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Table 5 SNPs significantly associated with CMT high and low risk breed groups after Bonferroni correction

From: The ESR1 gene is associated with risk for canine mammary tumours

SNP

NCBI SNP ID

Minor allele

Frequency minor allele

Major allele

OR

P Raw a

P Bonf b

P Perm c

P BPerm d

   

High risk breeds

Low risk breeds

      

CHEK2 INT 8-9

ss244244336

G

0.269

0.040

T

8.8

8.6E-19

7.8E-18

<1.0E-07

0.076

ESR1 EX 2

rs21960513

T

0.629

0.305

C

3.9

5.0E-21

4.5E-20

<1.0E-07

0.107

ERBB2 EX 14

rs24537331

A

0.253

0.511

G

0.3

8.4E-15

7.6E-14

<1.0E-07

0.110

BRCA2 INT 18-19

ss244244323

G

0.000

0.133

A

_ e

1.8E-16

1.6E-15

<1.0E-07

0.110

ERBB2 INT 3-4

ss244244348

G

0.330

0.681

A

0.2

2.4E-24

2.2E-23

<1.0E-07

0.112

BRCA2 EX 11

rs23244160

G

0.174

0.346

T

0.4

8.4E-09

7.6E-08

4.2E-05

0.151

CHEK2 INT 5-6

ss244244335

G

0.051

0.000

A

_ e

9.6E-06

8.6E-05

0.005

0.182

ESR1 EX 4

ss244244343

G

0.061

0.394

A

0.1

9.8E-33

8.8E-32

<1.0E-07

0.204

PTEN EX 9

ss244244369

T

0.112

0.346

C

0.3

1.3E-16

1.2E-15

<1.0E-07

0.209

BRCA2 EX 5

rs23250374

C

0.429

0.23

T

2.5

1.1E-09

1.0E-08

1.0E-05

0.321

ERBB2 INT 12-13b

rs24537327

A

0.485

0.283

G

2.4

2.2E-09

1.9E-08

2.0E-05

0.362

ERBB2 EX 13b

rs24537329

T

0.486

0.285

C

2.4

2.4E-09

2.2E-08

2.1E-05

0.368

PTEN INT 7-8

ss244244368

A

0.183

0.356

G

0.5

8.0E-09

7.2E-08

4.0E-05

0.385

BRCA2 5UTR

ss244244322

T

0.343

0.506

C

0.5

2.7E-06

2.4E-05

0.002

0.407

PTEN INT 3-4

ss244244367

G

0.191

0.346

A

0.6

2.8E-07

2.5E-06

5.0E-04

0.416

STK11 INT 1-2

rs22928814

T

0.241

0.362

C

0.6

1.1E-04

1.0E-03

0.031

0.476

BRIP1 EX 19b

ss244244329

T

0.538

0.386

T

1.9

9.9E-06

8.9E-05

0.006

0.521

ERBB2 INT 8-9

ss244244349

G

0.089

0.027

A

3.2

0.001

5.8E-03

0.101

0.566

ESR1 INT 7-8a

ss244244344

A

0.124

0.223

G

0.5

2.3E-04

2.2E-03

0.051

0.708

BRIP1 INT 8-9a

ss244244325

G

0.135

0.011

A

14.5

3.2E-11

2.9E-10

<1.0E-07

0.817

ERBB2 INT 1-2

ss244244347

T

0.021

0.000

C

_ e

0.005

0.045

0.340

0.845

BRIP1 INT 15-16

ss244244327

T

0.131

0.011

A

14.0

8.0E-11

7.2E-10

<1.0E-07

0.874

ERBB2 EX13a

rs24616607

G

0.044

0.005

C

8.5

0.001

5.2E-03

0.095

0.983

  1. (n = 237 and n = 191, respectively, after QC).
  2. aP-value from chi-square test.
  3. b Corrected for the number of across-breed LD blocks (9).
  4. c EMP1 value after 107 permutations.
  5. d EMP1 value after 10,000 breed permutations.
  6. e OR could not be calculated as the minor allele was absent in either cases or controls.
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BMC Veterinary Research

ISSN: 1746-6148

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