The availability of molecular genotyping assays, which can accurately detect the presence of paternal alloalleles, provide an important tool in managing pregnancies at risk for immune cytopenic disorders. Despite their utility and effectiveness, molecular diagnostic methodologies are not free of potential problems. Users must be aware that the presence of a gene does not necessarily correspond to the expression of the encoded protein antigen on the cell surface. A limitation of ASPCR, as well as other approaches, is that new allelic variants might not be detected because they might not possess sequences to which specific primers or probes are directed. Therefore, it is necessary to identify discordance between parental serotypes and genotypes when conducting prenatal genotyping for immune cytopenic disorders. When using fetal genotyping alone, failure to identify inconsistencies between parental serotypes and genotypes can lead to an incorrect assumption of fetal serology. Even with this precaution, although unlikely, it is conceivable that certain variants or combinations of variants might be undetectable. Additionally, the possibility of nonpaternity can negate the effort of establishing concordance between the "paternal" serotype and genotype.

The extreme sensitivity of PCR-based assays is beneficial when attempting to identify antigen incompatibilities between a pregnant woman and her fetus. Even extensive maternal contamination of an amniotic sample, which we have found to be infrequent, is unlikely to interfere with the detection of an incompatible allele in the fetus, because only a few copies of a template DNA are required for its detection. However, it is advisable to confirm the fetal origin of DNA used for genotyping by VNTR analysis before withdrawing further monitoring or therapy in fetuses identified as being not at risk.

In sensitized women, where the father's blood type is unknown or the father is heterozygous for the antigen system in question, establishing the fetal blood type can be accomplished through cordocentesis. However, the risk of pregnancy loss with cordocentesis is greater than the risk associated with amniocentesis, and the ability to serotype the fetal blood sample might be complicated by the presence of maternal antibody. Genotyping, using DNA isolated from amniocytes, is an especially useful tool for identifying fetuses at risk for immune cytopenic disorders. In cases where the father is potentially incompatible with the mother, or his phenotype is unknown, establishing that the fetus lacks the relevant allele and is, therefore, not at risk, obviates the need for expensive and invasive monitoring by amniocentesis throughout the pregnancy. Identifying a fetus as being at risk, on the other hand, allows for appropriate monitoring, early intervention, and improved care.

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