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Table 1 p-values and ranks of disease genes among all genes using the first simulated data set and their power estimates across 200 simulations

From: Identifying rare disease variants in the Genetic Analysis Workshop 17 simulated data: a comparison of several statistical approaches

Phenotype

Gene

p-values and ranks

Power

  

WS

CMC

RB

Price et al. [9] (Q-traits only)

 

Affected status

FLT1

9.0 × 10−4/1.9 × 10−3

(9.5/25)

2.1 × 10−5/4.3 × 10−3

(2/46)

8.0 × 10−4/3.0 × 10−3

(8/29)

–

0.78/0.685

 

VEGFA

3.3 × 10−3/1.4 × 10−3

(16/19)

3.6 × 10−3/2.2 × 10−3

(22/25)

3.0 × 10−3/2.0 × 10−3

(22/20)

–

0.06/0.06

 

PIK3C2B

7.1 × 10−3/6.1 × 10−3

(33/45.5)

7.0 × 10−3/9.3 × 10−3

(39/75)

1.0 × 10−2/7.0 × 10−3

(43/40)

–

0.64/0.71

Q1

FLT1

<1.0 × 10−4/<1.0 × 10−4

(1.5/1.5)

4.2 × 10−11/1.3 × 10−5

(1/3)

<1.0 × 10−4/<1.0 × 10−4

(1.5/1.5)

<1.0 × 10−7/<1.0 × 10−7

(1/1)

1/1

 

KDR

5.0 × 10−4/3.0 × 10−4

(6/10)

5.3 × 10−4/3.0 × 10−4

(8/9)

7.0 × 10−4/4.0 × 10−4

(7/7)

1.2 × 10−6/1.8 × 10−7

(2/2)

0.995/0.99

 

HIF1A

9.8 × 10−3/9.8 × 10−3

(41/89.5)

1.0 × 10−2/1.0 × 10−2

(40.5/96)

2.4 × 10−2/2.1 × 10−2

(45/104)

1.1 × 10−2/2.1 × 10−2

(96/256)

0.655/0.61

 

VEGFA

1.4 × 10−2/1.9 × 10−3

(51/28)

1.5 × 10−2/5.0 × 10−4

(49.5/13)

3.0 × 10−2/3.4 × 10−3

(59/27)

2.2 × 10−3/5.6 × 10−4

(22/33)

0.015/0.485

 

ARNT

1.6 × 10−2/9.0 × 10−4

(56/19)

1.7 × 10−2/1.5 × 10−3

(63/24)

2.2 × 10−2/1.9 × 10−3

(44/18.5)

2.0 × 10−2/5.9 × 10−3

(156/128)

0.845/0.88

 

VEGFC

0.5/0.5

(956/1521)

0.502/0.502

(913/1313)

1/1

(1460/2083)

1.4 × 10−3/1.4 × 10−3

(19/63)

0.355/0.345

Q2

VNN3

8 × 10−4/0.003

(2/7)

1.2 × 10−2/2.2 × 10−2

(9/40)

2.4 × 10−3/7.0 × 10−3

(5/12)

1.4 × 10−3/2.4 × 10−3

(6/19.5)

0.545/0.485

 

PDGFD

1.8 × 10−2/3.6 × 10−2

(30/113)

4.1 × 10−2/6.5 × 10−2

(46.5/118)

2.6 × 10−2/4.5 × 10−2

(27/79)

4.4 × 10−2/5.2 × 10−2

(238/420)

0.545/0.485

 

PLAT

1.6 × 10−2/3.2 × 10−1

(24/975)

6.3 × 10−2/4.2 × 10−1

(66/1030)

3.9 × 10−2/9.2 × 10−1

(46/1952)

1.2 × 10−1/4.9 × 10−1

(452/1960)

0.255/0.075

 

LPL

2.3 × 10−2/4.1 × 10−2

(42/124)

6.5 × 10−2/8.1 × 10−2

(70/172.5)

3.4 × 10−2/9.8 × 10−2

(40/186)

8.2 × 10−2/2.2 × 10−1

(1999/1166)

0.47/0.28

 

VNN1

1.2 × 10−1/2.2 × 10−1

(176/629)

1.6 × 10−1/3.8 × 10−1

(142/957)

2.2 × 10−1/3.3 × 10−1

(242/624)

1.9 × 10−3/3.2 × 10−1

(11/1468)

0.38/0.04

  1. In each cell the top line lists the p-values and the values in parentheses give the corresponding ranks. Results are computed using nonsynonymous rare variants (before slash) or all rare variants (after slash). Power is the replicability across 200 simulations using the WS method. Genes are sorted by their p-values in the WS method using nonsynonymous rare variants.
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BMC Proceedings

ISSN: 1753-6561

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