X-chromosome inactivation patterns at the HUMARA locus. Two controls of random inactivation (the presence of both alleles 1r and 2r before and after HpaII digestion) and skewed inactivation (presence of 2 alleles 1k and 2k before and 1 allele 2k after HpaII digestion) are included. The male patient has 1 allele 1p corresponding to his active X chromosome; the same allele is absent after HpaII digestion, indicating its normal active status. Two alleles were detected for the mother (1m and 2m) and the sister (1s and 2s) before and after HpaII digestion, indicating a normal random X-Chr inactivation in both. In most of the diagrams, peaks appear in duplicate, which is the result of unspecific flanking dATP added by the taq polymerase (for some of the product) at the 3′ end of the PCR product. The small peaks to the left side of each major peak are a result of slippage of the taq polymerase during the PCR reaction that results in amplifications of n-1 of the cag repeats.