Table 3 GMDR-based model for high-order gene–gene interactions in relation to breast cancer risk.

From: Pro-inflammatory cytokine polymorphisms and interactions with dietary alcohol and estrogen, risk factors for invasive breast cancer using a post genome-wide analysis for gene–gene and gene–lifestyle interaction

n

Model

TBA

P value

CVC

 

Overall

1

TRAIP rs2352975

0.5382

0.0010

10/10

2

TRAIP rs2352975, SALL1 rs10521222

0.5270

0.0010

8/10

3

TRAIP rs2352975, DUSP1 rs17658229, SALL1 rs10521222

0.5271

0.0547

5/10

4

TRAIP rs2352975, DUSP1 rs17658229, SALL1 rs10521222, APOC1 rs4420638

0.5249

0.0547

9/10

5

TRAIP rs2352975, DUSP1 rs17658229, SALL1 rs10521222, APOC1 rs4420638,

HLA-DQA1 rs9271608

0.5215

0.0107

10/10

 

Overall non-obese group, BMI < 30 kg/m2

1

APOC1 rs4420638

0.5179

0.1719

10/10

2

APOC1 rs4420638, SALL1 rs10521222

0.5244

0.1712

10/10

3

APOC1 rs4420638, SALL1 rs10521222, HLA-DQA1 rs9271608

0.4980

0.6230

10/10

 

Overall obese group, BMI ≥ 30 kg/m2

1

HNF1A-AS1 rs2243616

0.5551

0.0107

10/10

2

HNF1A-AS1 rs2243616, SALL1 rs10521222

0.5546

0.0107

9/10

3

HNF1A-AS1 rs2243616, DUSP1 rs17658229, SALL1 rs10521222

0.5533

0.0107

10/10

4

HNF1A-AS1 rs2243616, DUSP1 rs17658229, SALL1 rs10521222, HLA-DQA1 rs9271608

0.5510

0.0107

10/10

 

Non-viscerally obese group, WHR ≤ 0.85*

1

APOC1 rs4420638

0.4924

0.8281

9/10

2

DUSP1 rs17658229, APOC1 rs4420638

0.5058

0.6230

9/10

3

DUSP1 rs17658229, APOC1 rs4420638, SALL1 rs10521222

0.5009

0.6230

9/10

4

DUSP1 rs17658229, APOC1 rs4420638, SALL1 rs10521222, HLA-DQA1 rs9271608

0.4851

0.9453

10/10

 

Viscerally obese group, WHR > 0.85

1

TRAIP rs2352975

0.5306

0.1719

10/10

2

TRAIP rs2352975, SALL1 rs10521222

0.5233

0.3770

5/10

3

TRAIP rs2352975, SALL1 rs10521222, APOC1 rs4420638

0.5564

0.0547

10/10

4

TRAIP rs2352975, SALL1 rs10521222, APOC1 rs4420638, HLA-DQA1 rs9271608

0.5486

0.0547

10/10

 

Non-viscerally obese group, WST ≤ 88 cm

1

APOC1 rs4420638

0.5190

0.1719

10/10

2

APOC1 rs4420638, SALL1 rs10521222

0.5240

0.1719

10/10

3

APOC1 rs4420638, SALL1 rs10521222, HLA-DQA1 rs9271608

0.5047

0.3770

10/10

 

Viscerally obese group, WST > 88 cm

1

TRAIP rs2352975

0.5266

0.1719

10/10

2

TRAIP rs2352975, SALL1 rs10521222

0.5307

0.1719

10/10

3

TRAIP rs2352975, DUSP1 rs17658229, SALL1 rs10521222

0.5336

0.0547

10/10

4

TRAIP rs2352975, DUSP1 rs17658229, SALL1 rs10521222, HLA-DQA1 rs9271608

0.5291

0.1719

10/10

 

Active group, MET ≥ 10.0*

1

HLA-DQA1 rs9271608

0.4872

0.9453

6/10

2

HLA-DQA1 rs9271608, SALL1 rs10521222

0.4833

0.9893

10/10

 

Inactive group, MET < 10.0

1

SALL1 rs10521222

0.4727

0.9990

8/10

2

SALL1 rs10521222, HLA-DQA1 rs9271608

0.4796

0.8281

10/10

 

Low-fat diet group, % cal. from SFA < 9.0

1

SALL1 rs10521222

0.4346

0.9990

6/10

2

DUSP1 rs17658229, HLA-DQA1 rs9271608

0.4305

1.0000

4/10

3

DUSP1 rs17658229, HLA-DQA1 rs9271608, SALL1 rs10521222

0.4422

0.9990

10/10

 

High-fat diet group, % cal. from SFA ≥ 9.0

1

TRAIP rs2352975

0.5463

0.0010

10/10

2

TRAIP rs2352975, SALL1 rs10521222

0.5481

0.0010

10/10

3

TRAIP rs2352975, SALL1 rs10521222, HLA-DQA1 rs9271608

0.5458

0.0010

10/10

  1. BMI body mass index; CVC, cross-validation consistency; GMDR, generalized multifactor dimensionality reduction; MET, metabolic equivalent; SFA, saturated fatty acids; TBA, testing balance accuracy; WHR, waist-to-hip ratio; WST, waist circumference. Models in bold face are considered the best, with the highest TBA, 10/10 CVC, and p < 0.05.
  2. *The models have either the highest TBA or 10/10 CVC, without statistical significance. By placing a greater importance on 10/10 CVC, the best model was selected.
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