Oncomine™ Comprehensive Assay Plus

Variant type

Oncomine™ Gene class

Oncomine™ Variant class

Annotation criteria

Copy number amplification

Gain-of-Function

Amplification

  • SVTYPE = "CNV"

  • FILTER = "GAIN"

  • Occurs in a designated copy-gain gene

Copy number deletion

Loss-of-Function

Deletion

  • SVTYPE = "CNV"

  • FILTER = "LOSS"

  • Occurs in a designated copy-loss gene

Copy number exon deletion

Loss-of-Function

ExonDeletion
  • SVTYPE = "CNV"

  • FILTER = "LOSS"

  • SUBTYPE = "BigDel"

Copy number exon duplication

Loss-of-Function

ExonDuplication

  • SVTYPE = "CNV"

  • FILTER = "GAIN"

  • SUBTYPE = "BigDup"

Loss of Heterozygosity

Loss-of-Function

LOH

  • SVTYPE = "LOH"

  • LOH = "1"

  • FILTER = "GAIN" or "LOSS" or "PASS"

Gene fusion

Gain-of-Function

Fusion

  • SVTYPE = "Fusion"

  • FILTER = "PASS"

  • Is a targeted fusion isoform

Non-targeted fusion

Gain-of-Function

NonTargetedFusion

  • SVTYPE = "Fusion"

  • FILTER = "PASS"

  • Non-Targeted field is present

  • NT_FUSION_IN_FRAME is not FALSE

  • NT_FUSION_DRIVER_INVOLVED is not FALSE

  • NT_FUSION_SECONDARY is not TRUE

RNA exon variant

Gain-of-Function

RNAExonVariant

  • SVTYPE = "RNAExonVariant" or "Fusion"

  • FILTER = "PASS"

  • Is a targeted RNA exon variant

Expression imbalance

Gain-of-Function

ExpressionImbalance

  • SVTYPE = "RNAExonTiles"

  • FILTER = "PASS"

  • Record meets Targeted Isoforms Detected Requirement

Long deletion

Loss-of-Function

LongDel

  • Positive mutation call

  • SVTYPE = "LongDel"

Loss-of-function truncating de novo mutation

Loss-of-Function

Truncating

  • Positive mutation call

  • Functional impact is frameshift block substitution, frameshift deletion, frameshift insertion, or nonsense

  • Occurs in a loss-of-function or unclassified gene

Missense hotspot mutation

Gain-of-Function

Loss-of-Function

Hotspot

  • Positive mutation call

  • Functional impact is missense

  • Transcript and codon position occur in predefined missense hotspot list

In-frame hotspot mutation

Gain-of-Function

Loss-of-Function

Hotspot

  • Positive mutation call

  • Function, transcript, and coding syntax occur in predefined in-frame hotspot list

Splice site hotspot mutation

Gain-of-Function

Loss-of-Function

Hotspot

  • Positive mutation call

  • Transcript, location, and exon occur in predefined splice site hotspot list

Intronic hotspot mutation

Gain-of-Function

Loss-of-Function

Hotspot

  • Positive mutation call

  • Transcript, location, and coding syntax occur in predefined intronic hotspot list

Promoter hotspot mutation

Gain-of-Function

Loss-of-Function

Hotspot

  • Positive mutation call

  • Transcript, location, and coding syntax occur in predefined promoter hotspot list

Synonymous hotspot mutation

Gain-of-Function

Loss-of-Function

Hotspot

  • Positive mutation call

  • Functional impact is synonymous

  • Transcript and coding syntax occur in predefined synonymous hotspot list

Gain-of-function truncating hotspot mutation

Gain-of-Function

Hotspot

  • Positive mutation call

  • Function, transcript, and coding syntax occur in predefined truncating hotspot list

  • Occurs in a gain-of-function gene

Loss-of-function truncating hotspot mutation

Loss-of-Function

Truncating

  • Positive mutation call

  • Function, transcript, and coding syntax occur in predefined truncating hotspot list

  • Occurs in a loss-of-function gene

MNV hotspot mutation

Gain-of-Function

Loss-of-Function

Hotspot

  • Positive mutation call

  • Transcript and coding syntax occur in MNV hotspot list

EGFR exon 19 deletion[1]

Gain-of-Function

EGFRExon19Deletion

  • Positive mutation call

  • Functional impact is nonframeshift deletion, nonframeshift block substitution

  • Deletion impacts codons 744-761 of EGFR

EGFR exon 20 insertion1

Gain-of-Function

EGFRExon20Insertion

  • Positive mutation call

  • Functional impact is nonframeshift insertion, nonframeshift block substitution

  • Insertion impacts codons 762-775 of EGFR or variant is in EGFR exon 20 insertion confirmed list

ERBB2 exon 20 insertion1

Gain-of-Function

ERBB2Exon20Insertion

  • Positive mutation call

  • Functional impact is nonframeshift insertion, or nonframeshift block substitution

  • Insertion impacts codons 770-783 of ERBB2

JAK2Exon12indel1

Loss-of-Function

JAK2Exon12Indel

  • Positive mutation call

  • Functional impact is nonframeshift deletion, nonframeshift insertion, or nonframeshift block substitution

  • Indel impacts codons 536-547 of JAK2

KIT exon 11 deletion1

Gain-of-Function

KITExon11Deletion

  • Positive mutation call

  • Functional impact is nonframeshift deletion, or nonframeshift block substitution

  • Deletion impacts codons 550-580 of KIT

  • Alternatively, mutation occurs in splice site flanking the 5' end of exon 11

KIT exon 11 insertion1

Gain-of-Function

KITExon11Insertion

  • Positive mutation call

  • Functional impact is nonframeshift insertion, or nonframeshift block substitution

  • Insertion impacts codons 550-580 of KIT

MET exon 14 skipping1

Gain-of-Function

METExon14Skipping

  • Positive mutation call

  • Location is splice site in MET exon 14, is intronic >= 4bp deletion in 30 nucleotides preceding MET exon 14, or variant is in MET Exon 14 Skipping confirmed list

PDGFRA exon 18 deletion1

Gain-of-Function

PDGFRAExon18Deletion

  • Positive mutation call

  • Functional impact is nonframeshift deletion, or nonframeshift block substitution

  • Deletion impacts codons 841-847 of PDGFRA

1 For more information, see Ion Torrent Class-Based Variants.