Consensus DNA profiling of formalin-fixed paraffin-embedded tissues: from genetic puzzle to a clear picture

The report describes an intricate investigation performed on formalin-fixed paraffin-embedded (FFPE) specimens for forensic purposes. The judicial authority asked to verify whether the death of a stillborn fetus was due to an acute or chronic placental disease. Post-mortem fetal organs and placenta were stored in formalin, embedded in paraffin and sectioned to prepare slides for histopathological examination. However, it was necessary a genetic verification to ensure the identity of the paraffin blocks as originating from the fetus’ organs and from the mother’s placenta. Hence, an oral swab was collected from the mother (M). The investigation involved 26 paraffin blocks from which we cut three sections for DNA extraction. Each sample underwent two rounds of amplification. Capillary electrophoresis revealed partial DNA profiles, due to degradation of the genetic material. Therefore, we used the ‘consensus’ profile approach based on replications. Using this approach, we created a genetic profile by combining and analyzing multiple partial DNA profiles from different sources. For the organs, for which a single block was available, the sample was divided into separate aliquots and a consensus profile was generated from the replicates that included alleles that appeared in two or more of the replicates. For organs with multiple blocks, we created a unified consensus profile by integrating the various partial profiles obtained from each block. The consensus placenta profile (CPP) and the consensus umbilical cord/chorionic membrane profile (CPU) were mixture profiles. The likelihood ratio (LR) approach was used to verify the relationship between the CPP and M profile and between CPP and the CPU. Then, the analysis – performed with LRMix software – confirmed that the DNA mixture belonged to M and her fetus rather than two unknown individuals, while Familias 3 software confirmed the biological relationship between M and her foetus. In this case, the consensus profiling approach allowed us to obtain a reliable genetic identification, overcoming the challenges of DNA degradation and to assess the mother-fetus relationship.