Table 2 Clinical studies on DNA methylation as a diagnostic and prognostic cancer-related biomarker (deposited on https://clinicaltrials.gov/—last accessed October 16, 2024)

NCT00855348

CRC

Epi proColon

SEPT9

Diagnosis

7,929

C

[267, 268]

NCT01511653

CRC

qMS-PCR

VIM, BCAT1, IKZF1, LINE1

Diagnosis

13,000

C

N/A

NCT01397747

CRC

qMS-PCR

NDRG4, BMP3

Diagnosis

12,776

C

[269]

NCT02476682

CRC

Multi-plexed RT-PCR

BCAT1, IKZF1, ACTB

Diagnosis

205

C

N/A

NCT05508503

CRC

ctDNA dual-target test kit

NTMT1, MAP3K14-AS1

Diagnosis

1,378

C

[270, 271]

NCT04304131

CRC

RT-PCR

SDC2

Diagnosis

1,210

C

[272]

NCT02540850

CRC

SEPT9 gene meylation

SEPT9

Diagnosis

1,031

C

[273]

NCT04287335

CRC

qMS-PCR

BMP3, NDRG4

Diagnosis

4,758

C

N/A

NCT01270360

CRC

GoldenGate

Methylation Cancer Panel I

PENK, NPY, WIF1

Diagnosis

502

C

[274]

NCT05996458

GC

qMS-PCR

RNF180, SEPT9

Diagnosis

84,000

R

N/A

NCT05991947

GC

NGS

APC, BRAF, EGFR, CDKN2A, AKT1, CTNNB1, FBXW7, FGFR2, GNAS, HRAS, KRAS, NRAS, PIK3CA, RNF43, PPP2R1A, PTEN, TP53, TOP2A

Diagnosis

1,100

R

N/A

NCT04994197

BLCA

DNA Methylation-Lightning™ Kit

ONECUT2

Diagnosis

970

R

[275]

NCT05362539

BLCA

qMS-PCR

GATA4, p16, p14, APC, CDH1, CD99

Diagnosis

246

C

N/A

NCT05220189

BLCA

EarlyTect® Bladder Cancer test

PENK

Diagnosis

1,549

R

[276]

NCT04568512

CCA

qMS-PCR

HOXA1, NEUROG1

Diagnosis

67

C

[277]

NCT00835341

OC

qMS-PCR

p16

Diagnosis

93

C

[278]

NCT01695018

OC

MethyLight

p16

Diagnosis

180

C

[279]

NCT01945697

OC

qMS-PCR

ZNF582, PX1

Diagnosis

267

C

[280]

NCT05573217

HCC

qMS-PCR

PIVKA-II

Diagnosis

180

US

N/A

NCT03804593

HCC

HCCBloodTest

SEPT9

Diagnosis

175

C

[281]

NCT03483922

HCC

NGS

AHNAK, STAP1

Diagnosis

403

C

N/A

NCT05801263

OV

CDO1/HOXA9 methylation assay

CDO1, HOXA9

Diagnosis

5,000

R

N/A

NCT03311152

HCC

Epi proColon 2.0 CE

SEPT9

Diagnosis

530

US

N/A

NCT06367049

NPC

qMS-PCR

H4C6, SEPT9, RASSF1A

Diagnosis

470

C

N/A

NCT05680077

EC

Fluorescence PCR

KCNA3, OTOP2

Diagnosis

1,116

C

N/A

NCT04321499

LUAD

RT-PCR

SHOX2, PTGER4

Diagnosis

70

C

[282]

NCT00340717

PRAD

qMS-PCR

GSTPI, CD44, Cav-1, ANXA2

Diagnosis

100

C

N/A

NCT00509821

GBM

Pyrosequencing

MGMT

Prognosis

60

C

N/A

NCT00897819

CRC

Pyrosequencing

APBA1, APBA3, p14, p16

Prognosis

350

C

N/A

NCT02786602

CRC

Pyrosequencing

LRP1

Prognosis

345

C

N/A

NCT04893356

SARC

qMS-PCR

MGMT

Prognosis

75

A, NR

[283]

NCT02022995

CRC

qMS-PCR

EGFR

Prognosis

180

C

N/A

NCT01139944

NSCLC

qMS-PCR

p16, CDKN2A, APC, RASSF1A, DAPK1, CDH13

Prognosis

99

C

N/A

NCT04177316

HCC

Pyrosequencing

VTRNA2-1

Prognosis

92

C

[284]

NCT04830618

GC

quantitative MethyLight assay

MOS

Prognosis

300

C

[285]

NCT02159339

GC

MethyLight

E-cad, GFRA1, p16, SRF, ZNF382

Prognosis

198

C

[286]

NCT01715233

GC

qMS-PCR

CHFR

Prognosis

27

C

N/A

NCT04155242

EC

MethyLight

ZNF345, ZNF569, TFPI2

Prognosis

147

R

N/A

NCT03542097

EWS

qMS-PCR

MGMT

Prognosis

82

C

N/A

NCT02688491

KIRC

qMS-PCR

PITX1, FOXE3, RIN1, TWF2, EHBP1L1

Prognosis

300

NR

N/A