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

Oncomine™ Focus Assay on Ion S5™ System— Analytical Performance September 2016 The world leader in serving science For Research Use Only. Not for use in diagnostic procedures.

Analytical Performance 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. Test Samples Analytical sensitivity, specificity and reproducibility AcroMetrix™ Oncology Hotspot Control (AOHC), of SNV detection at an allele frequency ≥ 5% Horizon Quantitative Multiplex Reference Standard (HD200) Analytical sensitivity, specificity and reproducibility AcroMetrix™ Oncology Hotspot Control (AOHC) of indel detection at an allele frequency ≥10% Analytical sensitivity, specificity and reproducibility Mix of cell line derived RNA, of gene fusion detection Horizon ALK-RET-ROS1 Fusion RNA Reference Standard (HD784), FFPE tumor samples Analytical sensitivity, specificity and reproducibility FFPE tumor samples of CNV detection from FFPE-derived samples with ≥50% tumor content 2 For Research Use Only. Not for use in diagnostic procedures.

Single Nucleotide Variants (SNVs) Overall performance: PPV Sensitivity Reproducibility 99.63% 98.77% 99.6% AOHC Operator True False False HD200 Operator True False False Sample Positive Positive Negative Positive Positive Negative 1 CP 59 0 0 1 CP 9 0 0 2 CP 57 0 2 2 CP 9 1 0 3 CP 59 0 0 3 CP 9 1 0 4 CP 59 0 0 4 CP 9 0 0 5 CP 59 0 0 5 CP 9 0 0 6 CP 53 0 6 6 CP 9 0 6 7 KC 59 0 0 7 KC 9 1 0 8 KC 59 0 0 8 KC 9 0 0 9 KC 59 0 0 9 KC 8 0 1 10 KC 59 0 0 10 KC 9 0 0 11 KC 59 0 0 11 KC 9 0 0 12 KC 59 0 0 12 KC 8 0 1 Subtotal 700 0 8 Subtotal 106 3 2 3 For Research Use Only. Not for use in diagnostic procedures.

Insertions and Deletions (indels) Overall performance: PPV Sensitivity Reproducibility 100% 100% 100% AOHC Operator True Positive False Positive False Negative Sample 1 KC 2 0 0 2 CP 2 0 0 3 KC 2 0 0 4 KC 2 0 0 5 KC 2 0 0 6 CP 2 0 0 7 KC 2 0 0 8 CP 2 0 0 9 CP 2 0 0 10 CP 2 0 0 11 KC 2 0 0 12 CP 2 0 0 Total 24 0 0 4 For Research Use Only. Not for use in diagnostic procedures.

Gene Fusions Overall performance: PPV Sensitivity Reproducibility 100% 100% 100% Sample Expected Fusion(s) Replicates per True False False operator Positive Positive Negative FFPE 1 TMPRSS2-ERG 4 (CP, KC) 8 0 0 FFPE 2 PTPRZ1-MET 4 (CP, KC) 8 0 0 FFPE 3 TPM3-NTRK1 4 (CP, KC) 8 0 0 HD784 EML4-ALK; CCDC6-RET; SLC34A2- 4 (CP, KC) 24 0 0 ROS1 Cell line mix ALK-PTPN3; CCDC6-RET; EML4- 4 (CP, KC) 32 0 0 ALK; SLC34A2-ROS1 Total — 80 0 0 5 For Research Use Only. Not for use in diagnostic procedures.

Copy Number Variants (CNVs) Overall performance: PPV Sensitivity Reproducibility 100% 96.42% 96.42% 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 6 For Research Use Only. Not for use in diagnostic procedures.

Performance Summary Summary : The Oncomine Focus Assay demonstrates high sensitivity, specificity and reproducibility in detecting known variants present in commercially available reference and FFPE tissue materials. 2-Operator Test Sensitivity Specificity (PPV) Reproducibility Analytical sensitivity, specificity and reproducibility of SNV detection at an allele 98.77% 99.63% 99.6% frequency ≥ 5% Analytical sensitivity, specificity and reproducibility of indel detection at an 100% 100% 100% allele frequency ≥10% 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 96.42% 100% 96.42% content 7