SNP analysis of challenging bone DNA samples using the HID‑Ion AmpliSeq™ Identity Panel : facts and artefacts

Fattorini, Paolo (avtor), Previderè, Carlo (avtor), Livieri, Tommaso (avtor), Zupanc, Tomaž (avtor), Zupanič-Pajnič, Irena (avtor)

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.

• Jezik: Angleški jezik
• Ključne besede: bone DNA, SNP analysis, DNA degradation, SNPs, PCR-MPS, LT-DNA
• Vrsta gradiva: Članek v reviji
• Tipologija: 1.01 - Izvirni znanstveni članek
• Organizacija: MF - Medicinska fakulteta
• Status publikacije: Objavljeno
• Različica publikacije: Objavljena publikacija
• Leto izida: 2023
• Št. strani: Str. 981-993
• Številčenje: Vol. 137, iss. 4
• PID: 20.500.12556/RUL-148106
• UDK: 61
• ISSN pri članku: 0937-9827
• DOI: 10.1007/s00414-023-03019-9
• COBISS.SI-ID: 154212355
• Datum objave v RUL: 27.07.2023

Gradivo je del revije

• Naslov: International journal of legal medicine
• Skrajšan naslov: Int. j. leg. med.
• Založnik: Springer Nature
• ISSN: 0937-9827
• COBISS.SI-ID: 527892

Licence

• Licenca: CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
• Povezava: http://creativecommons.org/licenses/by/4.0/deed.sl
• Opis: To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.

Sekundarni jezik

• Jezik: Slovenski jezik
• Ključne besede: DNK kosti, analiza SNP, razgradnja DNK

Projekti

• Financer: ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
• Številka projekta: J3-3080
• Naslov: Določitev predniškega porekla iz DNA za identifikacijske namene