FFPE Tissue sample

RNA biomarkers can be effective indicators of biological processes, pathological processes, or potential responses to treatment. While RNA biomarkers are often identified using profiling methods such as RNA-seq or microarray, biomarker verification requires robust, cost-effective techniques that enable reproducible measurement of differential expression. QuantiGene Gene Expression Assays are ideal for verification of gene expression biomarkers.

QuantiGene Assays can quickly and robustly verify gene expression biomarkers:

  • Demonstrated concordance with biomarker discovery and expression profiling techniques such as whole-transcriptome microarrays (Hall, Linton)
  • Measure up to 80 genes simultaneously from classically difficult sample types such as formalin-fixed paraffin-embedded (FFPE) tissue sections or whole blood, with minimal sample preparation required

QuantiGene Assays are ideal for use with FFPE tissue samples because:

  • Probe hybridization approach is insensitive to formalin-induced chemical modifications such as RNA-protein crosslinking
  • Several short capture and detection probes enable the measurement of degraded RNA, with 28S:18S ratios as low as 0.1
  • Compatible with H&E-stained FFPE tissue sections

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Product image of Invitrogen Immune Response 80-Plex Human QuantiGene Plex Panel

NEW Invitrogen Immune Response 80-Plex Human QuantiGene Plex Panel

Analyze 80 cytokine, chemokine, and growth factor RNA targets simultaneously for efficient immune response profiling, biomarker discovery, and validation.

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Technical validity of QuantiGene Plex assay using sections from fixed breast cancer tissue

Publication showing QuantiGene Plex assay using sections from fixed breast cancer tissue

The hybridization and signal-amplification gene expression technology QuantiGene Plex is especially well suited for FFPE because it avoids the issues that are generated by FFPE RNA cross-linkage. It does this by hybridizing RNA directly, avoiding the need for RNA extraction and also by using signal rather than enzymatic amplification methods.

The multiple small oligo probes used for QuantiGene hybridization can generate a signal even if a particular region of the target RNA is degraded or fails to hybridize.

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QuantiGene Plex 384-well example data

The QuantiGene Plex 384-well assay is designed to increase sample throughput and decrease hands-on time while allowing for fast time to results for screening projects. Below is example data that was generated using the 384-well format using the recommended equipment listed.

Stimulation of cytokine production in HeLa cells

Cytokine production in cultured HeLa cells was stimulated using a Cell Stimulation Cocktail and monitored for various time points up to 24 hours. In this experiment, a full 80-plex panel was used for screening purposes focused on cytokine, and chemokine biomarkers.

Figure 2. Normalized gene expression of various targets in HeLa cells at different time points post stimulation with a Cell Stimulation cocktail. Y-axis: Average normalized expression; x-axis: mRNA targets; z-axis: time points of stimulation. Only a subset of gene targets tested is being displayed. HeLa cells were cultured in a 384-well format and stimulated with a Cell Stimulation cocktail for various times up to 24h (1h, 2h, 4h, 24h). Unstimulated cells served as baseline control. At the indicated time points, cells were lysed according to the QuantiGene sample prep protocol for cell lysates using liquid handling (Thermo Fisher Platemate). After all samples from all time points were prepared, the QuantiGene Plex 384-well assay was performed. Chart illustrates the normalized gene expression results.

The power of using branched-DNA technologies to validate melanoma biomarkers

Figure 3. QuantiGene Plex mRNA cluster analysis. Genes with the best 7 P values were analyzed using an unsupervised cluster analysis. Note: Sample 17 was not a melanoma sample (lymph node with pigmented histiocytes).



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