Oncomine Focus Assay on Ion S5 System Analytical Performance - - PowerPoint PPT Presentation

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September 2016

Oncomine™ Focus Assay on Ion S5™ System— Analytical Performance

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

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Analytical Performance

Test Samples Analytical sensitivity, specificity and reproducibility

• f SNV detection at an allele frequency ≥ 5%

AcroMetrix™ Oncology Hotspot Control (AOHC), Horizon Quantitative Multiplex Reference Standard (HD200) Analytical sensitivity, specificity and reproducibility

• f indel detection at an allele frequency ≥10%

AcroMetrix™ Oncology Hotspot Control (AOHC) Analytical sensitivity, specificity and reproducibility

• f gene fusion detection

Mix of cell line derived RNA, Horizon ALK-RET-ROS1 Fusion RNA Reference Standard (HD784), FFPE tumor samples Analytical sensitivity, specificity and reproducibility

• f CNV detection from FFPE-derived samples

with ≥50% tumor content FFPE tumor samples

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

Purpose: To determine the sensitivity, specificity, and reproducibility of the Oncomine Focus Assay in detecting known variants present in commercially available reference and FFPE tissue materials.

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Single Nucleotide Variants (SNVs)

AOHC Sample Operator True Positive False Positive False Negative 1 CP 59 2 CP 57 2 3 CP 59 4 CP 59 5 CP 59 6 CP 53 6 7 KC 59 8 KC 59 9 KC 59 10 KC 59 11 KC 59 12 KC 59 Subtotal 700 8

PPV Sensitivity Reproducibility 99.63% 98.77% 99.6%

HD200 Operator True Positive False Positive False Negative 1 CP 9 2 CP 9 1 3 CP 9 1 4 CP 9 5 CP 9 6 CP 9 6 7 KC 9 1 8 KC 9 9 KC 8 1 10 KC 9 11 KC 9 12 KC 8 1 Subtotal 106 3 2

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

Overall performance:

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Insertions and Deletions (indels)

AOHC Sample Operator True Positive False Positive False Negative 1 KC 2 2 CP 2 3 KC 2 4 KC 2 5 KC 2 6 CP 2 7 KC 2 8 CP 2 9 CP 2 10 CP 2 11 KC 2 12 CP 2 Total 24

PPV Sensitivity Reproducibility 100% 100% 100%

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

Overall performance:

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Gene Fusions

Sample Expected Fusion(s) Replicates per

• perator

True Positive False Positive False Negative FFPE 1 TMPRSS2-ERG 4 (CP, KC) 8 FFPE 2 PTPRZ1-MET 4 (CP, KC) 8 FFPE 3 TPM3-NTRK1 4 (CP, KC) 8 HD784 EML4-ALK; CCDC6-RET; SLC34A2- ROS1 4 (CP, KC) 24 Cell line mix ALK-PTPN3; CCDC6-RET; EML4- ALK; SLC34A2-ROS1 4 (CP, KC) 32 Total — 80

PPV Sensitivity Reproducibility 100% 100% 100%

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

Overall performance:

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Copy Number Variants (CNVs)

FFPE Sample Cellularity (%) Amplification Operator (TP) Wild type (TN) 1 90% 4/4(CP), 4/4(KC): CCND1 4/4(CP), 4/4(KC): ERBB2 2 85% 4/4(CP), 4/4(KC): MYC 4/4(CP), 4/4(KC): ERBB2 3 85% 3/4(CP), 4/4(KC): MYCN 4/4(CP), 4/4(KC): CDK6 4 100% 4/4(CP), 4/4(KC): CDK4 4/4(CP), 4/4(KC): FGFR1 5 100% 4/4(CP), 4/4(KC): CDK6 4/4(CP), 4/4(KC): CDK4 6 75% 2/4(CP), 4/4(KC): PIK3CA 4/4(CP), 4/4(KC): MYC 7 80% 4/4(CP), 4/4(KC): PIK3CA 4/4(CP), 4/4(KC): MET 8 65% 4/4(CP), 4/4(KC): CCND1 4/4(CP), 4/4(KC): EGFR 9 70% 4/4(CP), 4/4(KC): MYC 4/4(CP), 4/4(KC): CDK6 10 100% 4/4(CP), 4/4(KC): EGFR 4/4(CP), 4/4(KC): ERBB2 11 65% 4/4(CP), 4/4(KC): EGFR NA Total — 81/84 80/80

PPV Sensitivity Reproducibility 100% 96.42% 96.42%

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

Overall performance:

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Performance Summary

Test Sensitivity Specificity (PPV) 2-Operator Reproducibility Analytical sensitivity, specificity and reproducibility of SNV detection at an allele frequency ≥ 5% 98.77% 99.63% 99.6% Analytical sensitivity, specificity and reproducibility of indel detection at an allele frequency ≥10% 100% 100% 100% Analytical sensitivity, specificity and reproducibility of gene fusion detection 100% 100% 100% Analytical sensitivity, specificity and reproducibility of CNV detection from FFPE-derived samples with ≥50% tumor content 96.42% 100% 96.42%

Summary: The Oncomine Focus Assay demonstrates high sensitivity, specificity and reproducibility in detecting known variants present in commercially available reference and FFPE tissue materials.