Degradation in forensic trace DNA samples explored by massively parallel sequencing

Technical strategy for monozygotic twin discrimination by single-nucleotide variants

Monozygotic (MZ) twins are theoretically genetically identical. Although they are revealed to accumulate mutations after the zygote splits, discriminating between twin genomes remains a formidable challenge in the field of forensic genetics. Single-nucleotide variants (SNVs) are responsible for a substantial portion of genetic variation, thus potentially serving as promising biomarkers for the identification of MZ twins. In this study, we sequenced the whole genome of a pair of female MZ twins when they were 27 and 33 years old to approximately 30 × coverage using peripheral blood on an Illumina NovaSeq 6000 Sequencing System. Potentially discordant SNVs supported by whole-genome sequencing were validated extensively by amplicon-based targeted deep sequencing and Sanger sequencing. In total, we found nine bona fide post-twinning SNVs, all of which were identified in the younger genomes and found in the older genomes. None of the SNVs occurred within coding exons, three of which were observed in introns, supported by whole-exome sequencing results. A double-blind test was employed, and the reliability of MZ twin discrimination by discordant SNVs was endorsed. All SNVs were successfully detected when input DNA amounts decreased to 0.25 ng, and reliable detection was limited to seven SNVs below 0.075 ng input. This comprehensive analysis confirms that SNVs could serve as cost-effective biomarkers for MZ twin discrimination.

DNA degradation of bloodstains on cotton fabric caused by different washing procedures

DNA degradation in biological material needs to be better understood. Bloodstains on washed clothing are disturbed by washing procedures, sometimes transferred to other fabrics, often with latent bloodstains and usually with significantly degraded DNA. The samples (cotton fabric with bloodstains) are divided into six main groups, depending on the washing method regarding water temperature (95, 60, and 30 °C) and the detergent use. After completing the washing process, samples were stored for a certain period (1 day to 6 months) and subsequently analyzed. Analyses were performed using standard protocols and commercial kits to measure the remaining DNA quantity (concentration) and DNA degradation index in the processed samples. Our results revealed that the high washing temperature (60 and 95 °C) and the application of detergent have a synergic action on DNA degradation, while at 30 °C this effect is absent. Furthermore, the effect of detergent on accelerated DNA degradation is observed about a month after the washing. This delayed effect of detergent has no explanation in current literature data. To obtain optimal results from the bloodstains, we recommended that the period from the crime event and attempted cleaning by a perpetrator to the laboratory analysis should be less than 1 month.

Effects of DNA degradation and genotype imputation on high-density SNP microarray in pairwise kinship analysis

High-density single nucleotide polymorphisms (SNPs) can detect distant relatives even in the context of pairwise kinship analysis. Although DNA microarrays conveniently generate genome-wide SNP data, they require large quantities of high-quality DNA. Genotyping data obtained from low-quantity and low-quality samples are likely unreliable owing to the incidence of no-called or mistyped SNPs. In this study, we examined the effects of insufficient sample densities and sample degradation on the efficacy of kinship analysis. While low DNA amounts had a minor effect, DNA degradation led to a significant increase in no-call rates and error rates. Posterior probabilities of kinship determination, calculated using the index of chromosomal sharing, were markedly lower in proportion to the no-call rates and error rates. We also investigated the effect of genotype imputation to complement the no-called genome data utilizing SNPs reference panels. We found that the posterior probability of the relative-assumed person increased with genotype complementation in case of mild degradation, even with mistyped genotypes. Therefore, DNA microarray with imputation is a promising method for analyzing forensic DNA samples taken from situations where DNA quantity and quality may be compromised, such as disaster victim identification using pairwise kinship analysis.

Whole-genome sequencing of artificial single-nucleotide variants induced by DNA degradation in biological crime scene traces

The aim of this study was to identify artificial single-nucleotide variants (SNVs) in degraded trace DNA samples. In a preliminary study, blood samples were stored for up to 120 days and whole-genome sequencing was performed using the Snakemake workflow dna-seq-gatk-variant-calling to identify positions that vary between the time point 0 sample and the aged samples. In a follow-up study on blood and saliva samples stored under humid and dry conditions, potential marker candidates for the estimation of the age of a blood stain (= time since deposition) were identified. Both studies show that a general decrease in the mean fragment size of the libraries over time was observed, presumably due to the formation of abasic sites during DNA degradation which are more susceptible to strand breaks by mechanical shearing of DNA. Unsurprisingly, an increase in the number of failed genotype calls (no coverage) was detected over time. Both studies indicated the presence of artificial SNVs with the majority of changes happening at guanine and cytosine positions. This confirms previous studies and can be explained by depurination through hydrolytic attacks which more likely deplete guanine while deamination leads to cytosine to thymine variants. Even complete genotype switches from homozygote 0/0 genotypes to the opposite 1/1 genotypes were observed. While positions with such drastic changes might provide suitable candidate markers for estimating short-term time since deposition (TsD), 11 markers were identified which show a slower gradual change of the relative abundance of the artificial variant in both blood and saliva samples, irrespective of storage conditions.

CRISPR-CasB technology in forensic DNA analysis: challenges and solutions

CRISPR-Cas technology has revolutionized the field of biotechnology with its precise therapeutic use from genetic as well as infectious diseases point of view. This technology is rapidly evolving to single tool enabling site-directed cut in the genome and highly specific activation or inhibition of gene expression or the exchange of single bases. Besides clinical applications, CRISPR-Cas technology has also shown promising use in the field of forensic DNA analysis. Enrichment of targeted genetic marker for identification followed by sequencing and non-PCR-dependent technique ensures the use of CRISPR-Cas technology in challenging forensic biological samples. The use of this advanced technology is also deemed helpful in mixed profile attribution, mostly in LCN contributors and the generation of a useful DNA profile in degraded samples. Besides its useful applications in forensic DNA analysis, CRISPR-Cas technology poses a huge threat from the generation of ghost DNA profiles by modification/alteration of target genetic markers. Forensic DNA analysts should carry out analysis of additional markers such as non-CODIS markers, Y-, X-chromosome markers, and mitochondrial DNA sequencing in a suspected ghost DNA profile case. KEY POINTS: • CRISPR-Cas9 technique is useful in analyzing LCN, mixed and degraded samples • Alteration of DNA using this technique can lead to generation of ghost DNA profiles • Alternative genetic markers and methylation pattern may detect a ghost DNA profile.

A novel set of short microhaplotypes based on non-binary SNPs for forensic challenging samples

Short tandem repeats (STRs) are the most widely used genetic markers in forensic application, but they are not ideal genetic markers for the analysis of forensic challenging samples such as highly degraded or unbalanced mixed samples because of their relatively large amplicons and stutter peaks. In this study, we developed a set of short microhaplotypes based on non-binary SNPs with molecular extent sizes no longer than 60 bases and genotyped 100 unrelated individuals from northern Han groups. Our results showed this panel has similar discrimination power to STR kits, as the combined random match probability (CMP) reached 1.396 × 10^-22 and mean effective number of alleles (Ae) was 3.59. The cumulative probability of exclusion for duos (CPE-duos) was 0.999919 and the cumulative probability of exclusion for trios (CPE-trios) was 0.9999999987, suggesting this panel could be applied for forensic personal identification and parentage testing independently. Population differentiation in 26 populations from the 1000 Genomes Project indicated this panel could distinguish populations from Africa, East Asia, South Asia, America, and Europe. These microhaplotypes based on non-binary SNPs have short amplicons, good discrimination power, no stutter artifacts, and have great potential in detection of highly degraded and unbalanced mixtures for personal identification, paternity testing, and ancestry inference.

An 18 Multi-InDels panel for analysis of highly degraded forensic biological samples

DNA genotyping from trace and highly degraded biological samples is one of the most significant challenges of forensic DNA identification. There is a lack of simple and effective methods for genotyping highly degraded samples. In this study, a multiple loci insertion/deletion polymorphisms (Multi-InDels) panel was designed for detecting 18 autosomal Multi-InDels through capillary electrophoresis (CE) with amplicon sizes no longer than 125 bp. Studies of sensitivity, degradation, and species specificity were performed and a population study was carried out using 192 samples from Han populations in Hunan province in the south of China. The combined random match probability (CMP) of these 18 Multi-InDels was 3.23 × 10^-12 and the cumulative probability of exclusion (CPE) was 0.9989, suggesting this panel could be used independently for human identification and could provide efficient supporting information for parentage testing. Complete profiles were obtained from as low as 62.5 pg of total input DNA after increasing the number of PCR cycles. Moreover, all alleles were detected from artificially highly degraded DNA after 80 min of boiling water bath treatment. This 18 Multi-InDels panel is simple, fast, and effective for the forensic analysis of highly degraded DNA.

Assessment of PowerPlex® Fusion 5C's ability to type degraded DNA

DNA samples collected at crime scenes are often degraded so this research focused on the ability of the Promega PowerPlex® Fusion 5C amplification kit to type both naturally and artificially degraded DNA. DNA was degraded naturally by placing equal volumes of blood on white fabric that was stored either inside, outside in a shaded area, or outside in direct sunlight. Samples were then collected every 10 days for 60 days and the DNA extracted (QIAamp® DNA Investigator). Artificially degraded samples were created by exposing extracted DNA to either UV light or 95 °C heat for varying times. DNA was also degraded artificially by placing blood samples into a 50% bleach solution for varying times prior to extraction. Following sample treatment, standard forensic DNA analysis was performed including quantification (Investigator® Quantiplex) and amplification (PowerPlex® Fusion 5C). Separation and detection were performed on an ABI 3130xl capillary electrophoresis unit and analysis was performed using GeneMapper ID v3.2.1. While the time and shade samples showed similar amounts of degradation, the samples exposed to direct sun showed more degradation. The artificially degraded samples showed more signs of degradation such as reduced overall peak height and peak height imbalance at heterozygous loci. There were also some cases where an allele that was known to be in the profile exhibited total dropout. Although there were some instances of both allelic dropout and heterozygote peak imbalance, PowerPlex® Fusion was able to reliably type degraded DNA as all alleles detected were consistent with the known donor profile. The results show that PowerPlex® Fusion is a robust kit capable of handling forensically challenged samples.