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
Published online Feb 7, 2023. doi: 10.3748/wjg.v29.i5.780
RT-qPCR | Microarrays | RNA-seq | |
Basic steps | RNA isolation, genome DNA removal | RNA isolation, mRNA extraction | RNA isolation, mRNA extraction |
cDNA preparation with RT | cDNA library preparation | Quality and quantity check | |
Use of primers for amplification | Labeling with fluorescence | cDNA library preparation | |
Data analysis | Hybridization with transcript probes on slides | Sequencing | |
Scanning | Data analysis | ||
Image processing and data analysis | Validation | ||
Validation | |||
Throughput | Low | High | High |
Dynamic range/sensitivity | Widest/high | Narrow/low | Wide (compared to microarrays)/high |
Need for reference genome | No | No | Yes |
Known sequences of genes of interest | Required | Required | Not required |
Cost | Low | Low | High |
Advantages | Low cost, simple | High throughput | Ability to detect novel differential transcripts |
Highest dynamic range | Relatively low cost | Splice junctions, SNP, non-coding RNA | |
Gold standard | Good bioinformatics and statistical practices | ||
Downsides | Dependence on pre-existing knowledge of genes of interest | Difficulty to detect novel transcripts, non-coding RNA, splicing, or other dynamic natures of transcriptome | Large data storage |
High cost | |||
Low throughput | |||
Need for designing probes | |||
Low dynamic range | |||
Applications and main achievements in HCC recurrence-related research | Commonly 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] |
- Citation: Chiang CC, Yeh H, Lim SN, Lin WR. Transcriptome analysis creates a new era of precision medicine for managing recurrent hepatocellular carcinoma. World J Gastroenterol 2023; 29(5): 780-799
- URL: https://www.wjgnet.com/1007-9327/full/v29/i5/780.htm
- DOI: https://dx.doi.org/10.3748/wjg.v29.i5.780