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Table 1 Results of a CNV-based case-control association analysis of insect bite hypersensitivity in Friesian horses

From: Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity

      

CNV frequency

     
      

Case

Control

     

CNVR ID

ECAa

Start (bp)

End (bp)

Size (bp)

State

Gain

Loss

Total

Gain

Loss

Total

P-value Gain

P-value Loss

P-value

ORb

Genec

CNVR_1144_1

4

23,383,774

23,505,444

121,671

Gain

1

0

1

9

0

9

0.033

 

0.0332

0.100.01–0.84

 

CNVR_1296_1

4

79,687,222

79,957,793

270,572

Gain

11

0

11

26

0

26

0.009

 

0.0092

0.360.17–0.78

SPAM1

CNVR_2035_1

8

3,638,239

3,783,874

145,636

Mixed

7

2

9

1

1

2

0.046

0.580

0.0367

5.401.11–26.3

IGLV8–61, ENSECAG00000014327

CNVR_2452_1

10

12,948,489

13,075,518

127,030

Mixed

15

10

25

6

0

6

0.022

0.982

0.0003

5.922.24–15.7

AC011513.3, CEACAM1, CEACAM3-CEACAM8, PSG1-PSG9, PSG11

CNVR_2685_1

11

41,743,465

41,832,225

88,761

Mixed

8

5

13

2

2

4

0.055

0.265

0.0245

3.821.19–12.3

 

CNVR_2758_1

12

19,366,263

19,527,441

161,179

Gain

14

0

14

2

0

2

0.004

 

0.0038

9.862.09–46.5

OR4D10, OR4D11, ENSECAG00000008771

CNVR_2979_1

14

64,375,388

64,516,633

141,246

Gain

3

0

3

11

0

11

0.040

 

0.0395

0.250.07–0.94

 

CNVR_4066

20

20,271

503,862

483,592

Mixed

1

0

1

7

1

8

0.064

0.987

0.0450

0.110.01–0.95

 

CNVR_4114_1

20

24,230,088

24,296,409

66,322

Mixed

6

0

6

19

0

19

0.010

 

0.0100

0.280.10–0.74

BTN3A1, BTN3A2, BTN3A3

CNVR_4120_1

20

26,392,472

26,531,248

138,777

Gain

25

0

25

46

0

46

0.003

 

0.0034

0.410.23–0.74

ENSECAG00000001951, ENSECAG00000019806, ENSECAG00000002019, ENSECAG00000002140, ENSECAG00000002328, ENSECAG00000000865

CNVR_4132_1

20

29,805,544

29,821,078

15,535

Gain

23

0

23

9

0

9

0.007

 

0.0074

3.111.36–7.12

 

CNVR_4140_1

20

30,493,889

30,523,455

29,567

Mixed

34

8

42

56

4

60

0.003

0.248

0.0159

0.520.30–0.88

MICA, MICB

CNVR_4141_1

20

30,624,048

30,689,273

65,226

Gain

60

0

60

35

0

35

0.001

 

0.0006

2.651.52–4.61

ENSECAG00000017324, ENSECAG00000002838

CNVR_4142_1

20

30,743,179

30,775,429

32,251

Mixed

14

18

32

11

5

16

0.422

0.008

0.0092

2.451.25–4.79

ENSECAG00000019095

CNVR_4155_1

20

32,467,872

32,582,288

114,417

Mixed

3

10

13

7

19

26

0.231

0.086

0.0285

0.440.21–0.92

 

CNVR_4271_1

21

10,784,937

10,861,217

76,281

Mixed

8

1

9

3

0

3

0.077

0.987

0.0464

4.201.02–17.3

 

CNVR_4537

23

32,331,580

32,716,916

385,337

Gain

1

0

1

9

0

9

0.034

 

0.0342

0.110.01–0.85

ENSECAG00000026512, ENSECAG00000009426

CNVR_4747d

26

250,337

434,632

184,296

Mixed

1

8

9

8

8

16

0.048

0.966

0.0332

0.120.01–0.98

 

CNVR_4992_1d

28

4428

376,070

371,643

Mixed

3

11

14

12

13

25

0.066

0.620

0.0092

0.210.05–0.83

ENSECAG00000001173, ENSECAG00000003651

  1. Significance level (P-value) based on CNV frequency differences between cases (n = 111) and controls (n = 111) using logistic regression and 1 principal component as covariate, including CNVR identification (CNVR_ID), chromosome, start and end position of CNVR (in base pairs), state (gain, loss or complex), odds ratio (OR) and candidate genes based on Ensembl IDs and human orthologues
  2. aEquus caballus chromosome
  3. bOdds ratio of the CNV with 95% confidence interval in superscript
  4. cSPAM1 = sperm adhesion molecule 1 (OMIM:600930), IGLV8–61 = immunoglobulin lambda variable 8–61 (OMIM:147240), AC011513.3 = ENSG00000267881, CEACAM1 = carcinoembryonic antigen-related cell adhesion molecule 1 (OMIM:109770), CEACAM3 = carcinoembryonic antigen-related cell adhesion molecule 3 (OMIM:609142), CEACAM4 = carcinoembryonic antigen-related cell adhesion molecule 4 (ENSG00000105352), CEACAM5 = carcinoembryonic antigen-related cell adhesion molecule 5 (OMIM:114890), CEACAM6 = carcinoembryonic antigen-related cell adhesion molecule 6 (OMIM:163980), CEACAM7 = carcinoembryonic antigen-related cell adhesion molecule 7 (ENSG00000007306), CEACAM8 = carcinoembryonic antigen-related cell adhesion molecule 8 (OMIM:615747), PSG1 = pregnancy-specific beta-1-glycoprotein 1 (OMIM:176390), PSG2 = pregnancy-specific beta-1-glycoprotein 2 (OMIM:176391), PSG3 = pregnancy-specific beta-1-glycoprotein 3 (OMIM:176392), PSG4 = pregnancy-specific beta-1-glycoprotein 4 (OMIM:176393), PSG5 = pregnancy-specific beta-1-glycoprotein 5 (OMIM:176394), PSG6 = pregnancy-specific beta-1-glycoprotein 6 (OMIM:176395), PSG7 = pregnancy-specific beta-1-glycoprotein 7 (OMIM:176396), PSG8 = pregnancy-specific beta-1-glycoprotein 8 (OMIM:176397), PSG9 = pregnancy-specific beta-1-glycoprotein 9 (OMIM:176398), PSG11 = pregnancy-specific beta-1-glycoprotein 11 (OMIM:176401), OR4D10 = olfactory receptor family 4 subfamily D member 10, OR4D11 = olfactory receptor family 4 subfamily D member 11, BTN3A1 = butyrophilin subfamily 3 member A1 (OMIM:613593), BTN3A2 = butyrophilin subfamily 3 member A2 (OMIM:613594), BTN3A3 = butyrophilin subfamily 3 member A3 (OMIM:613595), MICA = major histocompatibility complex class I chain-related gene A (OMIM:600169), MICB = major histocompatibility complex class I chain-related gene B (OMIM:602436)
  5. dOdds ratio of CNV gain is mentioned