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14 pages, 2184 KiB

Open AccessArticle

Evaluation of Storage Conditions and the Effect on DNA from Forensic Evidence Objects Retrieved from Lake Water

by Muhammad Shahzad, Hanne De Maeyer, Ghassan Ali Salih, Martina Nilsson, Anastasia Haratourian, Muhammad Shafique, Ahmad Ali Shahid and Marie Allen

Genes 2024, 15(3), 279; https://doi.org/10.3390/genes15030279 - 23 Feb 2024

Viewed by 844

Abstract

DNA analysis of traces from commonly found objects like knives, smartphones, tapes and garbage bags related to crime in aquatic environments is challenging for forensic DNA laboratories. The amount of recovered DNA may be affected by the water environment, time in the water, [...] Read more.

DNA analysis of traces from commonly found objects like knives, smartphones, tapes and garbage bags related to crime in aquatic environments is challenging for forensic DNA laboratories. The amount of recovered DNA may be affected by the water environment, time in the water, method for recovery, transport and storage routines of the objects before the objects arrive in the laboratory. The present study evaluated the effect of four storage conditions on the DNA retrieved from bloodstains, touch DNA, fingerprints and hairs, initially deposited on knives, smartphones, packing tapes, duct tapes and garbage bags, and submerged in lake water for three time periods. After retrieval, the objects were stored either through air-drying at room temperature, freezing at −30 °C, in nitrogen gas or in lake water. The results showed that the submersion time strongly influenced the amount and degradation of DNA, especially after the longest submersion time (21 days). A significant variation was observed in success for STR profiling, while mtDNA profiling was less affected by the submersion time interval and storage conditions. This study illustrates that retrieval from water as soon as possible and immediate storage through air-drying or freezing before DNA analysis is beneficial for the outcome of DNA profiling in crime scene investigations. Full article

(This article belongs to the Special Issue Improved Methods in Forensic DNA Analysis)

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15 pages, 1216 KiB

Open AccessArticle

Complete Mitochondrial DNA Genome Variation in the Swedish Population

by Kimberly Sturk-Andreaggi, Martin Bodner, Joseph D. Ring, Adam Ameur, Ulf Gyllensten, Walther Parson, Charla Marshall and Marie Allen

Genes 2023, 14(11), 1989; https://doi.org/10.3390/genes14111989 - 25 Oct 2023

Viewed by 1215

Abstract

The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, [...] Read more.

The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies. Full article

(This article belongs to the Special Issue Improved Methods in Forensic DNA Analysis)

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20 pages, 7878 KiB

Open AccessArticle

Direct and Secondary Transfer of Touch DNA on a Credit Card: Evidence Evaluation Given Activity Level Propositions and Application of Bayesian Networks

by Martina Onofri, Cristina Altomare, Simona Severini, Federica Tommolini, Massimo Lancia, Luigi Carlini, Cristiana Gambelunghe and Eugenia Carnevali

Genes 2023, 14(5), 996; https://doi.org/10.3390/genes14050996 - 27 Apr 2023

Cited by 6 | Viewed by 2092

Abstract

In a judiciary setting, questions regarding the mechanisms of transfer, persistence, and recovery of DNA are increasingly more common. The forensic expert is now asked to evaluate the strength of DNA trace evidence at activity level, thus assessing if a trace, given its [...] Read more.

In a judiciary setting, questions regarding the mechanisms of transfer, persistence, and recovery of DNA are increasingly more common. The forensic expert is now asked to evaluate the strength of DNA trace evidence at activity level, thus assessing if a trace, given its qualitative and quantitative features, could be the result of an alleged activity. The present study is the reproduction of a real-life casework scenario of illicit credit card use by a co-worker (POI) of its owner (O). After assessing the shedding propensity of the participants, differences in DNA traces’ qualitative and quantitative characteristics, given scenarios of primary and secondary transfer of touch DNA on a credit card, a non-porous plastic support, were investigated. A case-specific Bayesian Network to aid statistical evaluation was created and discrete observations, meaning the presence/absence of POI as a major contributor in both traces from direct and secondary transfer, were used to inform the probabilities of disputed activity events. Likelihood Ratios at activity level (LRα) were calculated for each possible outcome resulting from the DNA analysis. In instances where only POI and POI plus an unknown individual are retrieved, the values obtained show moderate to low support in favour of the prosecution proposition. Full article

(This article belongs to the Special Issue Improved Methods in Forensic DNA Analysis)

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20 pages, 1582 KiB

Open AccessArticle

Evaluating the Usefulness of Human DNA Quantification to Predict DNA Profiling Success of Historical Bone Samples

by Jacqueline Tyler Thomas, Courtney Cavagnino, Katelyn Kjelland, Elise Anderson, Kimberly Sturk-Andreaggi, Jennifer Daniels-Higginbotham, Christina Amory, Brian Spatola, Kimberlee Moran, Walther Parson and Charla Marshall

Genes 2023, 14(5), 994; https://doi.org/10.3390/genes14050994 - 27 Apr 2023

Cited by 2 | Viewed by 4220

Abstract

This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation [...] Read more.

This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55–125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that human DNA quantity is a better predictor of success than the ratio of human to exogenous DNA. Accurate quantification with qPCR is feasible for historical bone samples, allowing for the screening of extracts to predict the success of DNA profiling. Full article

(This article belongs to the Special Issue Improved Methods in Forensic DNA Analysis)

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19 pages, 1844 KiB

Open AccessArticle

Applying Unique Molecular Indices with an Extensive All-in-One Forensic SNP Panel for Improved Genotype Accuracy and Sensitivity

by Adam Staadig, Johannes Hedman and Andreas Tillmar

Genes 2023, 14(4), 818; https://doi.org/10.3390/genes14040818 - 29 Mar 2023

Cited by 2 | Viewed by 1900

Abstract

One of the major challenges in forensic genetics is being able to detect very small amounts of DNA. Massively parallel sequencing (MPS) enables sensitive detection; however, genotype errors may exist and could interfere with the interpretation. Common errors in MPS-based analysis are often [...] Read more.

One of the major challenges in forensic genetics is being able to detect very small amounts of DNA. Massively parallel sequencing (MPS) enables sensitive detection; however, genotype errors may exist and could interfere with the interpretation. Common errors in MPS-based analysis are often induced during PCR or sequencing. Unique molecular indices (UMIs) are short random nucleotide sequences ligated to each template molecule prior to amplification. Applying UMIs can improve the limit of detection by enabling accurate counting of initial template molecules and removal of erroneous data. In this study, we applied the FORCE panel, which includes ~5500 SNPs, with a QIAseq Targeted DNA Custom Panel (Qiagen), including UMIs. Our main objective was to investigate whether UMIs can enhance the sensitivity and accuracy of forensic genotyping and to evaluate the overall assay performance. We analyzed the data both with and without the UMI information, and the results showed that both genotype accuracy and sensitivity were improved when applying UMIs. The results showed very high genotype accuracies (>99%) for both reference DNA and challenging samples, down to 125 pg. To conclude, we show successful assay performance for several forensic applications and improvements in forensic genotyping when applying UMIs. Full article

(This article belongs to the Special Issue Improved Methods in Forensic DNA Analysis)

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13 pages, 1677 KiB

Open AccessArticle

Development of Improved DNA Collection and Extraction Methods for Handled Documents

by Ashley G. Morgan and Mechthild Prinz

Genes 2023, 14(3), 761; https://doi.org/10.3390/genes14030761 - 21 Mar 2023

Cited by 1 | Viewed by 1683

Abstract

Handwritten documents may contain probative DNA, but most crime laboratories do not process this evidence. DNA recovery should not impair other evidence processing such as latent prints or indented writing. In this study, single fingermarks on paper were sampled with flocked swabs, cutting, [...] Read more.

Handwritten documents may contain probative DNA, but most crime laboratories do not process this evidence. DNA recovery should not impair other evidence processing such as latent prints or indented writing. In this study, single fingermarks on paper were sampled with flocked swabs, cutting, and dry vacuuming. In addition, two extraction methods were compared for the sample type. DNA yields were low across all methods; however, this work confirms the ability to recover DNA from paper and the usefulness of the vacuum sampling method combined with the Chelex-Tween method. Stability of touch DNA deposits were compared over an 11-month period to better understand degradation that may occur over time. No significant difference in DNA recovery was observed, suggesting DNA deposits on paper are stable over an 11-month span. Full article

(This article belongs to the Special Issue Improved Methods in Forensic DNA Analysis)

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16 pages, 2911 KiB

Open AccessArticle

Probabilistic Genotyping of Single Cell Replicates from Mixtures Involving First-Degree Relatives Prevents the False Inclusions of Non-Donor Relatives

by Kaitlin Huffman and Jack Ballantyne

Genes 2022, 13(9), 1658; https://doi.org/10.3390/genes13091658 - 15 Sep 2022

Cited by 5 | Viewed by 1760

Abstract

Analysis of complex DNA mixtures comprised of related individuals requires a great degree of care due to the increased risk of falsely including non-donor first-degree relatives. Although alternative likelihood ratio (LR) propositions that may aid in the analysis of these difficult cases can [...] Read more.

Analysis of complex DNA mixtures comprised of related individuals requires a great degree of care due to the increased risk of falsely including non-donor first-degree relatives. Although alternative likelihood ratio (LR) propositions that may aid in the analysis of these difficult cases can be employed, the prior information required for their use is not always known, nor do these alternative propositions always prevent false inclusions. For example, with a father/mother/child mixture, conditioning the mixture on the presence of one of the parents is recommended. However, the definitive presence of the parent(s) is not always known and an assumption of their presence in the mixture may not be objectively justifiable. Additionally, the high level of allele sharing seen with familial mixtures leads to an increased risk of underestimating the number of contributors (NOC) to a mixture. Therefore, fully resolving and identifying each of the individuals present in familial mixtures and excluding related non-donors is an important goal of the mixture deconvolution process and can be of great investigative value. Here, firstly, we further investigated and confirmed the problems encountered with standard bulk analysis of familial mixtures and demonstrated the ability of single cell analysis to fully distinguish first-degree relatives (FDR). Then, separation of each of the individual donors via single cell analysis was carried out by a combination of direct single cell subsampling (DSCS), enhanced DNA typing, and probabilistic genotyping, and applied to three complex familial 4-person mixtures resulting in a probative gain of LR for all donors and an accurate determination of the NOC. Significantly, non-donor first-degree relatives that were falsely included (LRs > 10²–10⁸) by a standard bulk sampling and analysis approach were no longer falsely included using DSCS. Full article

(This article belongs to the Special Issue Improved Methods in Forensic DNA Analysis)

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12 pages, 1298 KiB

Open AccessArticle

Empirical Evidence on Enhanced Mutation Rates of 19 RM-YSTRs for Differentiating Paternal Lineages

by Faqeeha Javed, Muhammad Shafique, Dennis McNevin, Muhammad Usama Javed, Abida Shehzadi and Ahmad Ali Shahid

Genes 2022, 13(6), 946; https://doi.org/10.3390/genes13060946 - 26 May 2022

Viewed by 1893

Abstract

Rapidly mutating Y-chromosomal short tandem repeats (RM Y STRs) with mutation rates ≥ 10⁻² per locus per generation are valuable for differentiating amongst male paternal relatives where standard Y STRs with mutation rates of ≤10⁻³ per locus per generation may not. [...] Read more.

Rapidly mutating Y-chromosomal short tandem repeats (RM Y STRs) with mutation rates ≥ 10⁻² per locus per generation are valuable for differentiating amongst male paternal relatives where standard Y STRs with mutation rates of ≤10⁻³ per locus per generation may not. Although the 13 RM Y STRs commonly found in commercial assays provide higher levels of paternal lineage differentiation than conventional Y STRs, there are many male paternal relatives that still cannot be differentiated. This can be improved by increasing the number of Y STRs or choosing those with high mutation rates. We present a RM Y STR multiplex comprising 19 loci with high mutation rates and its developmental validation (repeatability, sensitivity and male specificity). The multiplex was found to be robust, reproducible, specific and sensitive enough to generate DNA profiles from samples with inhibitors. It was also able to detect all contributor alleles of mixtures in ratios up to 9:1. We provide preliminary evidence for the ability of the multiplex to discriminate between male paternal relatives by analyzing large numbers of male relative pairs (536) separated by one to seven meioses. A total of 96 mutations were observed in 162 meioses of father–son pairs, and other closely related male pairs were able to be differentiated after 1, 2, 3, 4, 5, 6 and 7 meiosis in 44%, 69%, 68%, 85%, 0%, 100% and 100% of cases, respectively. The multiplex offers a noticeable enhancement in the ability to differentiate paternally related males compared with the 13 RM Y STR set. We envision the future application of our 19 RM Yplex in criminal cases for the exclusion of male relatives possessing matching standard Y STR profiles and in familial searching with unknown suspects. It represents a step towards the complete individualization of closely related males. Full article

(This article belongs to the Special Issue Improved Methods in Forensic DNA Analysis)

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Review

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12 pages, 311 KiB

Open AccessReview

Forensic Applications of Markers Present on the X Chromosome

by Fernanda M. Garcia, Bárbara G. O. Bessa, Eldamária V. W. dos Santos, Julia D. P. Pereira, Lyvia N. R. Alves, Lucas A. Vianna, Matheus C. Casotti, Raquel S. R. Trabach, Victor S. Stange, Débora D. Meira and Iuri D. Louro

Genes 2022, 13(9), 1597; https://doi.org/10.3390/genes13091597 - 07 Sep 2022

Cited by 11 | Viewed by 3847

Abstract

Microsatellite genetic markers are the gold standard for human genetic identification. Forensic analyses around the world are carried out through protocols using the analysis of STR markers in autosomal chromosomes and in the Y chromosome to solve crimes. However, these analyses do not [...] Read more.

Microsatellite genetic markers are the gold standard for human genetic identification. Forensic analyses around the world are carried out through protocols using the analysis of STR markers in autosomal chromosomes and in the Y chromosome to solve crimes. However, these analyses do not allow for the resolution of all cases, such as rape situations with suspicion of incest, paternity without a maternal sample for comparison, and biological traces with DNA mixture where the profile sought is female, among other situations. In these complex cases, the study of X-chromosome STR markers significantly increases the probability of identification by complementing the data obtained for autosomal and Y-chromosome markers, due to the unique structure of the X chromosome and its exclusive method of inheritance. However, there are currently no validated Brazilian protocols for this purpose, nor are there any population data necessary for statistical analyses that must be included in the issuance of expert reports. Thus, the aim of this article is to provide a literary review of the applications of X-chromosomal markers in population genetics. Full article

(This article belongs to the Special Issue Improved Methods in Forensic DNA Analysis)

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