Oncology Biomarker Panel

Transcription

1 Oncology Biomarker Panel

2 HTG EdgeSeq Oncology Biomarker Panel The HTG EdgeSeq Oncology Biomarker Panel profiles tumor samples in order to identify therapeutic targets and drug response markers using an NGS-based gene expression assay powered by HTG EdgeSeq chemistry. 2,0 genes, 2 groups and pathways AMPK Pathway Angiogenesis Apoptosis Cardio Toxicity Cell Cycle Cluster of Differentiation DMPK DNA Repair EGF / PDGF Pathway EGFR / HER Pathway FGGR Pathway Hedgehog Pathway Hypoxia Immuno Oncology Includes 1 key drug targets JAX / STAT Pathway MAP Kinase Pathway NFkB Pathway Other Genes of Interest Pl3K AKT Pathway Receptors Stem Cells Stress Toxicity Tissue Specific WNT Pathway AKT CD1 CD30 CTLA EGFR FGFR1 FGFR2 HER2 HER3 IGFR1 IGFR2 MEK MET mtor PD-1 PDL-1 PI3K Generate high quality tumor profiles from FFPE through extraction-free chemistry Counts KLK3 (PSA) Cancer Marker Counts 30,000,000 CDX2 Colorectal Cancer Marker Counts 1,00 1, Counts KRT and Cancer Marker Counts,000,000 2,000 NKX2-1 (TTF-1) Cancer Marker Counts 1,000 00,, and FFPE tissue were processed with the HTG EdgeSeq Oncology Biomarker Panel at the same sample input amount. Sequencing was performed on the Illumina MiSeq instrument. Data for selected tissue-specific markers are shown plotted with samples on the x-axis and raw counts on the y-axis.

3 The routine use of complex molecular profiling is enabled by the portfolio of automated HTG EdgeSeq products, which includes the HTG EdgeSeq Oncology Biomarker Panel. Achieve consistent and reproducible performance through automation A. Different days, same instruments... r= Day 1 r=0. r=0.3 Day 2 r=0. r=0. r=0. Day 3 B. Same day, different instruments Instrument 1... r=0.. r=0.... r=0. Instrument 2 r=0.1 r=0. r=0.1 Instrument 3 Figure 1. To demonstrate robust chemistry and automation, 2 ng of universal RNA was processed using the HTG EdgeSeq Oncology Biomarker Panel across 3 days and 3 HTG EdgeSeq systems. Pearson correlation, r, 0. for day-to-day replicates (A) and 0. for instrument vs instrument replicates (B). Data was log 2 transformed and correlation plots were prepared.

4 Gain the most from samples with minimal sample utilization. A. Total RNA ( ng) B. Cell line (1,-23 cells) r=0.2 r=0. r=0. r=0.2 r=0. r= ng RNA 2 1, cells 0,000 0,000 0,000 0,000 r=0.2 r=0. r=0. r=0.2 r=0. r=0.1 1,000 0,000.2 ng RNA 1,000 0,000 3 cells 0,000 0,000,000 0,000 2,000,000 r=0. r=0. r=0. r= ng RNA r=0.3 r=0.3 3,000 30,000 2,000 1,000,000 0,000 r=0. r=0.0 r=0. r=0.1 cells r=0. r=0. 22,000 1, ng RNA 1,000, cells,000 2,000,000 0,000 0,000,000 0,000,000 1,000 0,000 0, ,000 2,000,000 3,000 Figure 2. To measure the sensitivity of the assay, titration experiments were performed to (1) establish linearity (not shown) and (2) determine sample input limitations. -point titrations were performed with total RNA (A) and a human cell line (B). Expression profile remained consistent across the titration series demonstrating excellent correlation as measured by Pearson is coefficient of correlation, r. A. FFPE B. FFPE C. Melanoma FFPE. r=0. r=0.1 r= mm 2 FFPE Tissue 1. mm 2 FFPE Tissue 1. mm 2 FFPE Melanoma Tissue.. r=0. r=0.1 r= mm 2 FFPE Tissue 12. mm 2 FFPE Tissue 12. mm 2 FFPE Melanoma Tissue Figure 3. Three FFPE tissues were lysed and processed with the HTG EdgeSeq Oncology Biomarker Panel at two sample inputs amounts (equivalent to 12. mm 2 and 1. mm 2 ), and sequenced on the Illumina MiSeq sequencing platform. Across all sample types, data correlations between the two input amounts were above 0. as measured by Pearson correlation, r.

5 HTG EdgeSeq Oncology Biomarker Panel Sample Requirements Sample Type FFPE Tissue Cell Lines 20,000 cells PAXgene 32 µl Purified RNA 1. ng Optimal Sample Input mm 2 of a µm section Process Controls Positive Negative positive probes ANT probes Endogenous Controls ACTB EE1G OAZ1 RPL SOD1 ATPF1 GAPDH PPIA RPS TBP DDX NCL RPL3 SLC2A3 YWHAZ Ordering Information Catalog # Product Name Description illumina (ILM) Next-Generation Sequencing Systems HTG EdgeSeq OBP ILM (2x) 2 plates, samples/plate HTG EdgeSeq OBP ILM (x) plates, samples/plate HTG EdgeSeq OBP ILM (1x2) 1 plate, 2 samples/plate HTG EdgeSeq OBP ILM (x2) plates, 2 samples/plate HTG EdgeSeq OBP ILM (1x) 1 plate, samples/plate Ion Torrent (IT) Next-Generation Sequencing Systems HTG EdgeSeq OBP IT (2x) 2 plates, samples/plate HTG EdgeSeq OBP IT (x) plates, samples/plate HTG EdgeSeq OBP IT (1x2) 1 plate, 2 samples/plate HTG EdgeSeq OBP IT (x2) plates, 2 samples/plate Visit for a detailed gene list. Ordering information orders@htgmolecular.com or contact your local sales representative. C US

6 Empowering precision medicine at the local level HTG Molecular Diagnostics, Inc. 330 E. Global Loop, Tucson, AZ 0 Call info@htgmolecular.com Website For Research Use Only. Not for use in diagnostic procedures. HTG EdgeSeq, HTG Edge and qnpa are trademarks of HTG Molecular Diagnostics, Inc. Any other trademarks or trade names used herein are the intellectual property of their respective owners. Revision 3: 1-JUL-201