Assessing accuracy in linkage analysis by means of confidence regions

When statistical linkage to a certain chromosomal region has been found, it is of interest to develop methods which quantify the accuracy with which the disease locus can be mapped. In this paper, we investigate the performance of three different types of confidence regions with asymptotically correct coverage probability as the number of pedigrees grows. Our setup is that of a saturated map of marker data. We show that the expected length of the confidence region is inversely proportional to the square of the noncentrality parameter and to a certain normalized slope-to-noise ratio. Our investigations reveal that testing performance criteria (such as the power to detect linkage) can be quite different from estimation based performance criteria (such as the expected length of a confidence region).