Is MPS always the answer? Use of two PCR-based methods for Y-chromosomal haplotyping in highly and moderately degraded bone material. (September 2019)

• Record Type: Journal Article
• Authors: Szargut, Maria; Diepenbroek, Marta; Zielińska, Grażyna; Cytacka, Sandra; Arciszewska, Joanna; Jałowińska, Katarzyna; Piątek, Jarosław; Ossowski, Andrzej
• Is Part Of: Forensic science international. Volume 42(2019)
• Page Start: 181
• Page End: 189
• Publication Date: 2019-09
• Subjects: Y-STR -- Haplotyping -- MPS -- Bone material -- Human identification -- Degradation -- Flanking region; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2019.07.016
• Languages: English
• ISSNs: 1872-4973

Abstract

Highlights: 75 bone samples from different time periods have been analyzed, the extracts obtained varied in DNA quantity and quality. Y-STR haplotypes were obtained from samples by CE allele calling (YFiler Plus PCR Amplification Kit) and MPS (ForenSeq Signature DNA Prep Kit). Differences in amplification rates were found within common markers. There was an allele call disconcordance in one sample. Significant number of variants have been found by sequence analysis of repetitive and flanking regions of the Y-STRs. Abstract: Forensic and population genetics often rely on Y-chromosomal studies. Whether it is a human identification case, trace evidence examination or phylogenetic analysis, a Y-STR haplotype is an important tool in the hands of law enforcement agencies. A common obstacle in achieving satisfactory results in all of the above mentioned circumstances, is low DNA quantity and quality within samples obtained. In this study we have examined Y-STR haplotypes in 75 bone material samples, coming from different time periods. For this purpose we have chosen YFiler Plus PCR Amplification Kit (ThermoFisher Scientific) and ForenSeq Signature DNA Prep Kit (Verogen Inc.), which use two different allele calling technologies – capillary electrophoresis and Massively Parallel Sequencing respectively. Full profiles were obtained from DNA extracts with as little as 0.1896 ng (Degradation Index 1.3) (ForenSeq) and 0.0591 ng (Degradation Index 26.8) (YFiler Plus) DNA input. The results that we present in this paper show differences in amplification rates between common markers in both kits. The differences strictly reflect mean amplicon length of markers. This, however, does not seem to influence Y-haplogroup estimation results noticeably. In one sample a discordance occurred between haplotypes obtained with both methods, where a 24 allele was called in DYS390 marker by capillary electrophoresis, while for the same sample in this locus a 23 allele was shown with MPS. A reason for this is yet to be investigated. The sequence analysis revealed a significant variation between isometric alleles, especially within repetitive regions of studied Y-STR markers.