When, in a case of uncertain paternity, a biological sample from a putative father is not available and DNA from paternal relatives has to be analysed instead, the situation is called a 'deficiency paternity test'. This branch of kinship testing is the main field of ChrX marker application and the major advantage of ChrX markers can be demonstrated here. Again, as illustrated using the royal pedigree, X-chromosomal traits or ChrX marker testing can connect pedigree members through large distances with respect to X-chromosomal tracks, however they fail when X-chromosomal lines are interrupted by father-son relationship. The benefit of ChrX testing can be shown by the presentation of some examples.
When ChrX markers are investigated in a deficiency case, the mother of the unavailable putative father (i.e. the putative grandmother) is the key figure. Instances in which she is available for genotyping, strictly speaking, do not represent deficiency cases. All ChrX alleles of the putative father can be determined by investigating her, and the MEC can be calculated using the respective formula for AS markers (Krüger et al., 1968; Table 7.1). The ChrX marker genotype of the putative grandmother can also be reconstructed to some extent from her children. If she has several daughters, it is possible to determine the parental origin of most of their ChrX alleles and therefore the grandmaternal genotype. If brothers of the putative father are available, the data are even more informative (Figure 7.2). Then, the grandmaternal genotype must have been heterozygous for all ChrX loci for which brothers of the putative father carry different alleles. If they carry identical alleles, the constellation is uninformative: the mother can be either homozygous or heterozygous at the corresponding locus. If closely linked loci have already been identified as being heterozygous, the probability of homozygosity at the original locus can be assessed by haplo-typing. This is exemplified in Figure 7.2 for DXS6801, DXs6809 and DXS6789. In this case a woman 'Nora', and her putative uncles 'Jim' and 'Joe' were tested for kinship. We typed 18 ChrX markers, including the Xp21 cluster (Szibor et al., 2005b). For some loci the constellation is informative in the sense that it narrows down the set of possible alleles of the putative grandmother (PGM) and consequently of the putative father (PF). In the present case, single STR typing revealed such a pattern and a consequent exclusion of paternity for DXS8378 and DXS10011. However, since DXS10011 is strongly prone to mutation, the exclusion was still regarded as weak. Anyhow, whilst single STR results for the Xp21 cluster were uninformative, haplotyping showed that the necessary paternal allele combination of 14-31-14 could not have been inherited from the PF. For the PF to have received this haplotype from the PGM,
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