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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