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

Table 1 Results of linkage analyses of replicate 4 using redefined 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	0.90	0.79	0.87	0.96
Two-point LOD score^b	3.91	2.22	2.22	3.19
Multipoint Z_max/NPL p-values^c
GENEHUNTER
NPL p-value	0.000021	0.0026	3.23e-06	2.16e-07
Multipoint HLOD (α)	3.65 (1.00)	2.45 (0.96)	5.93 (1.00)	6.36 (1.00)
MERLIN
NPL p-value	<0.00001	0.00004	<0.00001	<0.00001
SIMWALK2
NPL p-value	0.0001	0.0066	0.0012	ND^e
SIBPAL
p-value	5.8 × 10^-7	9.5 × 10^-8	4.8 × 10^-6	7.0 × 10^-7
1-LOD interval (cM)^d	5.23	12.55	8.16	7.54

^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