Sample ID
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Name of the sequenced sample imported from a sequencing run.
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SNV/INDEL
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Gene
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HGNC reviewed official gene symbol.
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AA Chg
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Amino acid change resulting from non-synonymous DNA variant.
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Mutant Frequency %
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Frequency of mutant allele expressed as a percentage.
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Oncomine Variant Class
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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.
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Oncomine Gene Class
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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.
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Info
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HS (targeted hotspot) or PN (potentially novel TP53 variant). De novo variant calls available for the breast panel only.
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Genotype
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Genotype measured associated with a DNA variant call.
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Ref Allele
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Reference allele as defined in the human genome reference (hg19).
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Mut Molecular Cov.
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Molecular coverage of the mutant allele.
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WT Molecular Cov.
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Molecular coverage of the wild type allele from the reference genome.
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Depth
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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) %
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Quality control check for SNV/INDEL target regions based on molecular coverage.
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Transcript ID
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NCBI accession number for the transcript representing the gene target being measured.
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Locus
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Chromosome and position of detected variant. Click the hyperlink to open the Ion Reporter™ Genomic Viewer to the specified locus.
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CNV
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Gene
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Gene locus targeted for CNV measurement.
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Gain/Loss
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Detected copy number gain or loss.
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CNV ratio
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Ratio of measured CNV gene locus coverage relative to coverage on non-CNV loci.
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p-value
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Significance of CNV ratio measurement.
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Med. Mol Cov. Gene
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Median molecular coverage of targeted CNV gene.
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Med. Mol Cov. Ref
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Median molecular coverage of non-CNV reference loci.
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Med. Read Cov. Gene
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Median read coverage of targeted CNV gene.
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Med. Read Cov. Ref
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Median read coverage of non-CNV reference loci.
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QC Test
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Assay quality control as determined by amplicon coverage uniformity and number of amplicons remaining after outlier removal.
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Valid CNV Amplicons
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Number of CNV amplicons remaining after outlier removal.
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CNV Locus
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Chromosomal location of CNV gene being targeted.
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Fusion
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Variant (exons)
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Name of fusion targeted and respective acceptor and donor exons.
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Oncomine Driver Gene
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The gene thought to be associated with increased oncogenic properties due to inappropriate activation by the fusion.
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COSMIC/NCBI
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COSMIC mutation or NCBI accession number.
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Mol Cov. Mutant
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Median molecular coverage across fusion amplicon.
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Read Cov. Mutant
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Median read coverage across fusion amplicon.
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Detection
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Detection status from assay.
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QC Test
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Assay quality control measured from expression detection of housekeeping genes.
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Type
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Assay type (For example, Fusion, RNA exon variant (exon skipping), Proc Control).
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Locus
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Chromosomal locations of targets included in assay.
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Ratio To Wild Type
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Ratio molecular for exon skipping assay relative to wild type control amplicons.
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Norm count Within Gene
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Exon skipping assay coverage normalized to molecular coverage of wild type (WT) MET control amplicons. (Lung panel only).
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