Oncomine™ Childhood Cancer Research Assay

Copy number amplification

Gain-of-Function

Amplification

• SVTYPE = "CNV"

• FILTER = "GAIN"

• Occurs in a designated copy-gain gene

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

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

Promoter hotspot mutation

Gain-of-Function

Loss-of-Function

Hotspot

• Positive mutation call

• Transcript, location, and coding syntax occur in predefined promoter 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, nonframeshift block substitution

• Insertion impacts codons 770–783 of ERBB2

JAK2 exon 12 indel¹

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

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