HTG EdgeSeq Oncology Biomarker Panel 

Profile tumor samples in order to identify therapeutic targets and drug response markers using an NGS-based gene expression assay powered by the HTG EdgeSeq chemistry.  

Thousands of genes (2,560), 24 groups and pathways

Includes Key Drug Targets

AKT EGFR HER3 MEK PD-1
CD19 FGFR1 IGFR1 MET PDL-1
CD30 FGFR2 IGFR2 mTOR PI3K
CTLA4 HER2      

Select and download available oncology biomarker genes and pathways

 

Additional Features | Benefits

  • Low sample input | Consume only a single 5 µm FFPE tissue section
  • Results in 36 hours | Gain insights faster with minimal hands-on manipulation
  • Rapid alignment and data assembly | Obtain quantitative gene expression from sequence data in 30 minutes

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.

Performance

Achieve consistent and reproducible performance through automation

Figure 1. To demonstrate robust chemistry and automation, 25 ng of universal RNA was processed using the HTG EdgeSeq Oncology Biomarker Panel across 3 days and 3 HTG EdgeSeq systems. Pearson correlation, r, averaged 0.97 for technical replicates (A), 0.985 for day-to-day replicates (B) and 0.988 for instrument vs instrument replicates (C). Data was log(2) transformed and correlation plots were prepared.

 

Gain the most from samples with minimal sample utilization

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. 4-point titrations were performed with total RNA (A) and a human cell line (B). Fold expression changes remained consistent across the titration series through excellent correlation as measured by Pearson correlation, r. 

 

Generate comprehensive data from very small sample inputs

Figure 3.  Three types of FFPE tissue were processed with the HTG EdgeSeq Oncology Biomarker Panel at two sample inputs, 12.5 mm2 and 1.56 mm2 and sequenced on the Illumina MiSeq sequencing platform running v3 reagent chemistry. Across all sample types, data correlations between the two input amounts remained above 0.98 as measured by Pearson correlation, r. 

 

Generate high quality tumor profiles from FFPE through extraction-free chemistry

Figure 4.  Breast, Colon, Lung and Prostate FFPE tissue were processed with the HTG EdgeSeq Oncology Biomarker Panel. Sequencing was performed on the Illumina MiSeq instrument running v3 reagent chemistry. Data was first normalized against all reads per sample, and relative (%) expression measured across tissue types.

 

Product Specifications

Sample Type Sample Input
FFPE Tissue A single 5 µm FFPE tissue section 
Cells > 3,000 cells
PAXgene 500 µl
Extracted RNA > 25 ng
Housekeepers

ACTB, EE1G, OAZ1, RPL6, SOD1

ATP5F1, GAPDH, PPIA, RPS7, TBP

DDX5, NCL, RPL38, SLC25A3, YWHAZ

Controls  
Negative 5 ANT probes
Positive 4 POS1 assay controls
Catalog # Description
Illumina 
916-002-208 HTG EdgeSeq Oncology Biomarker Panel (2x8)
916-002-008 HTG EdgeSeq Oncology Biomarker Panel (4x8)
916-002-224 HTG EdgeSeq Oncology Biomarker Panel (1x24)
916-002-024 HTG EdgeSeq Oncology Biomarker Panel (4x24)
916-002-096 HTG EdgeSeq Oncology Biomarker Panel (1x96)
Ion Torrent 
916-002-308 HTG EdgeSeq Oncology Biomarker Panel (2x8)
916-002-108 HTG EdgeSeq Oncology Biomarker Panel (4x8)
916-002-324 HTG EdgeSeq Oncology Biomarker Panel (1x24)
916-002-124 HTG EdgeSeq Oncology Biomarker Panel (4x24)

2 – 4 million aligned sequencing recommended per sample are recommended.

Ordering

orders@htgmolecular.com

Learn more about HTG EdgeSeq products and chemistry

HTG EdgeSeq miRNA Expression Profiling
HTG EdgeSeq mRNA Expression Profiling
HTG EdgeSeq Future Applications
HTG EdgeSeq Chemistry

Resources:

Biopharma and HTG Molecular Diagnostics brochure
HTG EdgeSeq Oncology Biomarker Panel sales sheet
HTG EdgeSeq Oncology Biomarker Panel brochure
HTG EdgeSeq Oncology Biomarker Panel gene list

Posters:

HTG EdgeSeq Oncology Biomarker Panel Assay, an NGS-based gene expression assay for measuring 2,532 oncology-related genes in FFPE tissue in different sample types

 

HTG's GenomeWeb webinar: Expression-based Profiling of Challenging FFPE Tumor Samples

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

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Last updated: 03/10/2017 - 13:33