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Table 4 Statistically significant 2-SNP patterns relevant to esophageal squamous cell carcinoma. In 2000 runs of 10-fold cross-validation, 52 2-SNP patterns were found to be esophageal cancer relevant. They had frequencies greater than the critical value of 0.00024 at the 5% level of significance (P < 0.05). By applying these 2-SNP patterns to the SNP data set, 15 2-SNP patterns have 95% confidence intervals (CIs) whose upper and lower limits not cross with OR = 1.

From: Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method

No

OR

95% CI

SNP site 1

SNP site 2

   

Gene

RS number

Genotype

Gene

RS number

Genotype

1

2.33

1.29 – 4.19

NQO1

rs1800566

Heterozygous

GADD45B

E1122

Homozygous common

2

2.09

1.41 – 3.09

GADD45B

E1122

Homozygous common

COMT

rs4818

Homozygous common

3

2.03

1.37 – 3.00

ercc5_55

 

Homozygous common

GADD45B

E1122

Homozygous common

4

0.61

0.38 – 0.98

cyp1a2_5

 

Heterozygous

GADD45B

E1122

Heterozygous

5

0.60

0.39 – 0.94

GADD45B

E1122

Heterozygous

ERCC2

rs1799787

Heterozygous

6

0.60

0.38 – 0.94

GADD45B

E1122

Heterozygous

COMT

rs4818

Heterozygous

7

0.58

0.37 – 0.92

GADD45B

E1122

Heterozygous

CYP1A2

rs2472304

Heterozygous

8

0.58

0.37 – 0.89

GSTM3

rs1537234

Heterozygous

GADD45B

E1122

Heterozygous

9

0.57

0.36 – 0.90

GADD45B

E1122

Heterozygous

COMT

rs4818

Homozygous common

10

0.57

0.37 – 0.87

LIG1

rs20579

Heterozygous

GADD45B

E1122

Heterozygous

11

0.54

0.35 – 0.84

GADD45B

E1122

Heterozygous

ERCC2

rs1052559

Homozygous common

12

0.45

0.28 – 0.72

GADD45B

rs14384

Homozygous common

GADD45B

E1122

Heterozygous

13

0.40

0.26 – 0.63

GADD45B

E1122

Heterozygous

ERCC5

rs17655

Homozygous common

14

0.22

0.06 – 0.73

adh1b_55

 

Homozygous variant

GADD45B

E1122

Heterozygous

15

0.16

0.04 – 0.62

NQO1

rs1800566

Homozygous variant

GADD45B

E1122

Homozygous common