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Table 1 Detailed AF% of detected 5hmc at 17 Hotspots (Top: Tier 1; Bottom: Tier 2)

From: 5-Hydroxymethylcytosine (5hmC) at or near cancer mutation hot spots as potential targets for early cancer detection

Chromosome

Tier 1 Hotspot Location

Mutation name

Hotspot Mutation

Bases at hotspot

C of CpG Normal (PBMC)

G of CpG Normal (PBMC)

C of CpG Immprtalized (PAM3005)

G of CpG Immprtalized (PAM3005)

C of CpG Cancer (HCT116)

G of CpG Cancer (HCT116)

chr11

108247071

ATM R337C, c.1009C>T

C>T

CpG

  

2.1%

56.8%

0.7%

8.1%

chr19

11021837

SMARCA4 T910M, c.2729C>T

C>T

CpG

 

2.0%

6.1%

1.1%

2.2%

10.7%

chr2

208248388

IDH1 R132H, c.395G>A

C>T

CpG

 

1.4%

2.0%

9.1%

2.8%

0.5%

chr1

162776212

DDR2 R709, c.2125C>T

C>T

CpG

7.1%

0.3%

8.9%

9.6%

7.4%

20.5%

chr17

39711955

ERBB2 S310F, c.929C>T

C>T

CpG

3.8%

 

12.5%

 

16.6%

 

chr2

211623993

ERBB4 R711C, c.2131C>T

G>A

CpG

1.3%

2.1%

8.5%

25.3%

9.9%

7.8%

chr12

25245350

KRAS G12C, c.34G>T

C>A

CC

  

22.58%

 

32.14%

 

Chromosome

Tier 2 Hotspot Location

Mutation name

Hotspot Mutation

Bases at hotspot

C of CpG Normal (PBMC)

G of CpG Normal (PBMC)

C of CpG Immprtalized (PAM3005)

G of CpG Immprtalized (PAM3005)

C of CpG Cancer (HCT116)

G of CpG Cancer (HCT116)

chr17

7673802

TP53 R273H, c.818G>A

C>T

CpG

1.2%

4.1%

2.5%

4.8%

5.0%

3.3%

chr17

7674220

TP53 R248Q, c.743G>A

C>T

CpG

5.8%

0.6%

8.7%

0.4%

5.5%

2.4%

chr7

55181378

EGFR T790M, c.2369C>T

C>T

CpG

7.4%

4.8%

6.4%

 

6.0%

0.7%

chr17

7675088

TP53 R175H, c.524G>A

C>T

CpG

2.3%

4.8%

0.8%

6.3%

3.4%

6.6%

chr5

112839941

APC R1450, c.4348C>T

G>A

CpG

 

6.3%

 

6.7%

 

18.6%

chr15

66436824

MAP2K1 P124S, c.370C>T

C>T

CC

7.2%

 

5.7%

 

3.8%

 

chr14

104780214

AKT1 E17K, c.49G>A

C>T

CC

2.8%

 

1.9%

 

4.7%

 

chr3

41224646

CTNNB1 S45F, c.134C>T

C>T

TCT

2.1%

 

1.5%

 

1.0%

 

chr3

179218303

PIK3CA E545K, c.1633G>A

G>A

TGA

 

2.6%

 

4.2%

 

5.4%

chrX

71119404

MED12 G44D, c.131G>A

G>A

GG

 

5.1%

 

5.4%

 

5.9%