Estimating the effect of SNP genotype on quantitative traits from pooled DNA samples

Table 1 Simulated data, regression of results from logistic regression of pooled data on results from least squares regression of individual data

Number of pools			3000	1024	512	256	128	64	32	16	8	4	2
Parameter	Statistic	Subset	With no genotyping error simulated
α	R²	All SNP	0.998	0.998	0.998	0.998	0.998	0.998	0.998	0.996	0.994	0.987	0.957
		MLP < 5	0.999	0.999	0.999	0.999	0.999	0.998	0.997	0.992	0.983	0.955	0.849
	Slope	All SNP	0.967	0.967	0.967	0.967	0.966	0.967	0.967	0.967	0.966	0.962	0.965
		MLP < 5	0.997	0.998	0.998	0.997	0.998	0.996	0.995	0.989	0.979	0.980	0.993
MLP	R²	All SNP	0.999	0.999	0.999	0.999	0.999	0.999	0.999	0.998	0.997	0.993	0.978
		MLP < 5	0.999	0.999	0.999	0.999	0.998	0.997	0.993	0.983	0.964	0.903	0.686
	Slope	All SNP	0.923	0.923	0.922	0.922	0.922	0.921	0.918	0.909	0.886	0.819	0.622
		MLP < 5	0.997	0.997	0.996	0.997	0.998	0.994	0.991	0.971	0.920	0.825	0.618
			With genotyping error (SD = 0.05) simulated
α	R²	All SNP	-	0.975	0.929	0.895	0.861	0.808	0.705	0.597	0.388	0.110	0.024
		MLP < 5	-	0.911	0.693	0.527	0.385	0.318	0.181	0.100	0.059	0.004	0.015
	Slope	All SNP	-	0.929	0.900	0.903	0.915	0.894	0.908	0.911	0.947	0.829	0.873
		MLP < 5	-	0.773	0.618	0.587	0.543	0.572	0.639	0.503	0.721	-0.370	-1.586
MLP	R²	All SNP	-	0.996	0.988	0.982	0.971	0.942	0.881	0.819	0.677	0.455	0.195
		MLP < 5	-	0.909	0.765	0.680	0.577	0.334	0.139	0.076	0.053	0.039	0.016
	Slope	All SNP	-	0.910	0.907	0.916	0.928	0.909	0.917	0.902	0.906	0.758	0.531
		MLP < 5	-	0.924	0.882	0.871	0.831	0.823	0.757	0.670	0.953	1.424	1.112

Simulated data, 3000 individuals, regression of results from logistic regression (genotype on phenotype, 3000 individuals or pooled data) on results from least squares regression (phenotype on genotype, 3000 individuals); parameters are the estimated effect (α) and minus the log p-value (MLP); the coefficient of determination (R²) and slope of the regression line are shown; results are presented for all SNP, or for SNP with MLP from individual data less than 5 (p-value > 1E-05), and with no genotyping error simulated, or with genotyping error (SD = 0.05) simulated

ISSN: 1297-9686