Oncomine™ Tumor Mutation Load Assay


Variant type	Oncomine™ Gene class	Oncomine™ Variant class	Annotation criteria
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 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 and ID occur in predefined intronic hotspot list
MNV hotspot mutation	Gain-of-Function Loss-of-Function	Hotspot	Positive mutation call Transcript and coding syntax occur in 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^[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, nonframeshift block substitution Insertion impacts codons 770–783 of ERBB2^[2]
JAK2 exon 12 indel^[1]	Gain-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.