9-7: The AMP Guidelines Variant tab Relevant Clinical Assessments section.

It also turns out that his BRAF variant occur in a cancer hotspot, so we can also select the HR+1 criterion in the Hotspots & Active Binding Sites section. This section also shows us that the variant occurs in an active binding site, so the oncogenicity score is increased when adding the AR+1 criterion.

hotspot and binding site

Figure 9-8: The AMP Guidelines Variant tab Relevant Hotspots and Active Binding Sites section.

The final section on this page is Computational Evidence and shows the functional predictions and splice site results.

variant computational evidence

Figure 9-9: The AMP Guidelines Variant tab Computational Evidence section.

This section lets us see that all 4 functional prediction scores support that this variant will likely cause a deleterious effect on the gene, so an IP+1 is selected, but there does not appear to be a splice site disruption, so SP+0 was selected.

variant splice site

Figure 9-10: The AMP Guidelines Variant tab Splice Predictions section.

All of these scores combined give us an oncogenicity score of +10 and confirm that this is indeed an oncogenic variant.

Next, we will move on to the Biomarkers section clicking the tab in the title bar.