Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples

DNA quality and STR success rate in different formalin-fixed tissues

Formalin-fixed tissues possess irreplaceable value as a source of DNA for identification, especially when fresh samples are unavailable. Nonetheless, extracting and amplifying DNA from these tissues is challenging, primarily due to formaldehyde-induced cross-linking and nucleic acid fragmentation. In this study, two pre-extraction treatments, gradual dehydration using ethanol and pre-digestion heat treatments, and three DNA extraction methods, the Chelex-100 method, TIANamp FFPE DNA Kit, and ML Ultra-micro DNA extraction kit, were utilized to optimize DNA extraction from different tissues, which were fixed in 4% unbuffered formalin for different durations. The tissues include the heart, liver, spleen, lung, kidney, muscle, and brain. DNA quality was assessed, and quantification was conducted using Spectrophotometer and Quantifiler® Trio DNA Quantification Kits, while the GSTAR™ 25 kit was employed for STR detection. The results indicated that the two pre-extraction treatments exhibited no significant effect on the STR success rate. On day 9, allelic dropout was observed in the heart, liver, spleen, lung, and kidney tissues. Furthermore, allelic dropout was observed in muscle and brain at 12 days and 15 days, respectively. In conclusion, the results underscore the feasibility of effectively extracting DNA from formalin-fixed tissues within 9 days for subsequent STR analysis.

Establishment and validation of a DIP panel for forensic ancestry inference and personal identification

BACKGROUND

Biallelic Deletion/Insertion polymorphisms (DIPs), known for their significant diversity across various populations, serve as valuable markers for forensic ancestry inference and personal identification. In this study, we utilized DIPs to provide a potentially powerful forensic examination tool specifically tailored for East Asian populations. Our focus on ancestry allows us to delve deeper into the genetic signatures that characterize this diverse group, offering enhanced resolution in forensic analyses.

METHODS

A total of 56 autosomal DIPs, 3 Y-chromosome DIPs, and the Amelogenin were selected to build the 60-panel. Population genetic parameters, principal component analysis (PCA), STRUCTURE analysis, and phylogenetic tree construction were employed to evaluate the capacity for ancestry inference. The verification guidelines recommended by the Scientific Working Group on DNA Analysis Methods were followed in the developmental validations of the 60-panel.

RESULTS

The PCA, STRUCTURE, and phylogenetic tree constructions were not only consistent with each other but also corroborated by previous research. The combined probability of discrimination and the cumulative probability of paternity exclusion values were 0.999999999999 and 0.9937, respectively. These values indicate that the 60-panel is not only a useful tool for personal identification testing within the East Asian population but also provides valuable biogeographic information. Furthermore, the validation study of the 60-panel, which included assessments of PCR conditions, sensitivity, species specificity, stability, mixture analysis, reproducibility, and case sample studies, as well as analysis of degraded samples, demonstrated that the panel is well-suited for forensic testing. The panel's performance was particularly notable in the analysis of degraded samples, showcasing its potential for use in challenging forensic cases.

CONCLUSION

The newly developed 60-panel demonstrated robust performance in validation tests, yielding reliable genotypes even from poor-quality samples like degraded DNA. It offers valuable biogeographic insights and sufficient polymorphism for personal identification, which assisted forensic examinations in East Asian populations.

A study of strong nucleosomes in the human genome

Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, nucleosomes are highly dynamic and susceptible to experimental conditions, resulting in extreme variability across nucleosome maps, which complicates the generation of accurate nucleosome organization data. We mapped nucleosomes from different individuals using improved MNase-seq. The improvements included setting different digestion levels (low, medium, high) and naked DNA correction to remove the noise caused by experimental manipulation and comparing maps to obtain the accurate position and occupancy of strong nucleosomes (SNs) in the whole genome. In addition, the characteristics of SNs were further excavated. SNs were enriched in Alu elements and near the centromere of Chr12. SNs contain some specific sequences, and the GC content of SNs is different from that of dynamic nucleosomes. The findings suggest that nucleosome location in the genome and the DNA sequence may affect nucleosome stability.

•

Naked DNA correction improved the accuracy of nucleosome map in partial digestion

•

Level of MNase digestion has effects on nucleosome organization

•

A type of strong nucleosomes (SNs) exist across different nucleosome maps

•

Nucleosome stability may be related to its location and the DNA sequence

Ribosomal DNA as target for the assessment of DNA degradation of human and canine DNA

The assessment of DNA amount and DNA integrity can support forensic DNA analysis, in particular of problematic traces such as single telogen hairs where STR typing success is often hampered by low amounts and strong degradation of nuclear DNA. Common strategies consist of quantitative polymerase chain reaction (qPCR)-based analysis of the abundance of a short versus a long nuclear amplicon, the latter prone to DNA degradation. To increase sensitivity, commercial qPCR solutions rest on amplification of multi-copy DNA sequences. Here we show that ribosomal DNA (rDNA) sequences are well suited for the same purpose. Because rDNA sequences are present in high copy number in most eukaryotic species, qPCR strategies can easily be adapted to non-human species. In this paper, we establish qPCR-based assays for human or dog DNA, respectively, which allow for sensitive analysis of DNA amounts and DNA degradation. We show that the human system can be applied to DNA of single telogen hairs, where STR typing success correlates with measured amounts and integrity of the DNA. By adapting the system to dog rDNA sequences we found that single telogen dog hairs often displayed less DNA degradation than human telogen hairs, in most cases allowing for successful STR typing. Thus, qPCR-based analysis of rDNA represents a cost-effective, highly sensitive strategy to assess DNA amount and integrity that can be adapted to hairs or other traces from various animal species.