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Table 1 Differentially methylated loci (p < 5 × 10−6): high vs. low BMI cases (BE, LGD, HGD/EAC combined)

From: Global DNA methylation patterns in Barrett’s esophagus, dysplastic Barrett’s, and esophageal adenocarcinoma are associated with BMI, gender, and tobacco use

Probe ID

Gene

Average β low BMI

Average β high BMI (overall change)

p value

Probe location

Relation to CpG island

Relative expression BE vs. normal^

Relative expression EAC vs. normal^

Cancer associated?

cg11839020

LRRC8D

0.29

0.41 (↑)

4.06E-09

5′UTR

Shore

1.59–1.78*

1.44–1.86*

N

cg11027822

ITGA6

0.62

0.72 (↑)

1.97E-07

Body

Open sea

1.57–3.96*

1.48–2.66*

Y

cg25872281

TMUB1

0.66

0.81 (↑)

3.56E-07

TSS1500; body

Island

1.32*

NS

N

cg22984132

TMUB1

0.51

0.62 (↑)

3.64E-07

TSS1500; body

Island

1.32*

NS

N

cg26314478

ESPNP

0.49

0.60 (↑)

3.86E-07

Body

Shelf

NS

NS

N

cg09458237

HSPA12B

0.51

0.66 (↑)

4.46E-07

TSS1500

Shore

1.37*

1.89–6.50*

Y

cg06393286

FAM43B

0.48

0.36 (↓)

4.64E-07

1st exon

Island

NS

NS

Y

cg09058554

SLC25A33

0.39

0.51 (↑)

6.40E-07

Body

Shore

NS

1.23*

Y

cg14950321

PLIN5

0.31

0.42 (↑)

7.21E-07

Body

Shore

4.17*

NS

N

cg02134660

FAM83B

0.52

0.72 (↑)

1.17E-06

TSS1500

Shore

NS

NS

N

cg25302888

TMUB1

0.65

0.77 (↑)

1.23E-06

TSS1500; body

Island

1.32*

NS

N

cg05137975

C6orf168

0.53

0.70 (↑)

1.52E-06

Body

Open sea

NS

3.64*

N

cg16957569

IDO2

0.56

0.69 (↑)

1.68E-06

TSS1500

Open sea

NS

NS

N

cg00831127

EPHB2

0.26

0.49 (↑)

2.33E-06

Body

Shore

1.62–6.30*

1.40–7.83*

Y

cg25229964

CNKSR1

0.59

0.71 (↑)

2.39E-06

TSS1500

Open sea

NS

NS

N

cg19513232

CAMK2A

0.39

0.52 (↑)

2.43E-06

Body

Open sea

NS

NS

N

cg10976975

BMP10

0.72

0.83 (↑)

2.53E-06

5′UTR; 1st exon

Open sea

NS

NS

N

cg04025965

TMUB1

0.58

0.72 (↑)

2.66E-06

TSS1500; body

Island

1.32*

NS

N

cg02233614

PFKFB2

0.29

0.39 (↑)

2.82E-06

5′UTR

Shore

1.32*

1.12*

N

cg06020352

IRF8

0.36

0.50 (↑)

2.92E-06

TSS1500

Shore

1.80–6.36*

3.85–7.56*

N

cg08526705

MYC

0.61

0.74 (↑)

2.99E-06

Body

Shore

NS

3.89*

N

cg08943714

HECA

0.28

0.42 (↑)

3.66E-06

Body

Open sea

NS

NS

N

cg17161520

TBC1D10C

0.46

0.57 (↑)

3.92E-06

Body

Shelf

NS

1.14*

N

cg10583322

MEGF11

0.49

0.65 (↑)

4.15E-06

Body

Open sea

NS

1.69*

Y

cg02059867

RAPGEFL1

0.42

0.57 (↑)

4.50E-06

1st exon; 5′UTR

Island

NS

NS

N

  1. 5′UTR = 5′ untranslated region; TSS1500 = 1500 bp’s upstream from transcription start site; Shore = DNA sequence up to 2 kb from CpG island; Shelf = DNA sequence 2–4 kb from CpG island; Open sea = DNA sequence >4 kb from CpG island; NS = not significant; ^ = relative gene expression data obtained from www.oncomine.org; *p ≤ 0.05; (↑)/(↓) = increase/decrease in methylation in high BMI group vs. the low BMI group
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Clinical Epigenetics

ISSN: 1868-7083

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