Skip to main content

Table 1 Comparison of traditional and new microarray platforms with sequencing approaches

From: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches

TechnologyTechnology/PlatformBiochemistryApprox. ThroughputMax. no. probes/primer pairsNo. of mapped ENSG IDsRead DepthsInput FFPE RNA (ng)*Approx. cost per sample (£)**Success rate of FF samples (n)Success rate of FFPE samples (n)
3′ RNA sequencingLexogen QuantSeqRNA → RT, oligodT priming from 3′ end, random priming towards 3′ end → amplification and barcoding → sequencing96 samples per 5 days55,76525,61010 M50090N/A98% (318)
QiaSeq UPX 3′ TranscriptomeRNA → RT, oligodT priming for cDNA synthesis →template switching for 2nd strand synthesis priming → fragmentation → end repair addition, adapter ligation → PCR to add indices → sequencing96 samples per 5 days42,55320,00015 M1050N/A94% (48)
Specific Targeted SequencingBioSpyder TempO-SeqRNA → annealed 50 bp detector oligos are ligated then amplified and barcoded → sequencing192 samples per 4 days19,30019,30012 M20 μm FFPE Section160N/A95% (38)
Ion Ampliseq TranscriptomeRNA → RT, multiplex PCR → sequence barcoding → emulsion PCR → sequencing of ~ 150 bp targets96 samples per 5 days20,80219,0598 M10160100% (108)76% (76)
Targeted ProbesNanostringRNA → hybridisation to fluorescent barcoded probes in solution → immobilised in nCounter cartridge → scan12 samples per day (800 genes)800800N/A50250N/A100% (12)
Newer MicroarrayAffymetrix Clariom SRNA → cRNA amplification → hybridisation to GeneChip → scan192 samples per 4 days211,300> 20,000N/A50100100% (3)100% (8)
Traditional MicroarrayAffymetrix U133A192 per day250,83311,827N/A50360100% (178)100% (286)
Illumina BeadChip HT-12 v3 / v4RNA → RT, amplification, biotinylation (NuGEN WT Ovation kit) → hybridisation to 50 bp probes on chip → scan96 samples per 1.5 days47,32322,571N/A150019591% (348)21% (206)
Full RNA SequencingRNA-seqRNA → fragmentation → RT → barcoded library construction → genome-wide full RNA sequencing8 samples per 5 days20,02518,57s1136 M paired reads2000250–500100% (52)100% (87)
  1. *Input RNA reflects quantities used in this study – for input ranges refer to the manufacturer’s guidelines
  2. **Estimated costs (£, UK December 2019) include library preparation and sequencing. Costs can vary by sample numbers and sequencing infrastructure