Identifying single-nucleotide polymorphisms responsible for the linkage signal of rheumatoid arthritis on chromosome 6 by joint modeling of linkage and association

Table 1 Four models compared in the three likelihood-ratio tests

Model^a		Likelihood	d.f.	Parameters^b	LR tests
(1)	BM	L(θ = $\frac{1}{2}$ , r² = 0)	1	p _A
(2)	LE	L(θ = 0, r²= 0)	4	p_A, p_D, f_DD, f_Dd, f_dd	(2) vs. (1): test for linkage
(3)	GM	L(θ = 0, 0 <r² < 1)	5	p_DA, p_Da, P_dA, f_DD, f_Dd, f_dd	(3) vs. (2): test for association in the presence of linkage
(4)	LD	L(θ = 0, r² = 1)	3	p_A, f_DD, f_Dd, f_dd	(3) vs. (4): test for other linked variants

^aBM, base model; LE, linkage equilibrium; GM, general model; LD, linkage disequilibrium.
^bP_A= marker allele frequency; P_D= disease allele frequency; f_g= P(affected | g), g ∈ {DD, Dd, dd}; p_DA, p_Da, p_dAare the marker-disease haplotype frequencies.

ISSN: 1753-6561