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

BMC Proceedings

Table 2 Characteristics of genes for which gene-wise scoring methods performed differently

	MS vs. HT						MS vs. LA
	CR1%			CR5%			CR1%			CR5%
	MS better	HT better	p-value	MS better	HT better	p-value	MS better	LA better	p-value	MS better	LA better	p-value
Rank (MS)/rank (other method)	0.53 (0.14)	2.4 (2.56)		0.56 (0.15)	1.43 (0.31)		0.7 (0.23)	3.09 (3.81)		0.72 (0.58)	1.41 (0.34)
Genes with better ranks	13/27	8/27		12/29	13/29		7/27	4/27		7/29	5/29
Markers per gene	5.8 (2.6)	2 (0.8)	<0.001	4.8 (2.1)	1.5 (0.9)	<0.001	4.3 (2.7)	5.8 (4.9)		4.2 (2.2)	2.2 (1.1)
Causal SNPs per gene (number)	1.3 (0.5)	1.4 (0.7)		1.1 (0.3)	1.2 (0.4)		1.4 (0.5)	2.5 (1.3)		1.2 (0.4)	1.6 (0.5)
Causal SNPs/gene (%)	25.6 (11.6)	72.9 (29.5)	0.002	26 (10.7)	88.5 (21.9)	<0.001	42.8 (27.9)	68.4 (40)		39.6 (32)	80 (27.4)
Frequency-adjusted effect size of strongest variant	0.038 (0.024)	0.044 (0.023)		0.025 (0.02)	0.048 (0.025)	0.02	0.033 (0.022)	0.05 (0.023)		0.025 (0.022)	0.066 (0.028)	0.03
Frequency of strongest variant	0.047 (0.077)	0.053 (0.071)		0.046 (0.07)	0.049 (0.06)		0.066 (0.103)	0.083 (0.065)		0.085 (0.103)	0.077 (0.063)
Relative effect size of second strongest variant (%)	40.5 (29.8)	63.6 (51.3)		10.9 (NA)	54.5 (23.5)		34 (20.4)	87.9 (10.4)	0.03	10.9 (NA)	54.5 (23.5)

MS, maximum statistics method. HT, Hotelling’s T² test. LA, LASSO method. CR1% are CR5% the data sets with rare variants using a 1% or a 5% cutoff of allele frequency, respectively. Means and standard deviations are presented. p-values are based on a two-group t-test. Characteristics that show significant differences in CR1% as well as in CR5% are in boldface.

ISSN: 1753-6561