Collapsing-based and kernel-based single-gene analyses applied to Genetic Analysis Workshop 17 mini-exome data

BMC Proceedings

Table 2 Top 10 disease-associated genes from different methods

Collapsing	Weighted-sum	Kernel (weighted IBS)	CMC (both synonymous and nonsynonymous SNPs)	CMC (synonymous SNPs only)	Collapsing (nonsynonymous SNPs only)	Weighted sum (nonsynonymous SNPs only)	Kernel (weighted IBS, nonsynonymous SNPs only)	CMC (nonsynonymous SNPs only)	Kernel (IBS, nonsynonymous SNPs only)
*PIK3C3*	*PIK3C3*	FLT1	FLT1	PRH1	FLT1	FLT1	MAP3K6	FLT1	OR2T3
FLT1	FLT1	TAS2R48	PRH1	TAS2R48	*PIK3C3*	*PIK3C3*	NOTCH2NL	*PIK3C3*	OR2T34
PRH1	PRH1	PRH1	*PIK3C3*	ZNF91	KDR	KDR	FLT1	KDR	HLA-A
PRR4	PRR4	PRR4	OR52E4	*PTK2B*	KCNJ12	OR52E4	OR2T34	OR2T3	OR52E4
*PTK2B*	*PTK2B*	*PIK3C3*	TAS2R48	LOC645118	ZNF77	NOTCH2NL	RGPD4	MAP3K6	FLT1
ZNF91	ZNF91	SUSD2	KDR	INSR	NOTCH2NL	ZNF77	LRP1B	HLA-L	KCNJ12
NOTCH2NL	NOTCH2NL	KCNJ12	NOTCH2NL	TERT	OR9G1	BRCA1	*PIK3C3*	VNN1	*PIK3C3*
TAS2R48	TAS2R48	OR52E4	*PTK2B*	EPHB1	OR2T3	OR9G1	VNN1	PATE	SUSD2
MUSK	MUSK	HLA-B	ZNF91	PRR4	EPHA5	OR2T3	MYO3A	E2F2	HLA-L
KIT	KIT	*PTK2B*	LRP1B	TNK1	E2F2	MAP3K6	TACC2	C1ORF147	SSTR4

For the kernel-based methods, there are 43 genes (Kernel, weighted IBS) and 19 genes (Kernel, weighted IBS, nonsynonymous SNPs only) that have p-values less than 10⁻¹⁶ and thus are reported as 0. These genes cannot be ranked effectively. Genes in bold and italic are causal genes for disease liability; genes in bold are associated with Q1 or Q2.

ISSN: 1753-6561