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Table 1 Results of linkage analyses of replicate 4 using redefined affection status.

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

Results from linkage analyses Type of marker set
  STR-7.5 cM SNP-3 cM SNP-1 cM SNP-0.3 cM
Information contenta 0.90 0.79 0.87 0.96
Two-point LOD scoreb 3.91 2.22 2.22 3.19
Multipoint Zmax/NPL p-valuesc     
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 NDe
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
  1. 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.
  2. bReflected the highest LOD scores obtained at the telomeric region.
  3. 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.
  4. dEstimated from multipoint LOD-score curves obtained from GENEHUNTER analyses.
  5. eNot determined because of the failure in convergence.