Evaluation and SNP typing of DNA from ultraviolet-irradiated human bloodstains using TaqMan assay

Jian Tie,Seisaku Uchigasaki,Eiji Isobe

doi:10.1038/s41598-021-87313-9

Abstract

When detecting DNA profiles from forensic materials, it is pivotal to know the extent of degradation and which DNA marker can be genotyped. Ultraviolet (UV) is one of the common external factors that causes DNA damage, through which, an attempt to reveal cardinal genetic information can be made. In this study, after irradiation with three different UV wavelengths, UV-damaged DNA in the bloodstains was analyzed with long and short TaqMan assays using real-time PCR. In addition, both short tandem repeat (STR) profiles and single nucleotide polymorphisms (SNPs) from the damaged DNA at different stages of UV exposure were also assessed. With increasing in UV irradiation cycles, there was a delay of the amplification curves accompanied with a decrease in the DNA amounts collected. Despite the amplification of STR genotype was not altered after 75 cycles of UVC irradiation, all 12 SNP loci could still be detected. Furthermore, a short-assay line was detected in the absence of an amplification of the evaluation curve. The results indicate that, although the DNA template might not be useful and suitable for analysis of STR profile, this approach is of some values in detecting SNPs.

Highlights

Retrieving evidence of genetic information from the degraded DNA samples is an important approach to reveal an individual identification in forensic medicine
Some approaches have been suggested to improve the results of low copy number (LCN) DNA template analysis, such as optimizing DNA extraction methods, increasing the number of cycles of PCR, repairing degraded DNA specimens, and using whole-genome amplification (WGA)[3,4,5]
Many studies have reported that Single nucleotide polymorphisms (SNPs) have some advantages over short tandem repeat (STR) in the forensic identification of individuals and paternity testing[8,9], for example, the amplicons involved in SNP analysis are very small; so they can used for analysis of highly degraded samples[10]

Summary

Results and discussion

When the amount of UV irradiation was increased to 75 cycles, short-assay amplification became more difficult, but amplification curve could still be observed for all UVA-, UVB-, and UVC-irradiated dried blood samples. The results indicated that each allele in each diluted template was amplified at all concentrations and that 0.02 ng of DNA template was required for SNP genotyping in the TaqMan assays in the present study (Fig. 2). Even the evaluation curve of amplification by real-time PCR was not amplified and only showed a short-assay line, indicating that the DNA template could not be analyzed for STR profiles, but it might be possible to detect SNPs. In other words, when the long assay of a sample cannot be amplified, the DNA template might be inappropriate for STR profile amplification. SNP locus amplification may be an appropriate choice in cases where STR profile amplification cannot be used to analyze LCN forensic samples

Materials and methods

Allele Chromosome MAF

Additional information