Custom panels

The Oncomine™ Variant Annotator plugin applies universal annotation rules for user-defined analysis workflows for use with custom Ion AmpliSeq™ and Ion AmpliSeq™ HD panels from AmpliSeq.com. To apply the rules, the Apply Oncomine Variant Annotator plugin option must be selected when an analysis workflow is created. For more information, see Steps in analysis workflow creation.

IMPORTANT! Because these annotations are generic, the annotations can be different from annotations that are generated with a system-installed analysis workflow.


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 Unclassified	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 Unclassified	Hotspot	Positive mutation call Transcript and ID occur in predefined intronic hotspot list
Synonymous hotspot mutation	Gain-of-Function Loss-of-Function Unclassified	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 Unclassified	Hotspot	Positive mutation call Transcript and coding syntax occur in predefined MNV hotspot list
CEBPA‑⁠bZIP^[1]	Loss-of-Function	CEBPA‑⁠bZIP	Positive mutation call Functional impact is nonframeshift deletion, nonframeshift insertion, or nonframeshift block substitution INDEL impacts codons 282–345 of CEBPA^[2]
CEBPA‑⁠N‑⁠terminal^[1]	Loss-of-Function	CEBPA‑⁠N‑⁠terminal	Positive mutation call Functional impact is nonframeshift deletion, nonframeshift insertion, nonframeshift block substitution, frameshift deletion, frameshift insertion, or frameshift block substitution INDEL impacts codons 1–120 of CEBPA^[2]
EGFR exon 19 deletion	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, 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]
FLT3 internal tandem duplication	Gain-of-Function	FLT3ITD	Positive mutation call Functional impact is a non-frameshift insertion in exon 14/15 of FLT3 or SVTYPE = "FLT3ITD"

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

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