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Table 4 WHI: Differentially DNA-methylated CpGs in IR significantly associated with an invasive BC risk, 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

Crude

DM and BMI adjusted

DM, BMI, and WHR adjusted

CpG context

Gene

Gene region

HR (95% CI)

p

HR (95% CI)

p

HR (95% CI)

p

Overall

           

chr1

cg05399785

3,564,031

1.43 (1.05, 1.94)

0.022

1.42 (1.04, 1.93)

0.027

1.43 (1.05, 1.95)

0.023

N Shelf

WDR8

Body

chr1

cg11832534

3,563,998

1.35 (1.03, 1.76)

0.030

1.34 (1.02, 1.76)

0.035

1.35 (1.03, 1.78)

0.030

N Shelf

WDR8

Body

chr1

cg16395997

3,562,798

1.49 (1.05, 2.10)

0.026

1.49 (1.04, 2.11)

0.028

1.50 (1.05, 2.13)

0.024

S Shore

WDR8

Body

chr1

cg16246545

120,255,941

0.76 (0.60, 0.96)

0.021

0.77 (0.61, 0.97)

0.028

0.76 (0.60, 0.97)

0.025

S Shore

PHGDH

Body

chr6

cg01254034

28,543,667

0.80 (0.66, 0.98)

0.033

0.79 (0.64, 0.97)

0.023

0.79 (0.64, 0.96)

0.021

OpenSea

SCAND3

Body

chr16

cg05807722

67,697,020

0.81 (0.65, 1.00)

0.054

0.80 (0.65, 1.00)

0.048

0.81 (0.65, 1.00)

0.049

S Shore

C16orf48

3'UTR

chr17

cg24366564*

2,843,149

1.39 (1.07, 1.80)

0.015

1.37 (1.05, 1.79)

0.019

1.38 (1.06, 1.80)

0.018

OpenSea

RAP1GAP2

Body

ER/PR + 

           

chr1

cg05399785

3,564,031

1.62 (1.16, 2.24)

0.004

1.61 (1.15, 2.23)

0.005

1.62 (1.16, 2.26)

0.004

N Shelf

WDR8

Body

chr1

cg11832534

3,563,998

1.48 (1.11, 1.98)

0.008

1.47 (1.10, 1.98)

0.010

1.49 (1.10, 2.00)

0.009

N Shelf

WDR8

Body

chr1

cg16395997

3,562,798

1.61 (1.11, 2.34)

0.013

1.61 (1.10, 2.35)

0.014

1.62 (1.11, 2.37)

0.013

S Shore

WDR8

Body

chr1

cg20671910

151,262,619

1.35 (1.03, 1.78)

0.031

1.35 (1.02, 1.78)

0.033

1.37 (1.04, 1.80)

0.027

OpenSea

ZNF687

Body

chr7

cg01676795*

75,586,348

1.72 (1.13, 2.63)

0.012

1.72 (1.12, 2.64)

0.013

1.75 (1.14, 2.69)

0.011

OpenSea

POR

Body

chr10

cg00541500

45,642,600

1.33 (1.01, 1.74)

0.042

1.32 (1.00, 1.73)

0.047

1.32 (1.01, 1.74)

0.044

OpenSea

LOC100133308

Body

chr10

cg01391548*

97,068,696

1.31 (1.00, 1.71)

0.049

1.36 (1.04, 1.78)

0.026

1.36 (1.04, 1.79)

0.026

OpenSea

 

Intergenic

chr17

cg24366564*

2,843,149

1.55 (1.17, 2.06)

0.003

1.53 (1.15, 2.05)

0.004

1.54 (1.16, 2.06)

0.003

OpenSea

RAP1GAP2

Body

HER2/neu -

           

chr1

cg05399785

3,564,031

1.52 (1.06, 2.18)

0.022

1.49 (1.03, 2.14)

0.033

1.49 (1.03, 2.15)

0.032

N Shelf

WDR8

Body

chr1

cg11832534

3,563,998

1.47 (1.07, 2.02)

0.018

1.44 (1.04, 1.99)

0.028

1.44 (1.04, 2.00)

0.027

N Shelf

WDR8

Body

chr1

cg16395997

3,562,798

1.60 (1.06, 2.42)

0.026

1.57 (1.03, 2.40)

0.037

1.57 (1.03, 2.41)

0.036

S Shore

WDR8

Body

chr1

cg16246545

120,255,941

0.75 (0.57, 1.00)

0.048

0.77 (0.58, 1.02)

0.067

0.76 (0.57, 1.02)

0.065

S Shore

PHGDH

Body

chr8

cg20907614*

29,914,963

0.63 (0.42, 0.95)

0.028

0.66 (0.43, 1.01)

0.053

0.66 (0.43, 1.01)

0.054

OpenSea

 

Intergenic

chr10

cg00541500

45,642,600

1.38 (1.02, 1.87)

0.035

1.36 (1.01, 1.85)

0.044

1.37 (1.01, 1.85)

0.042

OpenSea

LOC100133308

Body

chr10

cg08284263*

92,958,627

1.32 (0.96, 1.82)

0.090

1.39 (1.00, 1.92)

0.047

1.38 (1.00, 1.91)

0.050

OpenSea

 

Intergenic

chr11

cg17058475

68,607,737

0.61 (0.42, 0.90)

0.013

0.65 (0.44, 0.97)

0.033

0.65 (0.44, 0.96)

0.030

N Shore

CPT1A

5'UTR

chr17

cg24366564*

2,843,149

1.66 (1.21, 2.28)

0.002

1.64 (1.19, 2.25)

0.003

1.64 (1.19, 2.27)

0.002

OpenSea

RAP1GAP2

Body

  1. BC Breast cancer, BMI Body mass index, Chr Chromosome, CI Confidence interval, CpG CpG dinucleotide, DM ever been treated for diabetes mellitus; ER/PR + Estrogen receptor/progesterone receptor–positive, HER2/neu– Human epidermal growth factor receptor-2–negative, HR Hazard ratio, IR Insulin resistance, UTR Untranslated region, WHI Women’s Health Initiative, WHR Waist-to-hip ratio
  2. § Annotation used R v.0.6.0.IlluminaHumanMethylation450kanno.ilmn12.hg19: Annotation for Illumina's 450 k methylation arrays
  3. a HR adjusted by age and leukocyte heterogeneities (CD8+CD28−CD45RA− T cell, naïve CD8 T cell, plasma blast, CD4+ T cell, natural killer cell, monocyte, and granulocyte)
  4. * Enhancer associated