Use of principal components to aggregate rare variants in case-control and family-based association studies in the presence of multiple covariates

Table 1 Average P-values obtained with the three methods for the nine genes containing variants with an effect on phenotype Q1 over 200 replicates

Gene	Number of variants		Principal components and collapsing method	Weight-based collapsing method	Step-up method
	Total	With effect
ARNT	18	5	0.044	0.066	0.041
ELAVL4	10	2	0.177	0.303	0.388
FLT1	35	11	4 × 10⁻²¹	<10⁻⁵	<10⁻⁵
FLT4	10	2	0.132	0.182	0.186
HIF1A	8	4	0.008	0.091	0.074
HIF3A	21	3	0.51	0.488	0.320
KDR	16	11	0.003	0.587	0.059
VEGFA	6	1	0.289	0.2345	0.262
VEGFC	1	1	0.054	0.067	0.080

ISSN: 1753-6561