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"
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	Truncating	Positive mutation call SVTYPE = "LongDel"
Loss-of-function truncating de novo mutation	Loss-of-Function Unclassified	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 Unclassified	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 Unclassified	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 and ID occur in predefined intronic 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^[2]
EGFR exon 20 insertion^[1]	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^[2]
ERBB2 exon 20 insertion^[1]	Gain-of-Function	ERBB2Exon20Insertion	Positive mutation call Functional impact is nonframeshift insertion, or nonframeshift block substitution Insertion impacts codons 770-783 of ERBB2^[2]
JAK2 exon 12 INDEL^[1]	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^[2]
KIT exon 11 deletion^[1]	Gain-of-Function	KITExon11Deletion	Positive mutation call Functional impact is nonframeshift deletion, or nonframeshift block substitution Deletion impacts codons 550-580 of KIT^[2] Alternatively, mutation occurs in splice site flanking the 5' end of exon 11
KIT exon 11 insertion^[1]	Gain-of-Function	KITExon11Insertion	Positive mutation call Functional impact is nonframeshift insertion, or nonframeshift block substitution Insertion impacts codons 550-580 of KIT^[2]
MET exon 14 skipping^[1]	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 deletion^[1]	Gain-of-Function	PDGFRAExon18Deletion	Positive mutation call Functional impact is nonframeshift deletion, or nonframeshift block substitution Deletion impacts codons 841-847 of PDGFRA^[2]

¹ For more information, see Ion Torrent class-based variants.

² In some cases the assay design may not cover the entire codon range.