Comparison of multipoint linkage analyses for quantitative traits in the CEPH data: parametric LOD scores, variance components LOD scores, and Bayes factors

Table 2 Highest LOD score or log (Bayes factor) and run time (in minutes)

			CHI3L2 147 cM (chr 1)^a		GSTM1 142 cM (chr 1)		PSPH 80 cM (chr 7)		VAMP8 113 cM (chr 2)
Model	Program	Scans	Stat^b	Time	Stat	Time	Stat	Time	Stat	Time
1Q	Exact	NA	11.5	1229	6.3	1234	10.1	470	3.6	1044
	lm_multiple	3 k	11.3–11.5	44	6.2–6.3	45	9.9–10.1	33	3.6–3.6	43
	lm_markers	3 k	10.7–11.6	21	5.7–6.3	21	8.1–10.3	13	3.5–3.6	20
	lm_markers	30 k	10.6–11.6	177	5.7–6.3	168	8.1–10.1	110	3.2–3.6	153
1Q + P	lm_twoqtl	30 k	13.7	563	7.2	604	10.8	401	3.8	535
1Q + UQ	lm_twoqtl	3 k	13.4	3568	5.6	816	40.4	542	4.1	808
VC	Merlin	NA	13	2	5.7	2	14.3	1	5	2
Bayesian	Loki	999 k	2.9	707	2.6	700	2.6	504	1.9	513

^apeak position (± 1 cM) from all analyses and gene location except VAMP8 (120–123 cM).
^bMORGAN and VC programs, the statistic (stat) is the LOD score with range (min and max) over 10 runs and time is the median of 10 runs for MCMC programs; Loki, stat is the log₁₀ (Bayes factor) for one run.