Modeling the effect of an associated single-nucleotide polymorphism in linkage studies

BMC Genomic Data

Table 1 Single-point LOD scores at five microsatellite markers at the end of chromosome 3.

Model and SNPs	Chromosomes
	D3S0123		D3S0124		D3S0125		D3S0126		D3S0127
Null model (linkage only)
	l₁^a		l₁		l₁		l₁		l₁
	1.65		4.51		0.41		1.97		3.06
Including parental SNP genotypes
	l₂ – l₁^c	l₂^b	l₂ – l₁	l₂	l₂ – l₁	l₂	l₂ – l₁	l₂	l₂ – l₁	l₂
B03T3056	0.33	1.98	0.22	4.73	0.10	0.51	0.42	2.39	0.25	3.31
B03T3057	0.00	1.65	0.02	4.53	0.04	0.46	0.02	1.99	0.03	3.09
B03T3066	0.17	1.82	0.03	4.54	0.11	0.54	0.00	1.97	0.42	3.48
Including siblings' SNP genotypes
	l₂ – l₁^c	l₂^b	l₂ – l₁	l₂	l₂ – l₁	l₂	l₂ – l₁	l₂	l₂ – l₁	l₂
B03T3056	0.60	2.25	0.64	5.15	0.02	0.43	0.18	2.15	1.10	4.16
B03T3057	0.81	2.46	0.13	4.64	0.17	0.58	0.49	2.46	0.11	3.17
B03T3066	0.78	2.43	0.39	4.90	0.66	1.07	0.10	2.07	0.15	3.21

^al₁is LOD score under linkage only (one degree of freedom)
^bl₂is LOD score for linkage including SNP genotypes (two degrees of freedom)
^cl₂ – l₁is LOD score for comparing model with SNP genotypes to model without SNP genotypes (one degree of freedom)

ISSN: 2730-6844