Overview Tab

The Overview tab displays a high-level view of the most relevant variants in the case. This tab contains a list of genes and shows variants detected in that case within those genes. The variants in this list are filtered according to the filter that was selected as part of the test definition. The key genes are predefined by Connected Insights based on cancer type.

Lab QC

The Lab QC section provides an overview of the following information contained under the Lab QC tab:

• Metric

• Value

• Status (Pass/Fail)

For more information on configuring metrics that display in the Lab QC section and their thresholds, refer to Pipeline and QC Configuration.

Tumor Content and Ploidy Metrics

View the % Estimated Tumor Purity and Estimated Tumor Ploidy in the Overview tab. This information displays under Tumor Characteristics.

Biomarkers

The following biomarkers provide an overview of the measurable biological markers. The content in these fields comes from secondary analysis files and is displayed here.

• Tumor Mutational Burden (TMB) — Displays the TMB in mut/MB. The TMB section also shows TMB-Low and TMB-High statuses.

• Microsatellite Instability (MSI) — Displays the MSI as a percentage. The MSI section also shows MS-Stable and MSI-High statuses.

• Genomic Instability Score (GIS) — Displays the GIS. The GIS section also shows GIS-Low and GIS-High statuses.

For more information on setting thresholds for the statuses, refer to Disease Configuration.

Select Interpret to open the biomarker details. For more information, refer to Interpret a Variant.

Tumor Mutational Burden (TMB)

GIS Data

MSI Data

Key Findings

This section provides information on genes specific to the disease, gene coverage, and variants.

Genes Specific to the Disease

For more information on how to set up genes specific to the disease, refer to Disease Configuration.

Gene Coverage

Gene coverage tracks show the following data in a graph:

• Transcript exons and introns — Transcript is the preferred transcript (if specified) or the RefSeq transcript. For more information on specifying a preferred transcript for a gene, refer to Preferred Transcripts.

• Gene coverage — The Y-axis indicates the gene coverage (for example, 50X).

• Hotspots — Hotspots are plotted along the X-axis and are derived from the Cancer Hotspots website.

• Variants — Variants in the gene that pass default filters. For more information on how to set up a default filter, refer to Test Definition Setup.

Variants

Variants for each gene are shown with My Knowledge Base and Other Knowledge Base assertions.

My Knowledge Base assertions include the following classifications:

• Highest biological classification across all diseases

• Highest actionability classification for therapeutic classifications across case and ancestor diseases

• Highest actionability classification for prognostic classifications across the case and ancestor diseases

• Diagnostic classifications across all diseases Other Knowledge Base assertions include the following classifications and filters:

• Highest actionability classifications for JAX-CKB and CIViC, including: – Therapeutic classifications across case and ancestor diseases – Prognostic classifications across the case and ancestor diseases – Diagnostic classifications across all diseases

• Default filters that show the variant To interpret variants from the Overview tab, select Interpret. For more information, refer to Interpret a Variant.