Two-stage study designs for analyzing disease-associated covariates: linkage thresholds and case-selection strategies

Table 2 Characteristics of simulated loci

			Average^a
Chr	Locus (closest SNP)	Distance between true locus and closest SNP (cM)	NPL (SD) at locus^b	SNP MAF^c in cases (one per family, n = 1500)	SNP MAF in controls (n = 2000)	r² between SNP and true locus
9	G (186)	0.08	0.01 (0.30)	0.374	0.384	0.01
11	F (389)	0.01	0.34 (0.49)	0.275	0.501	0.94
18	E (269)	0.05	0.92 (0.81)	0.297	0.223	0.15

^aAverages calculated across 100 replicates
^bNPL, nonparametric multipoint LOD score from MERLIN when analyzing binary RA affection status
^cMAF, minor allele frequency

ISSN: 1753-6561