| The effects of Misspecification of marker allele frequencies on lod-scores and NPL-scores in genetic linkage analysis, with key individuals unavailable for genotyping, are examined. Genotypes are simulated for (i) affected sib-pairs wich are analysed with nonparametric linkage (NPL) statistic and (ii) three-generation pedigrees which are analysed using the parametic lod score allele frequencies. Biallelic as well as five-allele markers are considered, and subsequent false positive rates and power to detect linkage are calculated. An extreme elevation of both false-positive rate and power is observed in the NPL analysis, whereas the lod-score analysis displays merely a mild increase. |