Genotyping and interpretation of STR-DNA: Low-template, mixtures and database matches-Twenty years of research and development

Cleaning protocols in forensic genetic laboratories

It is pivotal to avoid cross-sample contamination in forensic genetic laboratories and optimal cleaning protocols for the removal of DNA are essential. A survey was performed, and ten forensic genetic laboratories shared their cleaning protocols in pre-PCR and post-PCR laboratories. The cleaning frequencies on different surface areas were somewhat similar, whereas none of the laboratories used the same cleaning reagents. Therefore, the efficiencies of the cleaning protocol utilised were tested and compared. The results showed that freshly made household bleach and Virkon® removed all amplifiable DNA from the surfaces, whereas DNA AWAY™ and the disinfection reagents ethanol, isopropanol, and ChemGene HLD4L did not.

Identification of individuals from low template blood samples using whole transcriptome shotgun sequencing

Biological trace samples consisting of very few cells pose a challenge to conventional forensic genetic DNA analysis. RNA may be an alternative to DNA when handling low template samples. Whereas each cell only contains two copies of an autosomal DNA segment, the transcriptome retains much of the genomic variation replicated in abundant RNA fragments. In this study, we describe the development of a prototype RNA-based SNP selection set for forensic human identification from low template samples (50 pg gDNA). Whole blood from a subset of the Danish population (41 individuals) and blood stains subjected to degradation at room temperature for up to two weeks were analysed by whole transcriptome shotgun sequencing. Concordance was determined by DNA genotyping with the Infinium Omni5-4 SNP chip. In the 100 protein-coding genes with the most reads, 5214 bi-allelic SNPs with gnomAD minor allele frequencies > 0.1 in the African/African American, East Asian, and (non-Finnish) European populations were identified. Of these, 24 SNPs in 21 genes passed screening in whole blood and degraded blood stains, with a resulting mean match probability of 4.5 ∙ 10-9. Additionally, ancestry informative SNPs and SNPs in genes useful for body fluid identification were identified in the transcriptome. Consequently, shotgun sequencing of RNA from low template samples may be used for a vast host of forensic genetics purposes, including simultaneous human and body fluid identification, leading to direct donor identification in the identified body fluid.

A comparison of likelihood ratios calculated from surface DNA mixtures using MPS and CE Technologies

This study evaluates the performance of analysing surface DNA samples using massively parallel sequencing (MPS) compared to traditional capillary electrophoresis (CE). A total of 30 samples were collected from various surfaces in an office environment and were analysed with CE and MPS. These were compared against 60 reference samples (office inhabitants). To identify contributors, likelihood ratios (LRs) were calculated for MPS and CE data using the probabilistic genotyping software MPSproto and EuroForMix respectively. Although a higher number of sequences/peaks were observed per DNA profile in MPS compared to CE, LR values were found to be lower for MPS data formats. This might be the result of the increased complexity of MPS data, along with a possible elevation of unknown alleles and/or artefacts. The study highlights avenues for improving MPS data quality and analysis to facilitate more robust interpretation of challenging casework-like samples.

Statistical methods for discrimination of STR genotypes using high resolution melt curve data

Despite the improvements in forensic DNA quantification methods that allow for the early detection of low template/challenged DNA samples, complicating stochastic effects are not revealed until the final stage of the DNA analysis workflow. An assay that would provide genotyping information at the earlier stage of quantification would allow examiners to make critical adjustments prior to STR amplification allowing for potentially exclusionary information to be immediately reported. Specifically, qPCR instruments often have dissociation curve and/or high-resolution melt curve (HRM) capabilities; this, coupled with statistical prediction analysis, could provide additional information regarding STR genotypes present. Thus, this study aimed to evaluate Qiagen's principal component analysis (PCA)-based ScreenClust® HRM® software and a linear discriminant analysis (LDA)-based technique for their abilities to accurately predict genotypes and similar groups of genotypes from HRM data. Melt curves from single source samples were generated from STR D5S818 and D18S51 amplicons using a Rotor-Gene® Q qPCR instrument and EvaGreen® intercalating dye. When used to predict D5S818 genotypes for unknown samples, LDA analysis outperformed the PCA-based method whether predictions were for individual genotypes (58.92% accuracy) or for geno-groups (81.00% accuracy). However, when a locus with increased heterogeneity was tested (D18S51), PCA-based prediction accuracy rates improved to rates similar to those obtained using LDA (45.10% and 63.46%, respectively). This study provides foundational data documenting the performance of prediction modeling for STR genotyping based on qPCR-HRM data. In order to expand the forensic applicability of this HRM assay, the method could be tested with a more commonly utilized qPCR platform.

Ultrasensitive sequencing of STR markers utilizing unique molecular identifiers and the SiMSen-Seq method

Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the MPS-STR data partly limits the detection of low DNA amounts, e.g., in complex mixtures. Unique molecular identifiers (UMIs) have been applied in several scientific fields to reduce noise in sequencing. UMIs consist of a stretch of random nucleotides, a unique barcode for each starting DNA molecule, that is incorporated in the DNA template using either ligation or PCR. The barcode is used to generate consensus reads, thus removing errors. The SiMSen-Seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing) method relies on PCR-based introduction of UMIs and includes a sophisticated hairpin design to reduce unspecific primer binding as well as PCR protocol adjustments to further optimize the reaction. In this study, SiMSen-Seq is applied to develop a proof-of-concept seven STR multiplex for MPS library preparation and an associated bioinformatics pipeline. Additionally, machine learning (ML) models were evaluated to further improve UMI allele calling. Overall, the seven STR multiplex resulted in complete detection and concordant alleles for 47 single-source samples at 1 ng input DNA as well as for low-template samples at 62.5 pg input DNA. For twelve challenging mixtures with minor contributions of 10 pg to 150 pg and ratios of 1-15% relative to the major donor, 99.2% of the expected alleles were detected by applying the UMIs in combination with an ML filter. The main impact of UMIs was a substantially lowered number of artefacts as well as reduced stutter ratios, which were generally below 5% of the parental allele. In conclusion, UMI-based STR sequencing opens new means for improved analysis of challenging crime scene samples including complex mixtures.

An inter-laboratory comparison of probabilistic genotyping parameters and evaluation of performance on DNA mixtures from different laboratories

Probabilistic genotyping (PG) is becoming the preferred standard for evidence interpretation, amongst forensic DNA laboratories, especially those in the United States. Various groups have expressed concern about reliability of PG systems, especially for mixtures beyond two contributors. Studies involving interlaboratory testing of known mixtures have been identified as ways to evaluate the reliability of PG systems. Reliability means different things in different contexts. However, it suffices here to think about it as a mixture of precision and accuracy. We might also consider whether a system is prone to producing misleading results - for example large likelihood ratios (LRs) when the POI is truly not a contributor, or small LRs when the POI is a truly a contributor. In this paper we show that the PG system STRmix™ is relatively unaffected by differences in parameter settings. That is, a DNA mixture that is analyzed in different laboratories using STRmix™ will result in different LRs, but less than 0.05% of these LRs would result in a different, or misleading conclusion as long as the LR is greater than 50. For the purposes of this study, we define LRs assigned using different parameters for the same mixtures as similar if the LR of the true POI is greater than the LRs generated for 99.9% of the general population. These findings are based on an interlaboratory study involving eight laboratories that provided twenty known DNA mixtures of two to four contributors and their individual laboratory STRmix™ parameters. The eight sets of laboratory parameters included differences in STR kits and PCR cycles as well as the peak, stutter, and locus specific amplification efficiency variances.

Single-cell investigative genetics: Single-cell data produces genotype distributions concentrated at the true genotype across all mixture complexities

In the absence of a suspect the forensic aim is investigative, and the focus is one of discerning what genotypes best explain the evidence. In traditional systems, the list of candidate genotypes may become vast if the sample contains DNA from many donors or the information from a minor contributor is swamped by that of major contributors, leading to lower evidential value for a true donor's contribution and, as a result, possibly overlooked or inefficient investigative leads. Recent developments in single-cell analysis offer a way forward, by producing data capable of discriminating genotypes. This is accomplished by first clustering single-cell data by similarity without reference to a known genotype. With good clustering it is reasonable to assume that the scEPGs in a cluster are of a single contributor. With that assumption we determine the probability of a cluster's content given each possible genotype at each locus, which is then used to determine the posterior probability mass distribution for all genotypes by application of Bayes' rule. A decision criterion is then applied such that the sum of the ranked probabilities of all genotypes falling in the set is at least 1-α. This is the credible genotype set and is used to inform database search criteria. Within this work we demonstrate the salience of single-cell analysis by performance testing a set of 630 previously constructed admixtures containing up to 5 donors of balanced and unbalanced contributions. We use scEPGs that were generated by isolating single cells, employing a direct-to-PCR extraction treatment, amplifying STRs that are compliant with existing national databases and applying post-PCR treatments that elicit a detection limit of one DNA copy. We determined that, for these test data, 99.3% of the true genotypes are included in the 99.8% credible set, regardless of the number of donors that comprised the mixture. We also determined that the most probable genotype was the true genotype for 97% of the loci when the number of cells in a cluster was at least two. Since efficient investigative leads will be borne by posterior mass distributions that are narrow and concentrated at the true genotype, we report that, for this test set, 47,900 (86%) loci returned only one credible genotype and of these 47,551 (99%) were the true genotype. When determining the LR for true contributors, 91% of the clusters rendered LR>1018, showing the potential of single-cell data to positively affect investigative reporting.

Improving DNA mixtures analysis using compound markers composed of InDels and SNPs screened from the whole genome with next-generation sequencing

Next-generation sequencing (NGS) allows for better identification of insertion and deletion polymorphisms (InDels) and their combination with adjacent single nucleotide polymorphisms (SNPs) to form compound markers. These markers can improve the polymorphism of microhaplotypes (MHs) within the same length range, and thus, boost the efficiency of DNA mixture analysis. In this study, we screened InDels and SNPs across the whole genome and selected highly polymorphic markers composed of InDels and/or SNPs within 300 bp. Further, we successfully developed and evaluated an NGS-based panel comprising 55 loci, of which 24 were composed of both SNPs and InDels. Analysis of 124 unrelated Southern Han Chinese revealed an average effective number of alleles (Ae ) of 7.52 for this panel. The cumulative power of discrimination and cumulative probability of exclusion values of the 55 loci were 1-2.37 × 10-73 and 1-1.19 × 10-28 , respectively. Additionally, this panel exhibited high allele detection rates of over 97% in each of the 21 artificial mixtures involving from two to six contributors at different mixing ratios. We used EuroForMix to calculate the likelihood ratio (LR) and evaluate the evidence strength provided by this panel, and it could assess evidence strength with LR, distinguishing real and noncontributors. In conclusion, our panel holds great potential for detecting and analyzing DNA mixtures in forensic applications, with the capability to enhance routine mixture analysis.

Performance of a 74-Microhaplotype Assay in Kinship Analyses

Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (Ae) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory.

DNA Profiling in Human Identification: From Past to Present

Forensic DNA typing has been widely accepted in the courts all over the world. This is because DNA profiling is a very powerful tool to identify individuals on the basis of their unique genetic makeup. DNA evidence is capable of not only identifying the presence of specific biospecimens in a crime scene, but it is also used to exonerate suspects who are innocent of a crime. Technological advancements in DNA profiling, including the development of validated kits and statistical methods have made this tool to be more precise in forensic investigations. Therefore, validated combined DNA index system (CODIS) short tandem repeats (STRs) kits which require very small amount of DNA, coupled with real-time polymerase chain reaction (PCR) and the statistical strengths are used routinely to identify human remains, establish paternity or to match suspected crime scene biospecimens. The road to modern DNA profiling has been long, and it has taken scientists decades of work and fine tuning to develop highly accurate testing and analyses that are used today. This review will discuss the various DNA polymorphisms and their utility in human identity testing.

A multilocus DNA mini-barcode assay to identify twenty vertebrate wildlife species

The world faces significant challenges in preserving the diversity of vertebrate species due to wildlife crimes. DNA barcoding, an effective molecular marker for insufficient nuclear DNA, is an authentic and quick identification technique to trace the origin of seized samples in forensic investigations. Here, we present a multiplex assay capable of identifying twenty vertebrate wildlife species utilizing twenty species-specific primers that target short fragments of the mitochondrial Cyt b, COI, 16S rRNA, and 12S rRNA genes. The assay achieved strong species specificity and sensitivity with a detection limit as low as 5 pg of DNA input. Additionally, it effectively discriminated a minor contributor (≥1%) from binary mixtures and successfully identified of noninvasive samples, inhibited DNA samples, artificially degraded DNA samples, and case samples, demonstrating a sensitive, robust, practical and easily interpretable tool in screening, and investigating forensic wildlife crimes.

Application of SNPs with low minor allele frequencies in missing person identification (MPI) through kinship analysis of DNA mixtures

The need to identify a missing person (MP) through kinship analysis of DNA samples found at a crime scene has become increasingly prevalent. DNA samples from MPs can be severely degraded, contain little DNA and mixed with other contributors, which often makes it difficult to apply conventional methods in practice. This study developed a massively parallel sequencing-based panel that contains 1661 single-nucleotide polymorphisms (SNPs) with low minor allele frequencies (MAFs) (averaged at 0.0613) in the Chinese Han population, and the strategy for relationship inference from DNA mixtures comprising different numbers of contributors (NOCs) and of varying allele dropout probabilities. Based on the simulated dataset and genotyping results of 42 artificial DNA mixtures (NOC = 2-4), it was observed that the present SNP panel was sufficient for balanced mixtures when referenced to the closest relatives (parents/offspring and full siblings). When the mixture profiles suffered from dropout, incorrect assignments were markedly associated with relatedness, NOC and the dropout level. We, therefore, indicate that SNPs with low MAFs could be reliably interpreted for MP identification through the kinship analysis of complex DNA mixtures. Further studies should be extended to more possible scenarios to test the feasibility of this present approach.

Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity

Forensic investigation of DNA samples from multiple contributors has become commonplace. These complex analyses use statistical frameworks accounting for multiple levels of uncertainty in allelic contributions from different individuals, particularly for samples containing few molecules of DNA. These methods have been thoroughly tested along some axes of variation, but less attention has been paid to accuracy across human genetic variation. Here, we quantify the accuracy of DNA mixture analysis over 244 human groups. We find higher false inclusion rates for mixtures with more contributors, and for groups with lower genetic diversity. Even for two-contributor mixtures where one contributor is known and the reference group is correctly specified, false inclusion rates are 1e-5 or higher for 56 out of 244 groups. This means that, depending on multiple testing, some false inclusions may be expected. These false positives could be lessened with more selective and conservative use of DNA mixture analysis.

SNP analysis of challenging bone DNA samples using the HID-Ion AmpliSeq™ Identity Panel: facts and artefacts

PCR-MPS is an emerging tool for the analysis of low-quality DNA samples. In this study, we used PCR-MPS to analyse 32 challenging bone DNA samples from three Second World War victims, which previously yielded no results in conventional STR PCR-CE typing. The Identity Panel was used with 27 cycles of PCR. Despite that we only had an average of 6.8 pg of degraded DNA as template, 30 out of 32 libraries (93.8%) produced sequencing data for about 63/90 autosomal markers per sample. Out of the 30 libraries, 14 (46.7%) yielded single source genetic profiles in agreement with the biological identity of the donor, whereas 12 cases (40.0%) resulted in SNP profiles that did not match or were mixed. The misleading outcomes for those 12 cases were likely due to hidden exogenous human contamination, as shown by the higher frequencies of allelic imbalance, unusual high frequencies of allelic drop-ins, high heterozygosity levels in the consensus profiles generated from challenging samples, and traces of amplified molecular products in four out of eight extraction negative controls. Even if the source and the time of the contamination were not identified, it is likely that it occurred along the multi-step bone processing workflow. Our results suggest that only positive identification by statistical tools (e.g. likelihood ratio) should be accepted as reliable; oppositely, the results leading to exclusion should be treated as inconclusive because of potential contamination issues. Finally, strategies are discussed for monitoring the workflow of extremely challenging bone samples in PCR-MPS experiments with an increased number of PCR cycles.

Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology

In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 10⁷ (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed.

The effects of DNA profiles: Measuring the effectiveness of DNA banks in criminal investigations in Brazil

Since 2013, the Brazilian National Bank of Genetic Profiles (BNPG) of the Integrated Network of Genetic Profiles Bank (RIBPG) has been used to aid investigations, identifying who committed a crime based on biological samples found at crime scenes or on victims, which may be substantial evidence in a criminal case. This research evaluates the extent to which the types of genetic profiles and the number of hits influence the number of investigations aided. The study used data from institutions of the RIBPG adopting the period from 2016 to 2020 and organized them in a stacked panel with 98 observations. A regression mediation model was built to estimate the influence of the independent variables "forensic unknown profiles," "profiles of convicted offenders," and "profiles of suspected perpetrators or legal profiles" when mediated by the "hits" variable, influence the increase of the dependent variable "investigations aided," identified as a measure of the effectiveness of the forensic DNA banks. The results showed that the 1% increase in the variables "forensic unknown profiles" and "profiles of suspected perpetrators or legal profiles," mediated by "hits," was significant to produce "investigations aided." As for the variable "profiles of convicted offenders," there was no evidence that it contributed significantly to the increase in "hits" and "investigations aided." The study demonstrated that the increase in "forensic unknown profiles" by 126 and "profiles of suspected perpetrators or legal profiles" by 14 led to 12 "hits" in the RIBPG, offering support to 4 cases. The variable "profiles of convicted offenders" did not show significant results in terms of "hits" and "investigations aided."

Impact on touch DNA of an alcohol-based hand sanitizer used in COVID-19 prevention

In the last years, forensic research has been focused on touch DNA in order to improve its evidential value in criminal activity investigations as well as to understand the variables impacting touch DNA. One of the emerging variables is represented by the use of alcohol-based sanitizers, which was suggested for hand hygiene during the COVID-19 pandemic. The aims of the present study were to assess the effect of a hand sanitizer on touch DNA deposition, transfer, and recovery and also to evaluate STR typing success, quality of DNA profiles, and personal identification. Before and after the use of an alcohol-based hand sanitizer, 20 volunteers deposited on glass surfaces 120 fingerprints, containing skin-derived or salivary DNA. Samples were quantified by real-time quantitative PCR (q-PCR), and 76 samples yielding > 15 pg/μl were typed for 21 autosomal STRs by GlobalFiler® PCR Amplification Kit. DNA profiles were classified into single source, mixed, and inconclusive profiles, and a LR assessment was performed by comparison to the reference samples using LRmix Studio software. After the use of hand sanitizer, samples yielded lower quantities of recovered transferred DNA, especially considering samples containing salivary DNA (p < 0.05 by Friedman test). All the 76 amplified samples (63.3% of the total) showed at least 10 typed loci, and 83-100% of profiles were consistent with the reference ones on the basis of a LR value ≥ 10⁶. Results showed that, although the hand sanitizer reduces the DNA recovering, touch DNA samples might still be useful for forensic personal identification even when hand sanitizers are used.

LT-RPA: An Isothermal DNA Amplification Approach for Improved Microsatellite Genotyping and Microsatellite Instability Detection

Microsatellites are short tandem repeats of one to six nucleotides that are highly polymorphic and extensively used as genetic markers in numerous biomedical applications, including the detection of microsatellite instability (MSI) in cancer. The standard analytical method for microsatellite analysis relies on PCR amplification followed by capillary electrophoresis or, more recently, next-generation sequencing (NGS). However, their amplification during PCR generates undesirable frameshift products known as stutter peaks caused by polymerase slippage, complicating data analysis and interpretation, while very few alternative methods for microsatellite amplification have been developed to reduce the formation of these artifacts. In this context, the recently developed low-temperature recombinase polymerase amplification (LT-RPA) is an isothermal DNA amplification method at low temperature (32 °C) that drastically reduces and sometimes completely abolishes the formation of stutter peaks. LT-RPA greatly simplifies the genotyping of microsatellites and improves the detection of MSI in cancer. In this chapter, we describe in detail all the experimental steps necessary for the development of LT-RPA simplex and multiplex assays for microsatellite genotyping and MSI detection, including the design, optimization, and validation of the assays combined with capillary electrophoresis or NGS.

Evaluating DNA Mixtures with Contributors from Different Populations Using Probabilistic Genotyping

It is common practice to evaluate DNA profiling evidence with likelihood ratios using allele frequency estimates from a relevant population. When multiple populations may be relevant, a choice has to be made. For two-person mixtures without dropout, it has been reported that conservative estimates can be obtained by using the Person of Interest’s population with a θ value of 3%. More accurate estimates can be obtained by explicitly modelling different populations. One option is to present a minimum likelihood ratio across populations; another is to present a stratified likelihood ratio that incorporates a weighted average of likelihoods across multiple populations. For high template single source profiles, any difference between the methods is immaterial as far as conclusions are concerned. We revisit this issue in the context of potentially low-level and mixed samples where the contributors may originate from different populations and study likelihood ratio behaviour. We first present a method for evaluating DNA profiling evidence using probabilistic genotyping when the contributors may originate from different ethnic groups. In this method, likelihoods are weighted across a prior distribution that assigns sample donors to ethnic groups. The prior distribution can be constrained such that all sample donors are from the same ethnic group, or all permutations can be considered. A simulation study is used to determine the effect of either assumption on the likelihood ratio. The likelihood ratios are also compared to the minimum likelihood ratio across populations. We demonstrate that the common practise of taking a minimum likelihood ratio across populations is not always conservative when FST=0. Population stratification methods may also be non-conservative in some cases. When FST>0 is used in the likelihood ratio calculations, as is recommended, all compared approaches become conservative on average to varying degrees.

Isometric artifacts from polymerase chain reaction‐massively parallel sequencing analysis of short tandem repeat loci: An emerging issue from a new technology?

The recent introduction of polymerase chain reaction (PCR)‐massively parallel sequencing (MPS) technologies in forensics has changed the approach to allelic short tandem repeat (STR) typing because sequencing cloned PCR fragments enables alleles with identical molecular weights to be distinguished based on their nucleotide sequences. Therefore, because PCR fidelity mainly depends on template integrity, new technical issues could arise in the interpretation of the results obtained from the degraded samples. In this work, a set of DNA samples degraded in vitro was used to investigate whether PCR‐MPS could generate “isometric drop‐ins” (IDIs; i.e., molecular products having the same length as the original allele but with a different nucleotide sequence within the repeated units). The Precision ID GlobalFiler NGS STR panel kit was used to analyze 0.5 and 1 ng of mock samples in duplicate tests (for a total of 16 PCR‐MPS analyses). As expected, several well‐known PCR artifacts (such as allelic dropout, stutters above the threshold) were scored; 95 IDIs with an average occurrence of 5.9 IDIs per test (min: 1, max: 11) were scored as well. In total, IDIs represented one of the most frequent artifacts. The coverage of these IDIs reached up to 981 reads (median: 239 reads), and the ratios with the coverage of the original allele ranged from 0.069 to 7.285 (median: 0.221). In addition, approximately 5.2% of the IDIs showed coverage higher than that of the original allele. Molecular analysis of these artifacts showed that they were generated in 96.8% of cases through a single nucleotide change event, with the C > T transition being the most frequent (85.7%). Thus, in a forensic evaluation of evidence, IDIs may represent an actual issue, particularly when DNA mixtures need to be interpreted because they could mislead the operator regarding the number of contributors. Overall, the molecular features of the IDIs described in this work, as well as the performance of duplicate tests, may be useful tools for managing this new class of artifacts otherwise not detected by capillary electrophoresis technology.

A New Computational Deconvolution Algorithm for the Analysis of Forensic DNA Mixtures with SNP Markers

Single nucleotide polymorphisms (SNPs) support robust analysis on degraded DNA samples. However, the development of a systematic method to interpret the profiles derived from the mixtures is less studied, and it remains a challenge due to the bi-allelic nature of SNP markers. To improve the discriminating power of SNPs, this study explored bioinformatic strategies to analyze mixtures. Then, computer-generated mixtures were produced using real-world massively parallel sequencing (MPS) data from the single samples processed with the Precision ID Identity Panel. Moreover, the values of the frequency of major allele reads (F_MAR) were calculated and applied as key parameters to deconvolve the two-person mixtures and estimate mixture ratios. Four custom R language scripts (three for autosomes and one for Y chromosome) were designed with the K-means clustering method as a core algorithm. Finally, the method was validated with real-world mixtures. The results indicated that the deconvolution accuracy for evenly balanced mixtures was 100% or close to 100%, which was the same as the deconvolution accuracy of inferring the genotypes of the major contributor of unevenly balanced mixtures. Meanwhile, the accuracy of inferring the genotypes of the minor contributor decreased as its proportion in the mixture decreased. Moreover, the estimated mixture ratio was almost equal to the actual ratio between 1:1 and 1:6. The method proposed in this study provides a new paradigm for mixture interpretation, especially for inferring contributor profiles of evenly balanced mixtures and the major contributor profile of unevenly balanced mixtures.

Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device

The high variability characteristic of short tandem repeat (STR) markers is harnessed for human identification in forensic genetic analyses. Despite the power and reliability of current typing techniques, sequence-level information both within and around STRs are masked in the length-based profiles generated. Forensic STR typing using next generation sequencing (NGS) has therefore gained attention as an alternative to traditional capillary electrophoresis (CE) approaches. In this proof-of-principle study, we evaluate the forensic applicability of the newest and smallest NGS platform available - the Oxford Nanopore Technologies (ONT) MinION device. Although nanopore sequencing on the handheld MinION offers numerous advantages, including low startup cost and on-site sample processing, the relatively high error rate and lack of forensic-specific analysis software has prevented accurate profiling across STR panels in previous studies. Here we present STRspy, a streamlined method capable of producing length- and sequence-based STR allele designations from noisy, error-prone third generation sequencing reads. To assess the capabilities of STRspy, seven reference samples (female: n = 2; male: n = 5) were amplified at 15 and 30 PCR cycles using the Promega PowerSeq 46GY System and sequenced on the ONT MinION device in triplicate. Basecalled reads were then processed with STRspy using a custom database containing alleles reported in the STRSeq BioProject NIST 1036 dataset. Resultant STR allele designations and flanking region single nucleotide polymorphism (SNP) calls were compared to the manufacturer-validated genotypes for each sample. STRspy generated robust and reliable genotypes across all autosomal STR loci amplified with 30 PCR cycles, achieving 100% concordance based on both length and sequence. Furthermore, we were able to identify flanking region SNPs in the 15-cycle dataset with > 90% accuracy. These results demonstrate that when analyzed with STRspy ONT reads can reveal additional variation in and around STR loci depending on read coverage. As the first and only third generation sequencing platform-specific method to successfully profile the entire panel of autosomal STRs amplified by a commercially available multiplex, STRspy significantly increases the feasibility of nanopore sequencing in forensic applications.

DNA Transfer in Forensic Science: Recent Progress towards Meeting Challenges

Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to DNA quantities and profile types being obtained given particular scenarios and circumstances, is paramount when performing, and giving guidance on, evaluations of DNA findings given activity level propositions (activity level evaluations). In late 2018 and early 2019, three major reviews were published on aspects of DNA-TPPR, with each advocating the need for further research and other actions to support the conduct of DNA-related activity level evaluations. Here, we look at how challenges are being met, primarily by providing a synopsis of DNA-TPPR-related articles published since the conduct of these reviews and briefly exploring some of the actions taken by industry stakeholders towards addressing identified gaps. Much has been carried out in recent years, and efforts continue, to meet the challenges to continually improve the capacity of forensic experts to provide the guidance sought by the judiciary with respect to the transfer of DNA.

A proof-of-principle study on implementing polymerase chain displacement reaction (PCDR) to improve forensic low-template DNA analysis

Polymerase chain reaction (PCR) plays an important role in forensic DNA analysis. However, the amplification of low-template DNA (LTDNA) samples usually encounters unsatisfactory results for the limited efficiency of PCR, which would interfere with the subsequent profile interpretation. Polymerase chain displacement reaction (PCDR) is a highly-efficient technique characterized by combining PCR and strand displacement reaction into a single PCDR cycle. This study explored the feasibility of PCDR for improving forensic LTDNA analysis. STR markers commonly used in forensic genetics were subjected to PCDR amplification and capillary electrophoresis detection. The results of singleplex reactions indicated that PCDR surpassed original PCR in efficiency for STR amplification. The average peak height of alleles in PCDR profiles was linearly correlated to the number of outer primers adopted for initiating the strand displacement process. Further, we assessed the multiplexing potential of PCDR by incorporating 17 STRs included in the expanded CODIS core loci and Amelogenin gene into a multiplex PCDR system. For pristine DNA templates ranged from 200 pg to 12.5 pg, the multiplex PCDR system consistently exhibited higher allele peak height as well as less allele dropout compared to the multiplex PCR references. Meanwhile, a significant reduction of stutter ratio was extensively observed in PCDR profiles. We also tested mock casework samples to verify the practical ability of multiplex PCDR for LTDNA detection. With DNA input varying from 48.1 pg to 6.6 pg, the multiplex PCDR system consistently obtained more allelic information than multiplex PCR methods. Our data collectively suggested that it is feasible to apply PCDR in forensic LTDNA analysis.

A highly polymorphic panel of 40-plex microhaplotypes for the Chinese Han population and its application in estimating the number of contributors in DNA mixtures

Microhaplotypes (MHs) have great potential in multiple forensic applications and have proven to be promising markers in complex DNA mixture analysis. In this study, we developed a multiplex panel of 40 highly polymorphic MHs for the Chinese Han population, evaluated its forensic values, and explored its application in predicting the number of contributors (NOCs) in DNA mixtures. The panel consisted of 20 newly proposed loci and 20 previously reported loci with lengths spanning less than 120 bp. The average effective number of alleles (A_e) was 3.77, and the cumulative matching probability (CMP) and the cumulative power of exclusion (CPE) reached 1.2E-37 and 1-2.1E-12, respectively, in the Chinese Han population from the 1000 Genomes Project. Further validation on 150 Chinese Han individuals showed that A_e ranged from 2.62 to 4.41 with a mean value of 3.61, and CMP and CPE were 3.61E-36 and 1-1.84E-12, respectively, indicating that this panel was informative for personal identification and paternity testing in the studied population. To estimate NOC in DNA mixtures, we developed a machine learning model based on this panel. As a result, the accuracies in artificial DNA mixtures reached 95.24% for 2- to 4-person mixtures and 83.33% for 2- to 6-person mixtures. Furthermore, the NOC estimation on simulated profiles with allele dropout showed that this panel was still robust under slight dropout. In conclusion, this panel has value for forensic identification and NOC estimation of DNA mixtures.

Developments in forensic DNA analysis

The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.

A 2b-RAD parentage analysis pipeline for complex and mixed DNA samples

Next-generation sequencing technology has revolutionized genotyping in many fields of study, yet parentage analysis often still relies on microsatellite markers that are costly to generate and are currently available only for a limited number of species. 2b-RAD sequencing (2b-RAD) is a DNA sequencing technique developed for ecological population genomics that utilizes type IIB restriction enzymes to generate consistent, uniform fragments across samples. This technology is inexpensive, effective with low DNA inputs, and robust to DNA degradation. Here, we developed a probabilistic genotyping-by-sequencing genetic testing pipeline for parentage analysis by using 2b-RAD for inferring familial relationships from mixed DNA samples and populations. Our approach to partial paternity assignment utilizes a novel weighted outlier paternity index (WOPI) adapted for next-generation sequencing data and an identity-by-state (IBS) matrix-based clustering method for pedigree reconstruction. The combination of these two parentage assignment methods overcomes two major obstacles faced by other genetic testing methods: 1) It allows detection of parentage when closely related or inbred individuals are in the alleged parent population (e.g., in laboratory strains); and 2) it resolves mixed DNA samples. We successfully demonstrate this novel approach by correctly inferring paternity for samples pooled from multiple offspring (i.e., entire clutches) in a highly inbred population of an East African cichlid fish. The unique advantages of 2b-RAD in combination with our bioinformatics pipeline enable straightforward and cost-effective parentage analysis in any species regardless of genomic resources available.

Second GHEP-ISFG exercise for DVI: "DNA-led" victims' identification in a simulated air crash

The Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) has organized a second collaborative exercise on a simulated case of Disaster Victim Identification (DVI), with the participation of eighteen laboratories. The exercise focused on the analysis of a simulated plane crash case of medium-size resulting in 66 victims with varying degrees of fragmentation of the bodies (with commingled remains). As an additional difficulty, this second exercise included 21 related victims belonging to 6 families among the 66 missings to be identified. A total number of 228 post-mortem samples were represented with aSTR and mtDNA profiles, with a proportion of partial aSTR profiles simulating charred remains. To perform the exercise, participants were provided with aSTR and mtDNA data of 51 reference pedigrees -some of which deficient-including 128 donors for identification purposes. The exercise consisted firstly in the comparison of the post-mortem genetic profiles in order to re-associate fragmented remains to the same individual and secondly in the identification of the re-associated remains by comparing aSTR and mtDNA profiles with reference pedigrees using pre-established thresholds to report a positive identification. Regarding the results of the post-mortem samples re-associations, only a small number of discrepancies among participants were detected, all of which were from just a few labs. However, in the identification process by kinship analysis with family references, there were more discrepancies in comparison to the correct results. The identification results of single victims yielded fewer problems than the identification of multiple related victims within the same family groups. Several reasons for the discrepant results were detected: a) the identity/non-identity hypotheses were sometimes wrongly expressed in the likelihood ratio calculations, b) some laboratories failed to use all family references to report the DNA match, c) In families with several related victims, some laboratories firstly identified some victims and then unnecessarily used their genetic information to identify the remaining victims within the family, d) some laboratories did not correctly use "prior odds" values for the Bayesian treatment of the episode for both post-mortem/post-mortem re-associations as well as the ante-mortem/post-mortem comparisons to evaluate the probability of identity. For some of the above reasons, certain laboratories failed to identify some victims. This simulated "DNA-led" identification exercise may help forensic genetic laboratories to gain experience and expertize for DVI or MPI in using genetic data and comparing their own results with the ones in this collaborative exercise.

A poor prognostic metastatic nongestational choriocarcinoma of the ovary: a case report and the literature review

BACKGROUND

Pure ovarian choriocarcinoma can be gestational or nongestational in origin. Nongestational pure ovarian choriocarcinoma is extremely rare and the prognosis is thought to be worse than that of the gestational type in patients with metastatic disease. We present a case of metastatic pure ovarian choriocarcinoma with poor prognosis in which the origin was identified as nongestational by DNA short tandem repeat (STR) analysis.

CASE PRESENTATION

A nulliparous woman in her thirties with metastatic choriocarcinoma was referred to our hospital after initial treatment proved unsuccessful. Two months earlier, she had undergone brain tumor resection and histological examination confirmed choriocarcinoma. Serum human chorionic gonadotropin (hCG) concentration at initial diagnosis was 5030 IU/L. Two cycles of a combination chemotherapy regimen of methotrexate, etoposide, and actinomycin-D (MEA therapy), which is commonly used for gestational choriocarcinoma, was administered. However, the disease could not be controlled. Imaging modalities at presentation revealed tumor present in the left ovary and left lung, but not in the uterus, which led us think that the choriocarcinoma was nongestational. Bleomycin, etoposide, and cisplatin (BEP therapy) which is commonly used for nongestational choriocarcinoma (malignant germ cell tumor) and surgical resection of the uterus, bilateral ovaries, and an affected part of the left lung led to the nadir level of hCG, but the tumor relapsed and levels of hCG again increased. To investigate the origin of choriocarcinoma, we performed DNA STR analysis of tumor cells and oral mucosal cells. Analysis revealed the origin of the choriocarcinoma as nongestational, as the genotype of tumor cells entirely corresponded with that of oral mucosal cells. BEP therapy and chemotherapy regimens administered for nongestational choriocarcinoma and gestational choriocarcinoma proved ineffective, and the patient died 21 months after diagnosis of metastatic choriocarcinoma.

CONCLUSION

Metastaic nongestational pure choriocarcinoma of ovary is an extremely rare and an aggressive disease, frequently resulting in poor outcome.

Revisiting single cell analysis in forensic science

Forensic science has yet to take full advantage of single cell analysis. Its greatest benefit is the ability to alleviate the challenges associated with DNA mixture analysis, which remains a significant hurdle in forensic science. Many of the factors that cause complexity in mixture interpretation are absent in single cell analyses—multiple contributors, varied levels of contribution, and allele masking. This study revisits single cell analyses in the context of forensic identification, introducing previously unseen depth to the characterization of data generated from single cells using a novel pipeline that includes recovery of single cells using the DEPArray NxT and amplification using the PowerPlex Fusion 6c kit with varied PCR cycles (29, 30, and 31). The resulting allelic signal was assessed using analytical thresholds of 10, 100, and 150RFU. The mean peak heights across the sample sets generally increased as cycle number increased, 75.0 ± 85.3, 147.1 ± 172.6, and 226.1 ± 298.2 RFU, for 29, 30, and 31 cycles, respectively. The average proportion of allele/locus dropout was most significantly impacted by changes in the detection threshold, whereas increases in PCR cycle number had less impact. Overall data quality improved notably when increasing PCR from 29 to 30 cycles, less improvement and more volatility was introduced at 31 cycles. The average random match probabilities for the 29, 30, and 31 cycle sets at 150RFU are 1 in 2.4 × 10¹⁸ ± 1.46 × 10¹⁹, 1 in 1.49 × 10²⁵ ± 5.8 × 10²⁵, and 1 in 1.83 × 10²⁴ ± 8.09 × 10²⁴, respectively. This demonstrates the current power of single cell analysis in removing the need for complex mixture analysis.

Past, Present, and Future of DNA Typing for Analyzing Human and Non-Human Forensic Samples

Forensic DNA analysis has vastly evolved since the first forensic samples were evaluated by restriction fragment length polymorphism (RFLP). Methodologies advanced from gel electrophoresis techniques to capillary electrophoresis and now to next generation sequencing (NGS). Capillary electrophoresis was and still is the standard method used in forensic analysis. However, dependent upon the information needed, there are several different techniques that can be used to type a DNA fragment. Short tandem repeat (STR) fragment analysis, Sanger sequencing, SNapShot, and capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) are a few of the techniques that have been used for the genetic analysis of DNA samples. NGS is the newest and most revolutionary technology and has the potential to be the next standard for genetic analysis. This review briefly encompasses many of the techniques and applications that have been utilized for the analysis of human and nonhuman DNA samples.

Challenges with co-amplification of microbial DNA in interpretation of STR profiles obtained from human skeletal remains

STR-based DNA analysis is still the main tool for human DNA identification in most forensic DNA laboratories. DNA typing of aged human skeletal elements faces well-known interpretation challenges characteristic of degraded and low copy number DNA samples. Analyzing tens of thousands of human bone and teeth samples, we found that the occasional presence of artefactual peaks of presumed microbial origin adds another layer of complexity to the interpretation of STR profiles. In this paper, we present our approach and suggest guidelines for identifying and distinguishing non-human peaks, developed over the last 18 years. Additionally, we report a compendium of artefact peaks of presumed microbial origin recorded in human STR profiles obtained from bone and teeth samples, originating from Iraq, Chile, Maldives, Brazil and Western Balkans. Our experience has shown that these artefacts are not uncommon in bone STR testing, suggesting the possibility of occurrence in other forensic contexts, particularly trace DNA samples. Raising awareness among the forensic DNA community and accounting for this phenomenon is important for accurate STR interpretation.

Micromanipulation of single cells and fingerprints for forensic identification

Crime scene samples often include biological stains, handled items, or worn clothes and may contain cells from various donors. Applying routine sample collection methods by using a portion of a biological stain or swabbing the entire suspected touched area of the evidence followed by DNA extraction often leads to DNA mixtures. Some mixtures can be addressed with sophisticated interpretation protocols and probabilistic genotyping software resulting in DNA profiles of their contributors. However, many samples remain unresolved, providing no investigative information. Samples with many contributors are often the most challenging samples in forensic biology. Examples include gang rape situations or where the perpetrator's DNA is present in traces among the overwhelming amounts of the victim's DNA. If this is the only available evidence in a case, it is of paramount importance to generate usable information. An alternative approach, to address biological mixtures, could be the collection of individual cells directly from the evidence and testing them separately. This method could prevent cells from being inadvertently blended during the extraction process, thus resulting in DNA mixtures. In this study, multiple tools coupled with adhesive microcarriers to collect single cells were evaluated. These were tested on epithelial (buccal) and sperm cells, as well as on touched items. Single cells were successfully collected but fingerprints were swabbed in their entirety to account for the extracellular DNA of these samples and the poor DNA quality of shed skin flakes. Furthermore, micromanipulation devices, such as the P.A.L.M.® and the Axio Zoom.V16 operated manually or with a robotic arm aureka®, were compared for their effectiveness in collecting cells. The P.A.L.M.® was suitable for single cell isolation when smeared on membrane slides. Manual or robotic manipulations, by utilizing the Axio Zoom.V16, have wider applications as they can be used to isolate cells from various substrates such as glass or membrane slides, tapes, or directly from the evidence. Manipulations using the Axio Zoom.V16, either with the robotic arm aureka® or manually, generated similar outcomes which were significantly better than the outcomes by using the P.A.L.M.®. Robotic manipulations using the aureka® produced more consistent results, but operating the aureka® required training and often needed re-calibrations. This made the process of cell manipulations slower than when manually operated. Our preferred method was the manual manipulations as it was fast, cost effective, required little training, but relied on a steady hand of the technician.

Evaluation of a custom GeneRead™ massively parallel sequencing assay with 210 ancestry informative SNPs using the Ion S5™ and MiSeq platforms

A custom GeneRead DNAseq SNP panel with 210 markers was evaluated using the Ion S5 and MiSeq sequencing platforms. Sensitivity, PCR cycle number, and the use of half volume of reagents for target enrichment and library preparation were tested. Furthermore, genotype concordance between results obtained with the different sequencing platforms and with known profiles generated using other sequencing assays was analysed. The GeneRead DNASeq SNP assay gave reproducible results with an input of 200 pg DNA on both platforms. A total of 204 loci were successfully sequenced. Three loci failed completely in the PCR amplification, and three additional loci displayed frequent locus drop-outs due to low read depth or high heterozygote imbalance. Overall, the read depth across the loci was more well-balanced with the MiSeq, while the heterozygote balance was less variable with the Ion S5. Noise levels were low on both platforms (median< 0.2 %). Two simple criteria for genotyping were applied: A minimum threshold of 45 reads and an acceptable heterozygote balance range of 0.3-3.0. Complete concordance between platforms was observed except for three genotypes in one of the poorly performing loci, rs1470637. This locus had relatively low read depths on both platforms, skewed heterozygote balance, and frequent locus drop-outs. There was also full genotype concordance between the results from the GeneRead assay and known profiles generated with the QIAseq and Ion AmpliSeq assays. The few discordant results were either due to locus drop-outs in the poorly performing loci or allele drop-outs in the QIAseq assay. Profiles with a minimum of 179 SNPs were obtained from four challenging case work samples (blood swabs, bone, or blood from a corpse). Overall, the GeneRead DNASeq assay showed considerable potential and could provide a reliable method for SNP genotyping in cases involving identification of individuals, prediction of phenotypic traits, and ancestry inference.

Strategy for STR typing of bones from the Second World War combining CE and NGS technology: A pilot study

The genetic identification of skeletal remains found in Second World War mass graves is complicated because of the poor quality of the samples. The aim of this study was to set up a workflow for STR typing of such samples combining PCR/CE and PCR/NGS technologies. To this end, 57 DNA samples from an equal number of 75-year-old femurs were studied. After a first round of PCR typing using GlobalFiler CE, 42 samples yielded a full profile and were therefore submitted to our standard workflow. The 15 samples that yielded no or a limited number (2-17/21) of autosomal STR markers as well four bone control samples that provided a full profile with the conventional PCR/CE test were typed in duplicate by the GlobalFiler NGS kit. Despite the degradation of the samples, which resulted in lower coverage and a lower % of on-target reads, reliable sequencing data were obtained from 16/19 samples. The use of a threshold of 30× for the locus call led to a consensus profile (cp) of 20-31/31 STR autosomal loci in 10 samples and to a cp of 8-10/31 loci in two samples, whereas the four control samples yielded a cp of 26-31/31 loci. Finally, the data of the NGS typing were combined with those of the CE typing. This last task allowed us to recover (on average) three alleles per sample and to increase the number of the heterozygous patterns in 37 cases. In total, the combined approach proposed here made possible the genetic typing of 65-100% of the autosomal STR markers in 10/15 (66.6 %) skeletal remains that yielded no or very poor results with the conventional PCR/CE approach. However, because several artefacts (such as allelic drop-out and allelic drop-in) were scored, the risk of mistyping cannot be neglected.

Autosomal STR Profiling and Databanking in Malaysia: Current Status and Future Prospects

Science and technology are extensively used in criminal investigation. From the mid- to late-1980s, one of the scientific discoveries that has had a particularly remarkable impact on this field has been the use of highly variable DNA sequence regions (minisatellites) in the human genome for individual identification. The technique was initially referred to as DNA fingerprinting, but is now more widely referred to as DNA profiling. Since then, many new developments have occurred within this area of science. These include the introduction of new genetic markers (microsatellites also known as short tandem repeats/STRs), the use of the polymerase chain reaction for target amplification, the development of DNA databases (databanking), and the advancement and/or improvement of genotyping protocols and technologies. In 2019, we described the progress of DNA profiling and DNA databanking in Malaysia for the first time. This report included information on DNA analysis regulations and legislation, STR genotyping protocols, database management, and accreditation status. Here, we provide an update on the performance of our DNA databank (numbers of DNA profiles and hits) plus the technical issues associated with correctly assigning the weight of evidence for DNA profiles in an ethnically diverse population, and the potential application of rapid DNA testing in the country. A total of 116,534 DNA profiles were obtained and stored in the Forensic DNA Databank of Malaysia (FDDM) by 2019, having increased from 70,570 in 2017. The number of hits increased by more than three-fold in just two years, where 17 and 69 hits between the DNA profiles stored in the FDDM and those from crime scenes, suspects, detainees, drug users, convicts, missing persons, or volunteers were recorded in 2017 and 2019, respectively. Forensic DNA analysis and databanking are thus progressing well in Malaysia and have already contributed to many criminal investigations. However, several other issues are discussed here, including the need for STR population data for uncharacterized population groups, and pilot trials for adopting rapid DNA profiling technology. These aspects should be considered by policy makers and law enforcement agencies in order to increase the reliability and efficiency of DNA profiling in criminal cases and in kinship analysis in Malaysia.

Sequencing of human identification markers in an Uyghur population using the MiSeq FGxTM Forensic Genomics System

Massively parallel sequencing (MPS) offers a useful alternative to capillary electrophoresis (CE) based analysis of human identification markers in forensic genetics. By sequencing short tandem repeats (STRs) instead of determining the fragment lengths by CE, the sequence variation within the repeat region and the flanking regions may be identified. In this study, we typed 264 Uyghur individuals using the MiSeq FGx™ Forensic Genomics System and Primer Mix A of the ForenSeq™ DNA Signature Prep Kit that amplifies 27 autosomal STRs, 25 Y-STRs, seven X-STRs, and 94 HID-SNPs. STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs, respectively. Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were 3–4 times larger than those of alleles determined by repeat length alone. A relatively large number of flanking region variants (28 SNPs and three InDels) were observed in the Uyghur population. Seventeen of the flanking region SNPs were rare, and 12 of these SNPs had no accession number in dbSNP. The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E−36 and 1.49E + 16, respectively. This was 10 000 times lower and 1 000 times higher, respectively, than the same parameters calculated from STR repeat lengths.

Key Points

Sequencing data on STRs and SNPs used for human identification are presented for the Uyghur population.

STRinNGS v.1.0 was used to analyse the flanking regions of STRs.

The concordance between PCR-CE and PCR-MPS results was 99.86%.

Detection of sequence variation in STRs and their flanking regions increased the allelic diversity.

Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System

The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful Forensic DNA Phenotyping (FDP). The EU-funded VISAGE (VISible Attributes through GEnomics) Consortium has developed various targeted MPS-based lab tools to apply FDP in routine forensic analyses. Here, we present an evaluation of the VISAGE Basic tool for appearance and ancestry prediction based on PowerSeq chemistry (Promega) on a MiSeq FGx System (Illumina). The panel consists of 153 single nucleotide polymorphisms (SNPs) that provide information about EVCs (41 SNPs for eye, hair and skin color from HIrisPlex-S) and continental BGA (115 SNPs; three overlap with the EVCs SNP set). The assay was evaluated for sensitivity, repeatability and genotyping concordance, as well as its performance with casework-type samples. This targeted MPS assay provided complete genotypes at all 153 SNPs down to 125 pg of input DNA and 99.67% correct genotypes at 50 pg. It was robust in terms of repeatability and concordance and provided useful results with casework-type samples. The results suggest that this MPS assay is a useful tool for basic appearance and ancestry prediction in forensic genetics for users interested in applying PowerSeq chemistry and MiSeq for this purpose.

Low temperature isothermal amplification of microsatellites drastically reduces stutter artifact formation and improves microsatellite instability detection in cancer

Microsatellites are polymorphic short tandem repeats of 1–6 nucleotides ubiquitously present in the genome that are extensively used in living organisms as genetic markers and in oncology to detect microsatellite instability (MSI). While the standard analysis method of microsatellites is based on PCR followed by capillary electrophoresis, it generates undesirable frameshift products known as ‘stutter peaks’ caused by the polymerase slippage that can greatly complicate the analysis and interpretation of the data. Here we present an easy multiplexable approach replacing PCR that is based on low temperature isothermal amplification using recombinase polymerase amplification (LT-RPA) that drastically reduces and sometimes completely abolishes the formation of stutter artifacts, thus greatly simplifying the calling of the alleles. Using HT17, a mononucleotide DNA repeat that was previously proposed as an optimal marker to detect MSI in tumor DNA, we showed that LT-RPA improves the limit of detection of MSI compared to PCR up to four times, notably for small deletions, and simplifies the identification of the mutant alleles. It was successfully applied to clinical colorectal cancer samples and enabled detection of MSI. This easy-to-handle, rapid and cost-effective approach may deeply improve the analysis of microsatellites in several biological and clinical applications.

Development of an automated AmpliSeq™ library building workflow for biological stain samples on the Biomek® 3000

Here, we present the development of an automated AmpliSeq™ (ThermoFischer, MA, USA) workflow for library building using the Biomek^® 3000 Laboratory Automation Workstation (Beckman Coulter Inc., CA, USA), in which the total volume of PCR reagents and reagents for library preparation are reduced by one-half. The automated AmpliSeq workflow was tested using 43 stain samples (blood, bone, muscle tissue, semen, swab, nail scrape and cigarette butts) collected from crime scenes. The sequencing data were evaluated for locus balance, heterozygous allele balance and noise. The performance of libraries built with the automated AmpliSeq workflow using one-half of the recommended reagent volumes were similar to the performance of libraries built with the recommended (full) volumes of the reagents.

Developmental validation of the monSTR identity panel, a forensic STR multiplex assay for massively parallel sequencing

The 21-plex STR panel monSTR was designed for high-fidelity forensic genotyping on the Illumina MiSeq platform. In this study, the panel's performance was validated according to the recommended validation guidelines of the Scientific Working Group for DNA Analysis Methods (SWGDAM). Concordance, repeatability and reproducibility, sensitivity of detection, mixture analysis, species-specificity, and the ability to analyze mock samples were assessed. Sequence data was analyzed using the genotyping software toaSTR. The assay performance was evaluated by measuring the read on-target ratio, the genotype accuracy, the inter-locus balance, the heterozygosity balance, and the signal-to-noise ratio. Results showed that profiles of NIST reference DNA samples as well as GEDNAP proficiency samples were fully concordant with CE-based methods. In addition, inter-run and intra-run variation experiments indicated high precision. Furthermore, full profiles could be obtained using 62.5 pg of DNA input amount with proper inter-locus balance and read on-target ratio; 76.4% of alleles were correctly called with 7.8 pg DNA input amount. It was demonstrated that 94.4% of minor contributor alleles were resolved accurately in a 1:49 mixture. Results suggested that the minor contribution could be precisely calculated based on the minor component allele frequency. Validation results described here demonstrate that the monSTR forensic identity panel is a valid tool for forensic STR genotyping using massively parallel sequencing.