Somatic Sample Analysis

Dashboard

• Case Information

  • (Mandatory) Case-ID/Name: Specific ID/Name created by the user to identify each case
  • (Optional) Age (1-150)
  • (Optional) Gender (female | male | unspecified)

• Number of annotations: The number of variant annotations, off-target, and on-target counts are shown here.

• Number of reads: The distribution of aligned/unaligned and off/on geneset reads are shown

• Het/hom and Ts/tv ratio: The het/hom ratio and the ts/tv ratio of the sample are shown here together with the distribution of the values for all samples in the SEQ platform with the same machine/kit combination.

• Target region coverage: The target refers to the regions defined in the kit. The coverage for different sequencing depths is shown for all chromosomes, and per chromosome.

• Average depth: The average depth around the kit target regions

• % of on target: The target region coverage for all chromosomes with 1X sequencing depth threshold. This is identical to the value illustrated in the target region coverage section.

• Summary: In the summary table, drug resistance causing or drug sensitizing alterations and their related drugs are displayed with the level of evidence codes.

  • Columns
    • Alteration: Name of the gene or biomarker (PD-L1, TMB, MSI, etc.) and how it is altered (e.g. amino acid change, affected transcript position for spliced variant, copy number change, or high TMB)
    • Approved for the selected cancer type: List of FDA-approved drugs to treat the diagnosed condition by targeting the alteration or a downstream target. You can see the detailed summary for the drug by clicking each drug name.
    • Investigational for the selected cancer type: List of potential drugs that may target specified alterations or a downstream target and are being investigated as a potential therapy for the diagnosed condition. You can see the detailed summary for the drug and links to view the related clinical trials on ClinicalTrials.gov by clicking each drug name.
    • Approved for Other Indications: List of drugs that have not been approved to treat the diagnosed condition but have been approved to treat other cancer types.
    • Resistance: List of drugs to which at least one of the specified alterations is resistant.

TMB Calculation

Tumor Mutational Burden is defined as non-synonymous SNP mutations per megabase. If the covered region length is less than 1.1 megabases, TMB cannot be calculated and will be seen as 'N/A'. For tumor only samples, TMB is calculated by the total number of non-synonymous and unique/novel SNP variants found in the sample, divided by the covered region on CDS. For tumor/matched-normalsamples, the variants detected in the normal sample are used to eliminate germline mutations.

Please see the table below for detailed parameters used for TMB calculation.

Parameters	Tumor Only	T/N match
Minimum Allowed Covered Length	1.1mb	1.1mb
Minimum Depth	25	50
Minimum Allele Fraction	0.05	0.05
Population Database Allele Filter	0.1%	-
dbSNP filter	Yes	-
Chromosome Filter	-	MT
Filter Non-coding Regions	Yes	Yes
Filter MNVs	-	Yes
Filter No PASS Variants	Yes	Yes
Use SNV and Indels	Yes	Yes
Eligible Region Coverage	5X	50X

MSI Calculation

MSI calculation is only available for tumor/normal matched analyses. MSIsensor^{1 (opens new window)} is used for MSI calculation.