Pan-cancer patterns of DNA methylation

Table 3 DNA methylation biomarkers and their potential clinical applications

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]

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.