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Table 3 DNA methylation biomarkers and their potential clinical applications

From: Pan-cancer patterns of DNA methylation

Biomarker name Cancer type Tissue detected
Risk   
BRCA1 DNAm signature (1,829 CpGs) Breast Whole blood DNA [65]
140 variable CpGs Cervical Normal uterine cervix cells [58]
Diagnosis   
GSTP1 Prostate Serum, urine, ejaculate [70]
APC, EDNRB, GSTP1 Prostate Urine [71]
CDKN2A, ARF, MGMT, GSTP1 Prostate Urine [72]
GSTP1, APC, PTGS2 Prostate Paraffin-embedded tissues [110]
SETP9 Colorectal Blood plasma [77]
APC, MGMT, RASSF2A, WIF1 Colorectal Blood plasma [78]
SHOX2 NSCLC Bronchial fluid aspirates/ blood plasma [76]
CDKN2A, MGMT NSCLC Sputum [74]
CCND2, RASSF1A, APC, HIN1 Breast Fine needle aspiration biopsy [111]
ZNF154, HOXA9, POU4F2, EOMES Bladder Urine [112]
Prognosis   
20-gene signature ALL Leukemic cells from bone marrow and peripheral blood [88]
15-gene classifier AML  
RASSF1A, APC Breast Serum [82]
ZAP70 CLL CD19 sorted mononuclear cells [80]
CDKN2A CCR Blood plasma [81]
DAPK1 Head and neck Tumor samples [84]
DAPK1 NSCLC Tumor samples [83]
CDKN2A, RASSF1A, CDH13, APC NSCLC Primary tumors and lymph nodes [85]
HIST1H4F, PCDHGB6, NPBWR1, ALX1, HOX9 NSCLC Tumor samples [89]
ALDH1A, OSR2, GATA4, GRIA4, IRX4 OPSCC Tumor samples [59]
GSTP1, APC, PTGS2 Prostate Tumor samples [110]
Response to therapy   
BRCA1 Breast Tumor samples [92],[93]
BCL2 Breast Tumor samples [113]
PITX2 Breast Tumor samples [114]
TFAP2E Colon Tumor samples [115]
MGMT Glioma Tumor samples [90],[91]
APAF1 Melanoma Tumor samples/cell lines [116]
IGFBP3 NSCLC Tumor samples/cell lines [117]
BRCA1 Ovary Tumor samples [94]
  1. ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; CCR, colorectal cancer; CLL, chronic lymphocytic leukemia; DNAm, DNA methylation; NSCLC, non-small-cell lung cancer; OPSCC, oropharyngeal squamous cell carcinoma.