A new nonparametric linkage statistic for mapping both qualitative and quantitative trait loci

We describe an alternative nonparametric linkage (NPL) statistic to that of Kruglyak et al. [Am. J. Hum. Genet. 58:1347-63, 1996] that can be used wit h qualitative phenotypes, and is easily extended for use with quantitative phenotypes. We analyzed the Genetic Analysis Workshop 12 simulated isolated population data, replicate 1, using two phenotypes; affected status (AFF) a dichotomous phenotype and quantitative trait Q5, which was chosen since i t was the most strongly associated with AFF. One false positive significant NPL score was observed for the AFF phenotype. For Q5 a single region on ch romosome I reached genome-wide significance. The peak of this signal was fo r marker D01G137 at 135.1 cM with a quantitative trait locus (QTL)-NPL scor e of 4.19. The nearest marker to the true location of the major gene (MG5 a t 137.1 cM) was D01G139 at position 135.8 cM, where the QTL-NPL score was s till high at 4.08. ((C)) 2001 Wiley-Liss, Inc.