|
| Methods | Advantages | Limitations | Bioinformatics tools |
|
| Gene methylation analysis | Detects earlier stages of CRC and precancerous polyps with high sensitivity and specificity [35], genome-wide DNA methylation analysis with using NGS or microarrays [36] | Limited accuracy of discrimination [36] | ENCODE, modENCOD, Econsortia, QDNAseq, CancerLocator, CancerDetector [37] |
|
| Multibiomarker fecal cfDNA assays |
| Modified solid-phase minisequencing method, QuARTS method, and hemo quant test, oligonucleotide-based hybrid captures-based real-time PCR methods | A promising approach toward cost-efficient DNA diagnostics and comparative sequence analysis with high sensitivity (85%–91%) and specificity (60%–93%) comparable to that of FOBT for early detection and screening CRC [38–40] | Not declared | UMI-tools, MAGERI [41] |
| Infinium HumanMethylationEPIC BeadChip microarray | Increased genome coverage of regulatory regions, high reproducibility and reliability, easy to use, time-efficient and cost-effective [42] | | |
| Whole genome bisulfite sequencing (WGBS) | Single-nucleotide resolution of DNA methylation across the entire genome [43] | Not declared expensive, time consuming, and nonapplicable for high throughput [44] | Wg-blimp, msPIPE, MethGo [45–47] |
|
| qRT-PCR | Facility, quantification, high reproducibility, and accuracy similar to NGS and the agilent microarray [48–50] | Limited potency for low-expressed miRNAs detection, contamination, less precise in regions of homopolar (similar) bases [48–50] | QDNA-seq, WisecondorX, BIC-seq2, CNVkit [51–53] |
|
| RNA sequencing | Direct adapter-dependent ligation of less short noncoding RNAs (e.g., miRNAs, piRNAs, and endosiRNAs,) using NGS [54], cheaper, quicker, more accuracy compared to qPCR or Sanger sequencing [55] | Bias resulting from the impact of sequence on ligation especially for 5′ adapter ligation vs 3′ adapter ligation and contaminant PCR products devoid of each inserts [54] | FastQC, Cutadapt, STAR, HTseq [56] |
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