Mitochondrial DNA control region typing from highly degraded skeletal remains by single-multiplex next-generation sequencing

• Published in: Electrophoresis Vol. 44; no. 17-18; pp. 1423 - 1434
• Main Authors: Vinueza-Espinosa, Diana C, Cuesta-Aguirre, Daniel R, Malgosa, Assumpció, Santos, Cristina
• Format: Journal Article
• Language: English
• Published: Germany Wiley Subscription Services, Inc 01.09.2023
• Subjects: Degradation; Denaturation; Deoxyribonucleic acid; DNA; Gene sequencing; Human remains; Mitochondrial DNA; Multiplexing; Polymerase chain reaction; Software; protocol optimization; skeletal samples; NGS; PowerSeq CRM Nested System kit; mtDNA
• ISSN: 0173-0835; 1522-2683
• DOI: 10.1002/elps.202200052

Poor nuclear DNA preservation from highly degraded skeletal remains is the most limiting factor for the genetic identification of individuals. Mitochondrial DNA (mtDNA) typing, and especially of the control region (CR), using next-generation sequencing (NGS), enables retrieval of valuable genetic information in forensic contexts where highly degraded human skeletal remains are the only source of genetic material. Currently, NGS commercial kits can type all mtDNA-CR in fewer steps than the conventional Sanger technique. The PowerSeq CRM Nested System kit (Promega Corporation) employs a nested multiplex-polymerase chain reaction (PCR) strategy to amplify and index all mtDNA-CR in a single reaction. Our study analyzes the success of mtDNA-CR typing of highly degraded human skeletons using the PowerSeq CRM Nested System kit. We used samples from 41 individuals from different time periods to test three protocols (M1, M2, and M3) based on modifications of PCR conditions. To analyze the detected variants, two bioinformatic procedures were compared: an in-house pipeline and the GeneMarker HTS software. The results showed that many samples were not analyzed when the standard protocol (M1) was used. In contrast, the M3 protocol, which includes 35 PCR cycles and longer denaturation and extension steps, successfully recovered the mtDNA-CR from highly degraded skeletal samples. Mixed base profiles and the percentage of damaged reads were both indicators of possible contamination and can provide better results if used together. Furthermore, our freely available in-house pipeline can provide variants concordant with the forensic software.