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Table 3 Tests of association between variants and traits Q1 and Q2

From: Successful identification of rare variants using oligogenic segregation analysis as a prioritizing tool for whole-exome sequencing studies

Trait

SNP (Gene)

Family

Number of copies (number in founders)

Association p-value

Unadjusted LOD

Adjusted LOD

Variation due to SNP (%)

Q1

C4S4935 ( VEGFC )

7

31 (1)

7.87 × 10–12

4.96

0.00

33.11

  

Others

0 (0)

NA

NA

NA

NA

  

All

31 (1)

1.12 × 10–16

5.12

0.00

10.64

 

C6S2981 ( VEGFA )

7

22 (1)

1.25 × 10–7

2.80

0.03

28.90

  

Others

24 (2)

1.27 × 10–8

1.28

0.00

4.97

  

All

46 (3)

9.90 × 10–18

4.91

0.00

11.96

 

C6S2432 (PSMB8)

7

23 (1)

7.78 × 10–7

2.37

0.03

25.18

  

Others

0 (0)

NA

NA

NA

NA

  

All

23 (1)

3.95 × 10–11

4.58

0.94

8.94

 

C6S5169 (MCM9)

7

21 (2)

3.37 × 10–5

1.91

0.04

17.34

  

Others

15 (4)

0.90

0.08

0.08

0.00

  

All

36 (6)

4.39 × 10–5

1.60

0.34

3.05

 

C11S2779 (OR10W1)

7

16 (1)

1.64 × 10–4

0.60

0.00

15.19

  

Others

36 (9)

0.62

0.00

0.00

0.04

  

All

52 (10)

2.96 × 10–3

0.64

0.14

1.72

 

C11S2804 (OR5AN1)

7

16 (1)

1.64 × 10–4

0.60

0.00

15.19

  

Others

107 (24)

0.46

0.00

0.00

0.09

  

All

123 (25)

0.024

0.64

0.40

0.87

 

C11S3874 (FIBP)

7

16 (1)

1.64 × 10–4

1.08

0.09

15.19

  

Others

0 (0)

NA

NA

NA

NA

  

All

16 (1)

5.22 × 10–7

0.87

0.02

5.07

Q2

C21S1354 (U2AF1)

7

7 (1)

2.58 × 10–4

1.79

0.60

12.31

  

Others

4 (1)

0.81

0.23

0.23

0.02

  

All

11 (2)

6.56 × 10–4

1.07

0.52

1.99

 

C2S4965 (WDR75)

7

13 (1)

3.51 × 10–4

1.22

0.04

15.25

  

Others

0 (0)

NA

NA

NA

NA

  

All

13 (1)

7.04 × 10–5

0.00

0.00

3.62

 

C5S12 (PLEKHG4B)

7

24 (1)

3.80 × 10–4

0.71

0.00

12.92

  

Others

4 (2)

0.75

0.00

0.00

0.00

  

All

28 (3)

7.31 × 10–4

0.07

0.00

2.62

 

C5S252 (PLEKHG4B)

7

24 (1)

3.80 × 10–4

0.71

0.00

12.92

  

Others

4 (2)

0.75

0.00

0.00

0.00

  

All

28 (3)

7.31 × 10–4

0.07

0.00

2.62

 

C21S898 (BRWD1)

7

12 (2)

4.29 × 10–4

1.96

1.43

8.46

  

Others

20 (4)

0.21

0.32

0.26

0.05

  

All

32 (6)

9.69 × 10–4

1.30

0.85

0.99

 

C21S1096 (BRWD1)

7

12 (2)

4.29 × 10–4

1.96

1.43

8.46

  

Others

16 (3)

0.043

0.32

0.20

0.50

  

All

28 (5)

8.84 × 10–5

1.30

0.80

1.85

  1. The effect of a specific variant on the test of linkage (unadjusted LOD versus LOD adjusted for the variant) at the position of the gene is indicated as well as the proportion of the variance explained by the variant. Results are separated according to the set of families on which the analysis was restricted: in family 7 alone (7), in families other than family 7 (Others), and in all families combined (All). Causal SNPs and genes are in bold.
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BMC Proceedings

ISSN: 1753-6561

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