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Amplification Calling

TruSight Tumor 15 incorporates an algorithm to call CNVs that is designed for tumor samples without matched normals. It can detect amplifications in three genes: EGFR, ERBB2, and MET above a 1.6 fold change.

Amplification output for TruSight Tumor 15 is reported in the amplifications VCF file. Amplifications are reported using the semiquantitative AmpScore metric. A higher AmpScore reflects both a higher confidence in the likelihood of an amplification and a higher expected fold change. Each amplification gene is reported in one of the following four groups, with thresholds as shown in Table Amplification Thresholds. For more information on the amplification VCF file, see Amplification VCF File.

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Samples with AmpScore ≥ 100 are considered to be amplified, and are reported as ALT=<DUP>, FILTER=PASS (ie, X ≥ Amplification Threshold)

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Samples with borderline AmpScores are noted in the VCF as ALT=<DUP> FILTER=NoCall calls. These samples are not determined to be amplified or normal. (ie, AmplificationThreshold > X ≥ PositiveThreshold)

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Samples with normal read depth are called as ALT=., FILTER=PASS (ie, PositiveThreshold > X ≥ NegativeThreshold)

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Samples with very low AmpScore are called as ALT=<DEL>, FILTER=NoCall. These samples are suspected deletions. (ie, NegativeThreshold ≥ X)

note

A gene amplification in a sample with an AmpScore much greater than 100 can cause secondary amplifications to not be detected, or cause normally present genes to be called low confidence deletions.

Table 1 Amplification Thresholds
Gene	Amplification Threshold	Positive Threshold	Negative Threshold
EGFR	100	91.51	65.40
ERBB2	100	93.40	81.13
MET	100	97.17	72.64

For Research Use Only. Not for use in diagnostic procedures.