20.500.12556/RUL-148106 SNP analysis of challenging bone DNA samples using the HID‑Ion AmpliSeq™ Identity Panel facts and artefacts PCR-MPS is an emerging tool for the analysis of low-quality DNA samples. In this study, we used PCR-MPS to analyse 32 challenging bone DNA samples from three Second World War victims, which previously yielded no results in conventional STR PCR-CE typing. The Identity Panel was used with 27 cycles of PCR. Despite that we only had an average of 6.8 pg of degraded DNA as template, 30 out of 32 libraries (93.8%) produced sequencing data for about 63/90 autosomal markers per sample. Out of the 30 libraries, 14 (46.7%) yielded single source genetic profiles in agreement with the biological identity of the donor, whereas 12 cases (40.0%) resulted in SNP profiles that did not match or were mixed. The misleading outcomes for those 12 cases were likely due to hidden exogenous human contamination, as shown by the higher frequencies of allelic imbalance, unusual high frequencies of allelic drop-ins, high heterozygosity levels in the consensus profiles generated from challenging samples, and traces of amplified molecular products in four out of eight extraction negative controls. Even if the source and the time of the contamination were not identified, it is likely that it occurred along the multi-step bone processing workflow. Our results suggest that only positive identification by statistical tools (e.g. likelihood ratio) should be accepted as reliable; oppositely, the results leading to exclusion should be treated as inconclusive because of potential contamination issues. Finally, strategies are discussed for monitoring the workflow of extremely challenging bone samples in PCR-MPS experiments with an increased number of PCR cycles. bone DNA SNP analysis DNA degradation SNPs PCR-MPS LT-DNA DNK kosti analiza SNP razgradnja DNK true false true Angleški jezik Slovenski jezik Članek v reviji 2023-07-27 08:51:49 2023-07-27 08:51:57 2024-09-30 10:04:34 0000-00-00 00:00:00 2023 0 0 Str. 981-993 iss. 4 Vol. 137 2023 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 61 0937-9827 10.1007/s00414-023-03019-9 154212355 s00414-023-03019-9.pdf s00414-023-03019-9.pdf 1 BCCEBE629B09CC66A1BA0AEF96A1C234 08d77257c24235d9f883c99a4f304f8ac16b38d22f62640ef53d291060a83b0a 3b224dab-2c4a-11ee-aeaf-00155dcfd717 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=172061 https://link.springer.com/article/10.1007/s00414-023-03019-9 0 1aa60619-2c4a-11ee-aeaf-00155dcfd717 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=172060 Medicinska fakulteta 0 0 0