Comparison of scoring methods for the detection of causal genes with or without rare variants

BMC Proceedings

Table 1 Results of mixed model analysis of the ranked gene lists for all phenotypes

Phenotype	Gene list cutoff (N)	MS vs. HT	MS vs. MV	MS vs. LA	HT vs. MV	HT vs. LA	MV vs. LA	AF = 1% vs. AF = 5%	CV vs. RV	IA AF = 1% and CV
Q1	10	−0.27***	−0.25***	−0.15***	0.02	0.13***	0.10***	−0.18***	−0.73***	0.43***
	20	−0.19***	−0.18***	−0.11***	0.01	0.08***	0.07***	−0.10***	−0.71***	0.45***
	50	−0.14***	−0.12***	−0.03	0.02	0.11***	0.09***	0.01	−0.66***	0.51***
	100	−0.05	−0.03	0.06*	0.02	0.11***	0.09**	0.10***	−0.77***	0.76***
	200	−0.01	0.01	0.11***	0.02	0.12***	0.10***	0.21***	−1.09***	1.07***
	500	0.08*	0.09**	0.13***	0.01	0.05	0.04	0.42***	−2.00***	1.85***
Q2	10	−0.04	−0.06	0.03	−0.02	0.07*	0.09**	0.14***	−0.67***	0.32***
	20	−0.03	−0.03	−0.04	−0.00	−0.01	−0.01	0.14***	−1.05***	0.46***
	50	0.08	0.07	−0.01	−0.01	−0.09*	−0.08*	0.26***	−1.69***	0.56***
	100	0.14**	0.13**	−0.00	−0.01	−0.14**	−0.14**	0.22***	−2.32***	0.72***
	200	0.11*	0.12*	0.04	0.01	−0.07	−0.08	0.03	−3.14***	1.13***
	500	0.25***	0.25***	0.11*	0.00	−0.13*	−0.13*	0.18***	-3.88***	1.19***
AFF	10	0.03	−0.01	0.04**	−0.04*	0.02	0.06***	−0.15***	0.02	−0.03
	20	0.09***	0.08***	0.05**	−0.01	−0.04*	−0.03	−0.16***	0.03	−0.03
	50	0.16***	0.14***	0.03	−0.02	−0.13***	−0.11***	−0.14***	0.03	−0.05
	100	0.34***	0.29***	0.11***	−0.05	−0.23***	−0.18***	−0.13***	0.14***	−0.16***
	200	0.44***	0.34***	0.07	−0.10*	−0.37***	−0.27***	−0.20***	0.21***	−0.25***
	500	0.69***	0.60***	0.15***	−0.09*	−0.54***	−0.45***	−0.40***	0.39***	−0.33***

N is the cutoff value of the ranked gene lists for inclusion in a future replication study. MS, maximum statistics method. HT, Hotelling’s T² test. MV, multivariate analysis. LA, LASSO method. AF, cutoff for allele frequency denoting rare variants. CV, analysis of common variants alone. RV, analysis of both common and collapsed rare variants. IA = interaction term. For the comparisons, values denote the average difference in number of detected causal genes. Negative numbers indicate a lower number of causal genes under the first setting. Significant positive and negative effects are in boldface and italics, respectively.
* p < 0.05.
** p < 0.01.
*** p < 0.001.

ISSN: 1753-6561