Mapping Haplotype-haplotype Interactions with Adaptive LASSO

BMC Genomic Data

Table 3 List of selected genes, corresponding "risk" haplotype structure, effect estimates and permutation p-values

SNP ID (allele)	Gene (region)	"Risk" haplotype	a _s	d _s	a _t	d _t	i _aa	i _ad	i _da	i _dd
9508994 (C/T)	PON1 (intron 1)	[TC]^M	0	0	0	0	0	-0.45	0	0
20209376 (C/T)	PON1 (intron 5)	[CC]^O						p* = 0.001
659435566 (C/T)	NFKB1 (exon 12)	[CC]^M	0	0	0	0	-0.33	0	0	0
659435702 (C/G)	NFKB1 (intron 22)	[TC]^O					p* = 0.001
22767327 (A/T)	FLT4 (intron 7)	[AT]^M	0	0	0	0	0	-0.30	0	0
22175087 (C/T)	FLT4 (intron 8)	[TC]^O						p* < 0.001
1125300 (G/T)	SPARC (intron 3)	[TT]^M	0	-0.38	0	0	0	0	0	0.245
1125290 (G/T)	SPARC (intron 5)	[TT]^O		p* = 0.001						p* < 0.001
634841108 (A/C)	TIMP2 (intron 2)	[AG]^M	0	0	0	0	0	0	0	0.68
634841123 (A/G)	TIMP2 (exon 3)	[CG]^O								p* < 0.001
634018768 (A/G)	HPGD (promoter)	[AG]^M	0	0	0.44	0	0	0	0	0
636105057 (A/G)	HPGD (promoter)	[GA]^O			p* < 0.001
17252653 (G/T)	MMP9 (intron)	[GC]^M	0	0	0.53	0	0	0	0	0
17254821 (C/G)	MMP9 (exon 10)	[TC]^O			p* < 0.001

^M mother's "risk" haplotype information; ^O offspring's "risk" haplotype information
p* is the permutation p-value.

ISSN: 2730-6844