Table 4 The impact of misdiagnosis in estimating genetic parameter from genome-wide genotypes

							Proportion of variance explained by SNPs
M _TA	M _TB	‘True’ (T) or diagnosed (D) disorders	Estimated from data or calculated ^a	σ _uA ²	σ _uB ²	σ ² _uA,uB	Disorder A	Disorder B	r g
0	0	T	Estimated	0.096	0.112	0.002	0.391 (0.089)	0.470 (0.093)	0.023 (0.155)
0.1	0	D	Estimated	0.096	0.092	0.013	0.387 (0.029)	0.393 (0.023)	0.139 (0.055)
		D	Calculated	0.096	0.095	0.010	0.385	0.396	0.109
0.1	0.1	D	Estimated	0.075	0.093	0.024	0.304 (0.034)	0.388 (0.035)	0.296 (0.092)
		D	Calculated	0.079	0.093	0.021	0.316	0.383	0.244

Calculated using equations in text based on the estimates from the true disorders and misclassification rates.
M_TA proportion of disorder A cases labelled as disorder B cases; M_TB proportion of disorder B cases labelled as disorder A cases. Values in parentheses are the standard errors for the parameters estimated when M_TA=M_TB=0, but otherwise are the standard deviations over 100 replicates.

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