Construction of conditional lod tables from multiple-locus linkage data.

Abstract

Although multipoint linkage data are becoming quite common, economical and efficient methods for presenting these data are not yet in use. Tables giving the full likelihood function would be very voluminous, whereas reduction to standard lods destroys part of the information. We suggest a special lod table representation which preserves nearly all the information about both gene order and genetic map distance at a great reduction in data presented. Conditional lods, coined "c-lods" to distinguish them clearly from ordinary lods, are calculated for distances between each adjacent pair of loci, with all distances among other loci in the system conditionally optimized. Thus, in an n-locus system, conditional lods are presented for the n - 1 adjacent pairs of loci only. The principal reason for reporting lod scores is the potential for combining data from separate studies to reach conclusive evidence for linkage and gene order. Because estimates of recombination are different in each set of data, the crux of the problem is to present scores that provide a close approximation to the true likelihood away from maximum likelihood (ML). The sum of conditional lods closely approximates the likelihood throughout the domain. Therefore, conditional lods contribute appropriately when mapping from several sources of data, so contradictory estimates can be reconciled efficiently.