Linkage analysis of the GAW14 simulated dataset with microsatellite and single-nucleotide polymorphism markers in large pedigrees

Table 2 Results of linkage analyses of replicate 4 using original affection status.

Results from linkage analyses>	Type of Marker Set
	STR-7.5 cM	SNP-3 cM	SNP-1 cM	SNP-0.3 cM
Information content^a	0.84	0.75	0.86	0.96
Two-point LOD score^b	0.93	0.31	1.97	1.97
Multipoint Z_max/NPL p-values^c
GENEHUNTER
NPL p-value	0.0026	0.033	0.0028	0.00084
Multipoint HLOD (α)	1.34 (0.51)	0.49 (0.36)	2.54 (0.70)	2.91 (0.74)
MERLIN
NPL p-value	0.0006	0.005	0.0006	0.0001
SIMWALK2
NPL p-value	0.0016	0.1153	0.0055	ND^e
SIBPAL
p-value	0.0114	0.0203	0.0198	0.00014
1-LOD interval (cM)^d	7.85	20.16	12.14	5.16

^aAveraged information content estimated from all markers on STR, SNP-1 cM, SNP-0.3 cM marker sets and the telomeric 50 markers on SNP-3 cM map using the entropy function in MERLIN.
^bReflected the highest LOD scores obtained at the telomeric region.
^cLinkage signal at the telomeric region of chromosome 3 was successfully detected by all marker panels. LOD scores and p-values reflected the most significant results for each panel.
^dEstimated from multipoint LOD-score curves obtained from GENEHUNTER analyses.
^eNot determined because of the failure in convergence.

ISSN: 2730-6844