Visualization interpretation guidance

Oncomine™ Lung Cell‑Free Total Nucleic Acid Research Assay

Metric

Description

Copy Number Variation

CNV Ratio

Should be interpreted as the fold amplification (gain) as detected by the assay. CNV specific amplicon (MET) coverage levels are compared to non-CNV amplicon coverage.

P-value

Significance of CNV Ratio measurement based on amplicon coverage variability (MAPD level) and magnitude of the pairwise coverage differences between the CNV and non-CNV amplicons. High coverage variability will result in less significant p-values.

For QC and CNV calling rules, see Quality control (QC) thresholds .

Fusion detection

Nomenclature

Each reported fusion target follows a specific naming convention such that the 5'- and 3'‑genes are reported along with donor and acceptor exon numbers. Lastly, a COSMIC ID or NCBI transcript accession number is added to the end of each target name. For example, EML4-ALK.E13A20.COSF463 identifies the EML4-ALK fusion variant with exon 13 of EML4 fused to exon 20 of ALK.

Fusion QC genes

Two non-fused process control genes (HMBS and TBP) that have been shown to be consistently detected in cell-free nucleic acid extracts are included in the assay to inform quality of fusion variant calls.

Analysis detail

  • Fusion targets are reported as FUSION in the Type column.

  • Fusion QC genes are reported as ProcControl in the Type column.

For QC and Fusion calling rules, see Quality control (QC) thresholds.

MET Exon 14 Skipping Assay

Nomenclature

  • One assay is specific to the exon 14 skipping detection in the MET gene called MET-MET.M13M15.

  • Two additional wild type assays are provided to inform the quality of a MET exon 14 skipping variant call. These are named MET.E6E7.WT and MET.E11E12.WT.

Analysis detail

  • MET exon 14 targets are reported as RNAExonVariant in the Type column.

  • For QC and MET exon 14 skipping calling rules, see Quality control (QC) thresholds.

Oncomine™ Breast cfDNA Research Assay v2

Metric

Description

Copy Number Variation

CNV Ratio

Should be interpreted as the fold amplification (gain) as detected by the assay. CNV specific amplicon (CCND1, ERBB2, FGFR1) coverage levels are compared to non-CNV amplicon coverage.

P-value

Significance of CNV Ratio measurement based on amplicon coverage variability (MAPD level) and magnitude of the pairwise coverage differences between the CNV and non-CNV amplicons. High coverage variability will result in less significant p-values.

For QC and CNV calling rules, see Quality control (QC) thresholds.

De novo (non‑hotspot) variant calling in TP53

Analysis detail

  • Panel includes approximately 80% coverage of the TP53 gene.

  • These variants are reported as PN (potentially novel) in the Info column. If the variant is reported as HS in the Info column, this variant is a hotspot specifically targeted by the breast panel.

  • These variant calls must be at a frequency of ≥0.5% to be reported in the analysis visualization. To view de novo TP53 variants at lower frequencies, download a VCF file from the visualization pages.