Table 2.

Comparison of gene expression analysis techniques used for biopsy-based transcriptomics

Technique	Type of tissue sample	Maximum number of transcripts	Shortest realistic turnaround time	Cost	Advantages	Disadvantages	Validated for diagnostic use in transplantation
RT-qPCR	Usually requires RNA-later or Snap Frozen Tissue	Limited; depends on quantity if RNA	<8 h	Low per sample; Depends on number of target transcripts; requires staff, equipment, and expertise	Cheap, Easily Customisable	Genes need to be preselected, requires amplification step, not suitable for degraded RNA	No
RT-MLPA	Suitable for FFPE	60	<24 h	Low per sample; Depends on number of target transcripts; requires staff, equipment, and expertise	Cheap, Easily Customisable	Genes need to be preselected	No
Microarray	Usually requires RNA-later or Snap Frozen Tissue	47 000	48 h	High; As a send away test, does not require staff, equipment, expertise	Large selection of genes, suitable for Discovery Studies.	Requires a separate core of tissues, Not Suitable for Archived FFPE, currently available solutions require shipping to Central Lab	Yes (MMDx)
Nanostring	Suitable for FFPE	800	24--48 h	Intermediate; Depends on number of genes; requires staff, equipment, expertise	Suitable for Samples after routine histological processing or archived FFPE	Genes need to be preselected, access to Nanostring platform Required	No for Transplant (Yes in Cancer field)
RNA-Seq	Usually requires RNA-later or Snap Frozen Tissue	n/a Coding and noncoding RNA	Up to a week	High; Depends on number of reads	Whole Genome Sequencing, High Dynamic Range; suitable for discovery studies	Expensive, requires good quality RNA and library prep, data analysis time-consuming	No

FFPE, formalin-fixed paraffin-embedded.