Simulating autosomal genotypes with realistic linkage disequilibrium and a spiked-in genetic effect

BMC Bioinformatics

Table 1 Original genetic signals (indicated by p values) are absent in the simulated data

SNP	Original GWAS^a			Type I error rates using simulated data ^b
	Asian	Caucasian	Both	Asian	Caucasian	Both
	n = 1028	n = 871	n = 1899	n = 1000	n = 1000	n = 1000
rs560426	3.84E-08	1.73E-03	1.12E-09	0.063	0.044	0.045
rs481931	6.93E-05	1.22E-03	3.04E-07	0.054	0.041	0.049
rs4147811	3.08E-05	6.16E-04	6.99E-08	0.057	0.043	0.053
rs2073485	1.24E-07	5.93E-01	4.02E-06	0.054	0.043	0.050
rs2013162	7.98E-07	2.98E-01	1.02E-05	0.052	0.038	0.061
rs861020	1.38E-04	7.34E-03	4.01E-06	0.055	0.047	0.056
rs10863790	7.31E-09	1.14E-01	2.01E-09	0.048	0.045	0.049
rs987525	8.53E-04	2.94E-12	1.74E-14	0.042	0.054	0.051
rs6072081	1.90E-06	2.10E-03	2.52E-08	0.045	0.053	0.040
rs6065259	1.00E-05	1.19E-02	7.57E-07	0.055	0.047	0.048
rs17820943	1.50E-07	5.70E-03	9.81E-09	0.038	0.059	0.051
rs13041247	8.80E-08	4.56E-03	4.92E-09	0.040	0.058	0.048
rs11696257	9.39E-08	5.07E-03	5.88E-09	0.041	0.057	0.053
rs6102085	8.67E-08	1.23E-01	5.00E-07	0.046	0.055	0.050

^aThe p values were based on the complete triads, which were used in the simulation study
^bBased on a per-comparison α-level of 0.05 and 2000 simulated studies

ISSN: 1471-2105