At how many histocompatibility loci do congenic mouse strains differ? Probability estimates and some implications

An expression is derived for the probability that a congenic strain and its inbred partner will differ by multiple linked histocompatibility genes when the number of incompatibilities between the original donor and background strains is known and the number of backcrosses to produce the strain is specified. This probability is shown to be rather large for typical values of the pertinent variables. Potential complications in data interpretation arising from unsuspected multiple incompatibilities between a congenic pair are discussed in relation to antigenic strength, H-locus polymorphism tissue distribution of H antigens, and certain types of experiments in which the cell-mediated lympholysis assay is used.