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Table 1 Significant true-positive genes by pedigree found using PSGS analysis

From: Pairwise shared genomic segment analysis in high-risk pedigrees: application to Genetic Analysis Workshop 17 exome-sequencing SNP data

Replicate

Chromosome

p-value

Causal gene

Causal SNP

Frequency in cases (%)

Frequency in population (%)

Run length range in causal gene

25

1

1 × 10–4

PIK3C2B

C1S9189

4.35

0.65

1,152.577–1,192.443

 

9

1 × 10–5

VLDLR

C9S444

17.39

0.14

793.933–802.051

27

9

1 × 10–4

VLDLR

C9S444

14.29

0.14

798.038–816.491

29

1

0.001

PIK3C2B

C1S9189

4.76

0.65

1,065.976–1,106.357

 

4

0.001

VEGFC

C4S4935

90.48

0.07

639.6238

 

9

1 × 10–6

VLDLR

C9S444

9.52

0.14

801.038–809.448

 

10

0.001

SIRT1

C10S3109

61.90

0.07

870.229–870.229

49

10

0.001

SIRT1

C10S3109

56.52

0.07

919.134–919.134

75

1

2 × 10–4

PIK3C2B

C1S9189

4.76

0.65

1,127.395–1,159.105

85

1

2 × 10–4

PIK3C2B

C1S9189

4.35

0.65

1,159.779–1,188.854

 

9

1 × 10–4

VLDLR

C9S444

13.04

0.14

764.763–770.269

94

1

1 × 10–4

PIK3C2B

C1S9189

4.76

0.55

1,232.038–1,256.771

116

9

4 × 10–4

VLDLR

C9S444

13.64

0.14

772.983–776.619

129

9

5 × 10–4

VLDLR

C9S444

20.83

0.14

712.761–728.337

142

9

9 × 10–4

VLDLR

C9S444

19.05

0.14

708.8238–711.8381

 

10

3 × 10–4

SIRT1

C10S3109

57.14

0.07

863.629–863.629

184

9

7 × 10–4

VLDLR

C9S444

23.81

0.14

734.410–750.419

190

9

4 × 10–5

VLDLR

C9S444

18.18

0.14

779.281–782.654

199

10

6 × 10–4

SIRT1

C10S3109

71.43

0.07

984.443–984.443

  1. Replicates 15, 101, 144, 182, and 200 did not identify any true-positive genes. Significance threshold = 0.001. Frequencies of causal SNPs in case subjects were calculated from 18 pedigree replicates.