Detailed analysis metrics

Metric

Description

Sample ID

Name of the sequenced sample imported from a sequencing run.

SNV/INDEL

Gene

HGNC reviewed official gene symbol.

AA Chg

Amino acid change resulting from non-synonymous DNA variant.

Mutant Frequency %

Frequency of mutant allele expressed as a percentage.

Oncomine Variant Class

Variant class annotation that provides a high-level summary of the variant type (hotspot, fusion, amplification, and so on). The annotation is included when the Oncomine™ Variant Annotator plugin is run in Ion Reporter™ Software.

Oncomine Gene Class

Variant gene functional annotation that provides a high-level summary of gene type (Gain-of-Function, Loss-of-Function, or Unclassified). The annotation is included when the Oncomine™ Variant Annotator plugin is run in Ion Reporter™ Software.

Info

HS (targeted hotspot) or PN (potentially novel TP53 variant). De novo variant calls available for the breast panel only.

Genotype

Genotype measured associated with a DNA variant call.

Ref Allele

Reference allele as defined in the human genome reference (hg19).

Mut Molecular Cov.

Molecular coverage of the mutant allele.

WT Molecular Cov.

Molecular coverage of the wild type allele from the reference genome.

Depth

Total read coverage across amplicon containing SNV/INDEL hotspot locations. Count of chip-level reads aligned at this locus that participate in variant calling.

Note: This description applies to both, Ion AmpliSeq™ HD and non‑Ion AmpliSeq™ HD analyses.

QC Test (LOD) %

Quality control check for SNV/INDEL target regions based on molecular coverage.

Transcript ID

NCBI accession number for the transcript representing the gene target being measured.

Locus

Chromosome and position of detected variant. Click the hyperlink to open the Ion Reporter™ Genomic Viewer to the specified locus.

CNV

Gene

Gene locus targeted for CNV measurement.

Gain/Loss

Detected copy number gain or loss.

CNV ratio

Ratio of measured CNV gene locus coverage relative to coverage on non-CNV loci.

p-value

Significance of CNV ratio measurement.

Med. Mol Cov. Gene

Median molecular coverage of targeted CNV gene.

Med. Mol Cov. Ref

Median molecular coverage of non-CNV reference loci.

Med. Read Cov. Gene

Median read coverage of targeted CNV gene.

Med. Read Cov. Ref

Median read coverage of non-CNV reference loci.

QC Test

Assay quality control as determined by amplicon coverage uniformity and number of amplicons remaining after outlier removal.

Valid CNV Amplicons

Number of CNV amplicons remaining after outlier removal.

CNV Locus

Chromosomal location of CNV gene being targeted.

Fusion

Variant (exons)

Name of fusion targeted and respective acceptor and donor exons.

Oncomine Driver Gene

Cancer driver gene descriptions as reported when the Oncomine™ Variant Annotator plugin is run in Ion Reporter™ Software.

COSMIC/NCBI

COSMIC mutation or NCBI accession number.

Mol Cov. Mutant

Median molecular coverage across fusion amplicon.

Read Cov. Mutant

Median read coverage across fusion amplicon.

Detection

Detection status from assay.

QC Test

Assay quality control measured from expression detection of housekeeping genes.

Type

Assay type (For example, Fusion, RNA exon variant (exon skipping), Proc Control).

Locus

Chromosomal locations of targets included in assay.

Ratio To Wild Type

Ratio molecular for exon skipping assay relative to wild type control amplicons.

Norm count Within Gene

Exon skipping assay coverage normalized to molecular coverage of wild type (WT) MET control amplicons. (Lung panel only).