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Table 5 TCGA: Differentially DNA-methylated CpGs in IR significantly associated with primary invasive BC tissues, overall and stratified by BC molecular subtype

From: DNA methylation in peripheral blood leukocytes for the association with glucose metabolism and invasive breast cancer

Chr

CpG site§

Position

Overall

ER/PR + 

HER2/neu -

CpG Context

Gene

Gene region

HR (95% CI)

p

HR (95% CI)

p

HR (95% CI)

p

chr2

cg00765233*

235,877,260

0.10 (0.01, 0.42)

0.006

0.07 (0.003, 0.47)

0.030

0.11 (0.01, 0.39)

0.005

OpenSea

SH3BP4

5'UTR

chr2

cg14386946**

179,315,284

2.65 (1.36, 6.11)

0.010

5.40 (1.83, 26.55)

0.011

2.68 (1.36, 6.24)

0.010

Island

PRKRA

Body

chr7

cg01676795*

75,586,348

2.98 (1.06, 9.43)

0.046

5.18 (1.44, 43.15)

0.026

2.97 (1.10, 9.82)

0.039

OpenSea

POR

Body

chr7

cg24207108

98,600,653

1.14 (0.68, 1.73)

0.567

2.26 (1.09, 5.11)

0.034

1.12 (0.64, 1.77)

0.653

OpenSea

TRRAP

Body

chr8

cg04684553

89,339,819

25.73 (3.46, 305.72)

0.004

NA

NA

12.53 (2.68, 84.73)

0.004

N Shore

MMP16

TSS200

chr10

cg26712428*

105,218,771

0.45 (0.16, 1.22)

0.119

0.06 (0.01, 0.37)

0.006

0.47 (0.16, 1.22)

0.116

S Shore

CALHM1

TSS200

chr12

cg20554753*

16,940,870

0.25 (0.04, 1.12)

0.085

0.04 (0.002, 0.32)

0.007

0.26 (0.05, 1.12)

0.086

OpenSea

 

Intergenic

chr12

cg21565550

100,967,522

3.81 (1.48, 12.35)

0.012

3.71 (1.23, 16.33)

0.042

4.20 (1.58, 14.28)

0.009

Island

GAS2L3

5'UTR

chr17

cg06892217**

40,075,290

3.05 (1.44, 7.62)

0.008

5.33 (1.96, 20.16)

0.004

3.10 (1.45, 7.83)

0.008

Island

ACLY

TSS200

chr17

cg13274938

38,493,822

0.23 (0.05, 0.89)

0.046

0.12 (0.02, 0.61)

0.016

0.21 (0.04, 0.82)

0.035

N Shelf

RARA

Body

chr17

cg18772573

71,257,980

0.77 (0.26, 2.01)

0.617

0.11 (0.004, 0.74)

0.044

0.77 (0.25, 2.04)

0.626

OpenSea

CPSF4L

1stExon

chr19

cg01969586

45,663,415

0.36 (0.09, 1.11)

0.111

0.08 (0.01, 0.48)

0.015

0.40 (0.09, 1.15)

0.122

OpenSea

NKPD1

TSS200

chr19

cg15197202

10,488,965

0.66 (0.32, 1.28)

0.227

0.35 (0.11, 0.90)

0.047

0.67 (0.33, 1.30)

0.244

N Shelf

TYK2

Body

chr19

cg21066748

46,005,805

0.61 (0.21, 1.41)

0.283

0.10 (0.01, 0.50)

0.018

0.62 (0.22, 1.39)

0.286

N Shelf

 

Intergenic

chr21

cg06500161*

43,656,587

3.80 (1.15, 15.47)

0.043

1.01 (0.19, 5.51)

0.993

3.86 (1.20, 15.78)

0.034

S Shore

ABCG1

Body

chr21

cg08309687£

35,320,596

0.30 (0.10, 0.87)

0.031

0.28 (0.05, 1.30)

0.131

0.30 (0.10, 0.88)

0.033

OpenSea

 

Intergenic

chr21

cg27243685*

43,642,366

2.64 (1.39, 5.66)

0.005

2.17 (0.63, 9.31)

0.258

2.73 (1.37, 5.80)

0.007

S Shelf

ABCG1

Body

  1. BC Breast cancer, Chr Chromosome, CI Confidence interval, CpG CpG dinucleotide; ER/PR + Estrogen receptor/progesterone receptor–positive, HER2/neu– Human epidermal growth factor receptor-2–negative, HR Hazard ratio, IR Insulin resistance, NA Not available, TCGA The Cancer Genomic Atlas, TSS200, 0–200 bp upstream of transcription start site, UTR Untranslated region. Numbers in bold face are statistically significant
  2. § Annotation used R v.0.6.0.IlluminaHumanMethylation450kanno.ilmn12.hg19: Annotation for Illumina's 450 k methylation arrays
  3. aHR adjusted by age, tumor purity, and cell-type proportion (cancer epithelial cell types 1 to 5 and normal epithelial, stromal, and immune cells)
  4. * Enhancer associated
  5. ** Promoter associated
  6. £ Enhancer and promoter associated