Linkage analysis with adequate modeling of a parent-of-origin effect

We present an extension to parametric linkage analysis that allows modeling diseases with a parent-of-origin effect (i.e., imprinting). Different pene trances are assumed for individuals being heterozygous at the disease locus , depending on their having inherited the disease allele from the father or mother. Motivated by the finding of a maternally expressed locus influenci ng alcohol consumption in mice (Alcp2), the analysis method has been includ ed into the program GENEHUNTER for application to Problem 1, Collaborative Study on the Genetics of Alcoholism of Genetic Analysis Workshop 11. By thi s extension, a powerful tool is provided for adequately modeling an inherit ed disease in linkage analysis that supposedly has imprinting effects. The program has been used to analyze the data set on alcohol dependence in huma ns and can be applied to other genetically determined traits as well. (C) 1 999 Wiley-Liss, Inc.