Caution in the interpretation of MLS.

ABSTRACT

We study the statistical properties of the maximum likelihood score (MLS) test. We show that the criteria for reaching conclusions about linkage are not the same for single point analysis as for multipoint, where the maximization is performed over an additional parameter, the position in the marker interval where the MLS is computed. In addition, this test is shown to be very sensitive to errors in allele frequencies and recombination fraction.