Table 1.

Summary of advantages and disadvantages of current transcriptome assessment technologies

	Advantages	Disadvantages
QUANTITATIVE RT-PCR	Established ‘gold standard’ of quantitative expression profiling High sensitivity High dynamic range High reproducibility	Low throughput- limited number of genes/transcripts can be evaluated in a single experiment-often used for validation. Larger amounts of sample required compared to other methods Depends on fidelity of “housekeeping genes”
MICROARRAY	Well established method Widely available Medium to high throughput- thousands of genes/transcripts can be profiled in a single experiment High reproducibility (at mid to high expression range) Publicly available databases on thousands of microarray studies Relatively low cost	Reference genome required ie determines relative and not absolute expression Only detects sequences complementary to those on the array Lower dynamic range Lower specificity and sensitivity compared to other techniques Analysis can be difficult comparing datasets from different microarray platforms
NEXT GENERATION SEQUENCING	High throughput- entire transcriptome can be profiled in a single experiment Can identify novel transcripts Direct digital counting High dynamic range High sensitivity High reproducibility	Comparatively more expensive per sample Sequence-specific biases Complex /time-consuming computational data analysis
NANOSTRING® nCOUNTER ANALYSIS SYSTEM	Medium throughput- up to 800 genes/transcripts in a single experiment Direct digital counting No reverse transcription or RNA amplification step, therefore reducing technical biases High sensitivity and specificity High dynamic range High reproducibility Paraffin embedded tissues can be used Rapid turnaround time (from sample processing to data acquisition)	High upfront costs of code sets and consumables Prior knowledge of genes required Not ideal for non-targeted gene discovery studies-fewer genes/transcripts per experiment compared to NGS and/or microarray