The sizes of marker amplimers were determined (blinded to pedigree structure and subject characteristics) from the electropherogram using the Genotyper software package (ABI). All electropherograms were visually inspected and exported from Genotyper in base pair sizes relative to the standard measured to one hundredth of a base pair. Fragment sizes were binned to alleles by using an automated algorithm developed by one of the authors (K.C.W.), which assumes that the distribution of allele sizes will have a sine-squared distribution with a fitted periodicity near two base pairs. The program determines the best periodicity and phase for the modeled distribution relative to the observed distribution. Fragments that are distributed between minimums of the modeled distribution are assumed to be the same allele. Allele frequencies observed in the founders were used for all analysis. The sex-averaged marker map order obtained from the manufacturer was used and verified with the family data from the current sample.
