Skip to main content

Table 2 Epigenetic markers employed in the ddMSP assay

From: Circulating cell-free DNA-based epigenetic assay can detect early breast cancer

Gene

Name

Product length

Chr

CpG

Common BC markers

  JAK3

Tyrosine-protein kinase JAK3

129

19

s-shore

  RASGRF1

Ras-specific guanine nucleotide-releasing factor 1

104

15

island

  CPXM1

Carboxypeptidase X1

94

20

island

  SHF

Src homology 2 domain-containing adapter protein F

117

15

island

Luminal-dominant markers

  DNM3

Dynamin 3

105

19

n-shore

  CAV2

Caveolin 2

141

7

island

  HOXA10

Homeobox protein Hox-A10

135

7

island

  B3GNT5

UDP-GlcNAc:betaGal beta-1,3-N acetylglucosaminyltransferase 5

97

3

island

TN-dominant markers

  ST3GAL6

ST3 beta-galactoside alpha-2,3-sialyltransferase 6

82

3

s-shore

  DACH1

Dachshund homolog 1

110

13

n-shore

  P2RX3

P2X purinoceptor 3

118

11

island

 Chr8:23572595

Intergenic locus corresponding to probe cg23495581, located at chr 8: 23,572,595 in GRCh37

83

8

s-shore

Internal control markers for MSP

  CREM

cAMP-responsive element modulator

75

10

 

  GLYATL3

Glycine N-acyltransferase-like protein 3

107

6

 

  ELMOD3

ELMO/CED-12 domain containing 3

90

2

 

  KLF9

Kruppel-like factor 9

89

9

 
  1. ddMSP droplet digital methylation-specific PCR, Chr chromosome, island CpG island, shore CpG shore (region within 2000 bps from CpG island), n-shore/s-shore northern/southern CpG shore (CpG shore attached to upstream/downstream side of CpG island, respectively), GRC Genome Reference Consortium