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Table 1 Mean false discovery proportion (FDP), mean number of falsely rejected null hypotheses out of 99,600, i.e. false positives (FP) and mean number of correctly rejected non-null hypotheses i.e. true positives (TP) over 100 simulation runs and a covariate-modulated false discovery rate (cmfdr) cut-off of 0.05

From: A correction for sample overlap in genome-wide association studies in a polygenic pleiotropy-informed framework

Model

Independent

Independent, eq. power

Overlapping

Overlapping, corrected

Null

    

FDP

–

–

–

–

TP

–

–

–

–

FP

0

0

245.14 (237.9, 252.4)

0

Positive Pleiotropy A (400 non-null SNPs)

    

FDP

0.0053 (0.0044, 0.0063)

0.0030 (0.0024, 0.0037)

0.39 (0.39, 0.40)

0.0056 (0.0048, 0.0065)

TP

260.9 (259.6, 262.1)

283 (282.0, 284.1)

330.4 (329.5, 331.4)

243.4 (242.1, 244.7)

FP

1.4 (1.2, 1.7)

0.9 (0.7, 1.1)

215.7 (210.1, 221.4)

1.4 (1.2, 1.6)

Positive Pleiotropy + Univariate (400 non-null SNPs)

    

FDP

0.008 (0.007, 0.009)

0.005 (0.004, 0.006)

0.48 (0.48, 0.49)

0.01 (0.008, 0.01)

TP

233.4 (232.1, 234.7)

270.4 (269.4, 271.5)

306.1 (304.7, 307.4)

209.8 (208.4, 211.2)

FP

2.0 (1.7, 2.2)

1.3 (1.1, 1.5)

289.2 (282.4, 296.1)

2.08 (1.8, 2.4)

Positive + Antagonistic Pleiotropy (400 non-null SNPs)

    

FDP

0.005 (0.005, 0.006)

0.004 (0.003, 0.005)

0.46 (0.45, 0.47)

0.008 (0.007, 0.010)

TP

261.5 (260.4, 262.6)

290.8 (289.6, 291.9)

280.9 (280.0, 282.2)

228.7 (227.3, 230.1)

FP

1.4 (1.2, 1.6)

1.2 (1.0, 1.4)

240.1 (233.8, 246.4)

2.0 (1.7, 2.2)

Positive Pleiotropy B (1200 non-null SNPs)

    

FDP

0.018 (0.008, 0.020)

0.013 (0.012, 0.014)

0.32 (0.31, 0.33)

0.029 (0.027. 0.031)

TP

295.65 (293.01, 298.29)

425.38 (422.42, 428.34)

618.30 (615.22, 621.38)

310.94 (308.22, 313.66)

FP

5.51 (5.05, 5.97)

5.60 (5.11, 6.09)

294.64 (288.18, 301.10)

9.36 (8.70, 10.02)

Positive Pleiotropy C (2200 non-null SNPs)

    

FDP

0.019 (0.017, 0.021)

0.018 (0.016, 0.020)

0.36 (0.35, 0.36)

0.034 (0.032, 0.037)

TP

159.71 (157.63, 161.79)

243.98 (241.91, 246.04)

575.33 (570.58, 580.08)

184.10 (181.68, 186.52)

FP

3.16 (2.80, 3.52)

4.49 (4.05, 4.92)

324.94 (317.67, 332.20)

6.59 (6.08, 7.10)

  1. Results are presented for six different simulation scenarios: the null model, where both traits are independent from genotype (all SNPs are null); positive pleiotropy A with 400 SNPs that are non-null for both traits; positive pleiotropy plus univariate effects for trait 1, where 200 SNPs were non-null for traits 1 and 2 and 200 SNPs were non-null for trait 1 only; positive plus antagonistic pleiotropy, where 400 SNPs were non-null for both traits 1 and 2, and half of these non-null SNPs have an effect in opposing directions for trait 1 and 2; positive pleiotropy B with 1200 SNPs that are non-null for both traits, 200 with large effects and 1000 with small effects; positive pleiotropy C with 2200 SNPs that are non-null for both traits, 200 with large effects and 2000 with small effects. In all six scenarios d=100,000 SNPs were simulated, the correlation due to overlap is 0.4 and the test statistics for study 2 were used as a covariate for study 1 for the covariate-modulated fdr. For each simulation scenario, we divided the simulated subjects into the following GWAS pairs: Independent, independent GWASs with no overlap (each with n=10,000), Independent eq. power, independent equally-powered GWASs (each with n=12,500 like the GWASs with overlapping subjects), Overlapping, uncorrected overlapping GWAS with (each with n=12,500 including,5000 overlapping, subjects) and Overlapping, corrected, the GWAS with 5,000 overlapping subjects after correction for sample overlap. Data is presented as mean (95% confidence interval)
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BMC Genomics

ISSN: 1471-2164

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