TABLE 1.
Technical comparison of gene expression analysis using formalin‐fixed paraffin‐embedded (FFPE) tissue with NanoString nCounter vs fresh tissue with DNA microarrays
| Feature | FFPE tissue with NanoString nCounter | Fresh tissue with cDNA microarrays |
|---|---|---|
| Maximum number of transcript targets | 800 | >47 000 a |
| Off‐the‐shelf panels available | Yes | Yes |
| Custom panels available | Yes | Yes |
| Recommended RNA input quantity | 100 ng | 50‐500 ng |
| Requires reverse transcription/amplification | No | Yes |
| Approximate assay turnaround time b | 24‐40 h | 25.5‐37.5 h |
| Analysis software provided by manufacturer | Yes c | Yes d |
| Ability to use same sample for histology and gene expression analysis, that is, ability for histomolecular integration | Yes | No |
| Immediate access to long‐term clinical follow‐up data on archival clinical samples (FFPE) | Yes | No |
| Food and Drug Administration approved |
Yes for platform Yes for specific clinical assays e |
No for platform Yes for specific clinical assay f |
| Approximate assay cost per sample g | $275 | $1000‐3000 |
| Integration with local (decentralized) clinical workflow | Simple due to local testing (no shipment of samples) on regulatory approved platform using simple open source analytics | Complex (shipment of sample to referral lab, no regulatory approval of platform, complex analytics) |
Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.
Dependent on multiple variables: instrument settings, RNA input quantity, technician experience, etc. Time excludes RNA extraction time and sample shipment time if applicable.
NanoString nSolver Analysis Software.
Affymetrix Transcriptome Analysis Console Software.
NanoString Prosigna Breast Cancer Prognostic Gene Signature Assay.
Roche AmpliChip CYP450 Test, a pharmacogenetics assay to determine the genotype of two cytochrome P450 enzymes: 2D6 and 2C19.
Including RNA isolation but excluding instrument expenses and labor for RNA extraction. Reagent cost varies with number of transcript targets and samples. Microarrays costs vary on scale of economy by provider.