Figure 1.
Figure 2.
Figure 3.
Figure 4.
Sensitivity (%) and specificity (%) of each identified DNA methylation marker
| SI No. | DOI | Sample type | Markers identified | Sensitivity (%) | Specificity (%) |
|---|---|---|---|---|---|
| 1 | 10.1016/j.ygeno.2020.06.007 | FFPE tissue; Blood plasma | SFMBT2 | 92.20 | 94.60 |
| VAV3-AS1 | 92.20 | 89.20 | |||
| ZNF132 | 86.30 | 94.60 | |||
| KCNQ5 | 90.20 | 89.20 | |||
| ITGA4 | 90.20 | 94.60 | |||
| THBD | 86.30 | 94.60 | |||
| FBN1 | 86.30 | 91.90 | |||
| EVC | 84.30 | 86.50 | |||
| C9orf50 | 94.10 | 86.50 | |||
| TWIST1 | 72.60 | 100.0 | |||
| ZNF304 | 66.70 | 100.0 | |||
| 2 | 10.7150/jca.57114 | Blood plasma | SEPT9 | 75.80 | 94.70 |
| SDC2 | 60.40 | 86.80 | |||
| 3 | 10.1002/1878-0261.12942 | Tissue DNA samples; plasma cfDNA | SEPT9 | 48.20 | 91.50 |
| BCAT1/IKZF1 | 66.00 | 95.00 | |||
| cg10673833 | 89.70 | 86.80 | |||
| 4 | 10.1038/s41598-023-35631-5 | FFPE tissue | BCAT1 | 73.30–75.20 | 92.40–94.30 |
| GATA5 | 73.30–74.30 | 91.40–92.40 | |||
| IKZF1 (V1) | 75.20 | 93.30 | |||
| IKZF1 (V2) | 70.50 | 95.20 | |||
| IRF2 | 81.90–82.90 | 90.5–91.40 | |||
| ITGA4 | 82.90 | 88.60–89.50 | |||
| HIC1 | 43.80 | 78.10 | |||
| NPY | 80.00 | 90.50 | |||
| SDC2 | 75.20–76.20 | 94.30–95.20 | |||
| SEPT9 | 70.50–72.40 | 88.60–90.50 | |||
| WIF1 | 65.70 | 96.20 | |||
| 5 | 10.1002/cam4.6224 | Blood plasma | SEPT9 | 50.00 | 90.00 |
| BMP3 | 40.00 | 90.00 | |||
| 6 | 10.1038/s41416-023-02337-4 | Blood plasma | AGBL4 | 40.30 | 77.50 |
| ALX4 | - | - | |||
| BCAT1 | 43.10 | 64.80 | |||
| BMP3 | 41.70 | 76.10 | |||
| FLI1 | 38.90 | 76.10 | |||
| GRIA4 | - | - | |||
| IKZF1 | 43.10 | 78.90 | |||
| NDRG4 | 62.50 | 47.90 | |||
| NPTX2 | 48.60 | 74.60 | |||
| PRIMA1 | - | - | |||
| RARB | - | - | |||
| SEPT9 | 48.60 | 69.00 | |||
| SDC2 | 41.70 | 70.40 | |||
| SFRP1 | 40.30 | 77.50 | |||
| SFRP2 | 31.90 | 85.90 | |||
| SLC8A1 | 45.80 | 73.20 | |||
| TWIST1 | - | - | |||
| VIM | 45.80 | 70.40 | |||
| WNT5A | 51.40 | 60.60 | |||
| ZNF331 | 50.00 | 66.20 | |||
| 7 | 10.1002/cac2.12478 | Blood plasma | SEPT9 | 40.00 | 96.00 |
| RNF180 | 46.20 | 87.30 | |||
| 8 | 10.62347/TPTQ3682 | Blood plasma | SEPT9 | 68.00 | 80.00 |
| ATXN1 | - | - | |||
| PCDH10 | - | - | |||
| MYO1G | - | - | |||
| NGFR | - | - | |||
| IKZF1 | - | - | |||
| ITGA4 | - | - | |||
| 9 | 10.1186/s12920-024-01893-9 | Blood plasma | HAND1 | 93.33 | 80.00 |
| SEPT9 | 66.67 | 86.67 |
Methods used for the identification of CRC DNA methylation markers
| SI No. | DOI | Sample type | Extraction & isolation method | Quantification of methylation method | Markers identified |
|---|---|---|---|---|---|
| 1 | 10.1016/j.ygeno.2020.06.007 | FFPE tissue; Blood plasma | AllPrep DNA/RNA FFPE Kit (QIAGEN) | RT-PCR | SFMBT2, VAV3-AS1, ZNF132, KCNQ5, ITGA4, THBD, FBN1, EVC, C9orf50, TWIST1, ZNF304 |
| 2 | 10.7150/jca.57114 | Blood plasma | QIAamp DNA Blood Mini Kit (QIAGEN) | Bisulfite Sequencing and PCR Assays | SEPT9, SDC2 |
| 3 | 10.1002/1878-0261.12942 | Tissue samples; plasma | MagMAX Cell-Free DNA Isolation Kit (Thermo Fisher Scientific) | Bisulfite conversion and targeted sequencing | SEPT9, BCAT1, IKZF1, cg10673833 |
| 4 | 10.1038/s41598-023-35631-5 | FFPE tissue | QIAamp DNA Kit (QIAGEN) | ddPCR using Bio-Rad QX200 system | BCAT1, GATA5, IKZF1 (V1), IKZF1 (V2), IRF4, ITGA4, HIC1, NPY, SDC2, SEPT9, WIF1 |
| 5 | 10.1002/cam4.6224 | Blood plasma | QIAmp circulating Nucleic Acid Kit (QIAGEN) | ddPCR | SEPT9, BMP3 |
| 6 | 10.1038/s41416-023-02337-4 | Blood Plasma | MagMAX Cell-Free DNA Isolation Kit (Thermo Fisher Scientific) | MSP with Zymo Lightning Conversion Reagent | AGBL4, ALX4, BCAT1, BMP3, FLI1, GRIA4, IKZF1, NDRG4, NPTX2, PRIMA1, RARB, SEPT9, SDC2, SFRP1, SFRP2, SLC8A1, TWIST1, VIM, WNT5A, ZNF331 |
| 7 | 10.1002/cac2.12478 | Blood plasma | QIAamp Circulating Nucleic Acid Kit (QIAGEN) | qPCR | SEPTIN9, RNF180 |
| 8 | 10.62347/TPTQ3682 | Blood plasma | MagMAX Cell-Free DNA Isolation Kit (Thermo Fisher Scientific) | MSP with Zymo Lightning Conversion Reagent | SEPT9, ATXN1, PCDH10, MYO1G, NGFR, IKZF1, ITGA4 |
| 9 | 10.1186/s12920-024-01893-9 | Blood plasma | AddPrep Genomic DNA Extraction Kit (Addbio) | qMS-PCR | HAND1, SEPT9 |
Master list of CRC DNA methylation markers and their corresponding sample types based on the list of eligible research articles
| SI no. | Title, Year | Reference no. | Sample type | Population | Age range (years) | CRC stage | DNA methylation marker | ||
|---|---|---|---|---|---|---|---|---|---|
| Male | Female | 0–I | II | ||||||
| 1 | Identifying potential DNA methylation markers in early-stage CRC, 2020 | [10] | FFPE tissue; Blood plasma | 37 | 14 | 34–77 | 36 | 6 | SFMBT2, VAV3-AS1, ZNF132, KCNQ5, ITGA4, THBD, FBN1, EVC, C9orf50, TWIST1, ZNF304 |
| 2 | Blood leukocytes methylation levels analysis indicate methylated plasma test is a promising tool for CRC early detection, 2011 | [11] | Blood plasma | 55 | 36 | 22–89 | 13 | 31 | SEPT9, SDC2 |
| 3 | A novel cfDNA methylation-based model improves the early detection of CRC, 2021 | [12] | Tissue DNA samples; plasma cfDNA | 287 | 202 | 18–89 | 66 | 86 | SEPT9, BCAT1, IKZF1, cg10673833 |
| 4 | Evaluation of epigenetic methylation biomarkers for the detection of CRC using ddPCR, 2023 | [13] | FFPE tissue | 57 | 48 | - | 24 | 35 | BCAT1, GATA5, IKZF1 (V1), IKZF1 (V2), IRF4, ITGA4, HIC1, NPY, SDC2, SEPT9, WIF1 |
| 5 | Combined SEPT9 and BMP3 methylation in plasma for CRC early detection and screening in a Brazilian population, 2023 | [14] | Blood plasma | 11 | 32 | 57.1 (mean) | 9 | 9 | SEPT9, BMP3 |
| 6 | CRC detected by liquid biopsy 2 years prior to clinical diagnosis in the HUNT study, 2023 | [3] | Blood plasma | 32 | 40 | 69.8 (mean) | 0 | 11 | AGBL4, ALX4, BCAT1, BMP3, FLI1, GRIA4, IKZF1, NDRG4, NPTX2, PRIMA1, RARB, SEPT9, SDC2, SFRP1, SFRP2, SLC8A1, TWIST1, VIM, WNT5A, ZNF331 |
| 7 | Combining methylated SEPTIN9 and RNF180 plasma markers for diagnosis and early detection of gastric cancer, 2023 | [15] | Blood plasma | 384 | 176 | <65, >65 | 94 | 53 | SEPT9, RNF180 |
| 8 | cfDNA methylation profiles enable early detection of colorectal and gastric cancer, 2016 | [16] | Blood plasma | 28 | 42 | 25–89 | 10 | 25 | SEPT9, ATXN1, PCDH10, MYO1G, NGFR, IKZF1, ITGA4 |
| 9 | Circulating-tumor DNA methylation of HAND1 gene: a promising biomarker in early detection of CRC, 2017 | [17] | Blood plasma | 18 | 12 | 31–68 | - | 9 | HAND1, SEPT9 |
Quality assessment ratings using the QUADAS-2 scale for reviewed studies (n = 9)
| Signaling questions | Patient selection | Index test | Reference standard | Flow and timing | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Q1 | Q2 | Q3 | Risk of bias | Applicability concerns | Q4 | Q5 | Risk of bias | Applicability concerns | Q6 | Q7 | Risk of bias | Applicability concerns | Q8 | Q9 | Risk of bias | |
| (1) Zhang et al. [16] | Y | N | N | High | Low | N | U | Low | Unclear | U | Y | Unclear | High | Y | N | High |
| (2) Chen et al. [17] | N | N | Y | Low | High | Y | Y | Unclear | Low | Y | N | Low | Low | N | Y | High |
| (3) Wu et al. [18] | U | Y | U | Unclear | Low | N | N | High | Low | Y | N | Low | Low | Y | N | Low |
| (4) Petit et al. [19] | N | N | Y | High | Low | Y | U | Low | High | N | Y | High | Low | N | Y | High |
| (5) Lima et al. [6] | Y | Y | N | High | High | Y | Y | Low | Low | Y | Y | Low | Unclear | U | Y | Unclear |
| (6) Brenne et al. [3] | N | Y | U | Low | Unclear | N | Y | Unclear | Low | N | Y | High | Low | Y | U | Low |
| (7) Nie et al. [20] | U | N | Y | Unclear | Low | N | U | High | Unclear | Y | N | Low | High | N | Y | High |
| (8) Lei [21] | N | Y | N | Low | High | Y | N | Low | High | Y | U | Low | Low | Y | N | Low |
| (9) Shavali et al. [22] | Y | N | N | High | Low | N | U | Unclear | Low | U | N | Unclear | Low | Y | N | Low |