Review
Copyright ©The Author(s) 2023.
World J Gastroenterol. Feb 7, 2023; 29(5): 780-799
Published online Feb 7, 2023. doi: 10.3748/wjg.v29.i5.780
Table 1 Comparisons of real-time quantitative reverse transcription PCR, microarrays, and RNA-sequencing and their applications in hepatocellular carcinoma recurrence

RT-qPCR
Microarrays
RNA-seq
Basic stepsRNA isolation, genome DNA removalRNA isolation, mRNA extractionRNA isolation, mRNA extraction
cDNA preparation with RTcDNA library preparationQuality and quantity check
Use of primers for amplificationLabeling with fluorescencecDNA library preparation
Data analysisHybridization with transcript probes on slidesSequencing
ScanningData analysis
Image processing and data analysisValidation
Validation
ThroughputLowHighHigh
Dynamic range/sensitivityWidest/highNarrow/lowWide (compared to microarrays)/high
Need for reference genomeNoNoYes
Known sequences of genes of interestRequiredRequiredNot required
CostLowLowHigh
AdvantagesLow cost, simpleHigh throughputAbility to detect novel differential transcripts
Highest dynamic rangeRelatively low costSplice junctions, SNP, non-coding RNA
Gold standardGood bioinformatics and statistical practices
DownsidesDependence on pre-existing knowledge of genes of interestDifficulty to detect novel transcripts, non-coding RNA, splicing, or other dynamic natures of transcriptomeLarge data storage
High cost
Low throughput
Need for designing probes
Low dynamic range
Applications and main achievements in HCC recurrence-related researchCommonly used as a validation tool for confirming DGE results yielded from other high throughput analyses[56]Providing abundant information on carcinogenicity of primary HCC cells and carcinogenic stimuli; laid the foundation for our current understanding of the pathogenesis of HCC recurrence[18]Prospectively discovering DGE as potential novel classifiers for the carcinogenic profile of recurrent HCC cells; elucidating how HBV triggers HCC recurrence by interrupting the human genome[92,94,96]