Oncomine™ Comprehensive Assay v3

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

Gene fusion

Gain-of-Function

Fusion

  • SVTYPE = "Fusion"

  • FILTER = "PASS"

  • Is a targeted fusion isoform

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

Intronic hotspot mutation

Gain-of-Function

Loss-of-Function

Hostpot

  • 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

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

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 insertion

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 COSM26720

ERBB2 exon 20 insertion

Gain-of-Function

ERBB2Exon20Insertion

  • Positive mutation call
  • Functional impact is nonframeshift insertion, nonframeshift block substitution
  • Insertion impacts codons 770-783 of ERBB2

MET exon 14 skipping

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