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Special Issue "Improved Methods in Forensic DNA Analysis"

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Bioinformatics".

Deadline for manuscript submissions: closed (25 March 2023) | Viewed by 8900

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Special Issue Editor

Prof. Dr. Marie Allen

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Guest Editor

Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
Interests: challenging DNA analysis; degraded DNA; mtDNA; STRs; NGS

Special Issue Information

Dear Colleagues,

Forensic DNA analysis has developed into an essential tool in criminal investigations. However, many factors can challenge DNA analysis, such as only retrieving small amounts of DNA from important forensic evidence items. Furthermore, the integrity of the DNA may be influenced by environmental factors leading to damage and degradation of the DNA. Another challenge is that numerous inhibitors may be coextracted with the DNA, leading to less efficient DNA profiling. Although new technologies have been developed (e.g., next-generation sequencing), it is crucial to use optimal protocols in all analysis steps, including sampling, extraction, further purification, DNA profiling, and bioinformatic analysis. This Special Issue is dedicated to reports demonstrating optimised forensic protocols and strategies in all stages of forensic DNA analysis and for a variety of criminal cases.

Prof. Dr. Marie Allen
Guest Editor

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Keywords

forensic genetics
human identification
criminal cases
mitochondrial DNA
short tandem repeats
single nucleotide polymorphisms
DNA phenotyping
DNA extraction
DNA quantification
improved PCR
next-generation sequencing
bioinformatic pipelines

Published Papers (7 papers)

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Research

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Open AccessArticle

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

Cristiana Gambelunghe

and

Eugenia Carnevali

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

Cited by 1 | Viewed by 454

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 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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Open AccessArticle

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

Jacqueline Tyler Thomas

Courtney Cavagnino

Katelyn Kjelland

Elise Anderson

Kimberly Sturk-Andreaggi

Jennifer Daniels-Higginbotham

and

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

Viewed by 1411

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 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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Open AccessArticle

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

Adam Staadig

Johannes Hedman

and

Andreas Tillmar

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

Viewed by 653

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 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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Open AccessArticle

Development of Improved DNA Collection and Extraction Methods for Handled Documents

Ashley G. Morgan

and

Mechthild Prinz

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

Viewed by 814

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, 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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Open AccessArticle

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

Kaitlin Huffman

and

Jack Ballantyne

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

Cited by 1 | Viewed by 1120

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 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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Open AccessArticle

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

and

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

Viewed by 1320

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. 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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Open AccessReview

Forensic Applications of Markers Present on the X Chromosome

Fernanda M. Garcia

Bárbara G. O. Bessa

Eldamária V. W. dos Santos

and

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

Cited by 3 | Viewed by 1916

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 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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