Comparative evaluation of the MAPlex, Precision ID Ancestry Panel, and VISAGE Basic Tool for biogeographical ancestry inference

Biogeographical ancestry (BGA) inference from ancestry-informative markers (AIMs) has strong potential to support forensic investigations. Over the past two decades, several forensic panels composed of AIMs have been developed to predict ancestry at a continental scale. These panels typically comprise fewer than 200 AIMs and have been designed and tested with a limited set of populations. How well these panels recover patterns of genetic diversity relative to larger sets of markers, and how accurately they infer ancestry of individuals and populations not included in their design remains poorly understood. The lack of comparative studies addressing these aspects makes the selection of appropriate panels for forensic laboratories difficult. In this study, the model-based genetic clustering tool STRUCTURE was used to compare three popular forensic BGA panels: MAPlex, Precision ID Ancestry Panel (PIDAP), and VISAGE Basic Tool (VISAGE BT) relative to a genome-wide reference set of 10k SNPs. The genotypes for all these markers were obtained for a comprehensive set of 3957 individuals from 228 worldwide human populations. Our results indicate that at the broad continental scale (K = 6) typically examined in forensic studies, all forensic panels produced similar genetic structure patterns compared to the reference set (G′ ≈ 90%) and had high classification performance across all regions (average AUC-PR > 97%). However, at K = 7 and K = 8, the forensic panels displayed some region-specific clustering deviations from the reference set, particularly in Europe and the region of East and South-East Asia, which may be attributed to differences in the design of the respective panels. Overall, the panel with the most consistent performance in all regions was VISAGE BT with an average weighted AUC̅W score of 96.26% across the three scales of geographical resolution investigated

Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification

Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification

Allelic proportions of 16 STR loci—including the new European Standard Set (ESS) loci—in a Swiss population sample

Allele frequencies and forensically relevant population statistics of 16 STR loci, including the new European Standard Set (ESS) loci, were estimated from 668 unrelated individuals of Caucasian appearance living in different parts of Switzerland. The samples were amplified with a combination of the following three kits: AmpFlSTR® NGM SElect™, PowerPlex® ESI17 and PowerPlex® ESX 17. All loci were highly polymorphic and no significant departure from Hardy-Weinberg equilibrium and linkage equilibrium was detected after correction for sampling

STRoe deer: a validated forensic STR profiling system for the European roe deer (Capreolus capreolus)

European roe deer (Capreolus capreolus L.) are the most common game species in Europe, hunted for meat and trophies. Forensic investigations involving roe deer poaching may often benefit from an individual identification method to link a suspect to a specific incident. The current paper presents a forensically validated DNA profiling system for European roe deer called “STRoe deer”. This DNA profiling system consists of 12 novel unlinked tetra-nucleotide short tandem repeat (STR) loci and two sexing markers, with an allelic ladder to facilitate accurate genotyping. Validation results using 513 European roe deer samples collected from a single population from the Swiss Plateau demonstrated successful amplification of all 14 loci with as little as 0.05 ng of European roe deer DNA. Species-specificity tests showed that other members of the Cervidae family exhibited partial profiles and non-specific peaks, whereas most members of the Bovidae family showed just non-specific cross-species amplification products. Three different methods to calculate match probabilities for randomly sampled European roe deer genotypes resulted in median match probabilities ranging from 1.4 × 10−13 to 2.5 × 10−5. These methods accounted for possible population structure, occurrence of null alleles and individual relatedness. Based on these results, we conclude that STRoe deer is a robust genotyping system that should prove a valuable tool for individual identification and sexing of European roe deer to support criminal investigations

Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

n the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was en-acted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and as-sess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immi-gration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad- scale geographic origin assignment using nuclear markers to support law enforcement

Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement

Dem Täter auf der Spur – Nachweis von Körpersekreten mittels mRNA-Profiling

Bis anhin erfolgt die Spurenartbestimmung von Körpersekreten mit enzymatischen und immunologischen Tests, die aber zum Teil nicht sehr spezifisch sind. mRNA-Profiling ist eine vielversprechende neue Methode zum Nachweis von Körperfl üssigkeiten (vor allem Blut, Speichel, Sperma, Vaginalsekret und Menstrualblut), bei der die Expression sekretspezifischer Proteine untersucht wird. Mit einer RNA/DNA Co-Analyse aus derselben Probe kann sowohl das Körpersekret identifiziert werden, als auch mittels DNA-Analyse die Probe einer Person zugeordnet werden. Diese Methoden und Ergebnisse werden anhand eines Kriminalfalls erklärt. In der Schweizerischen DNA-Datenbank werden die DNA-Profile von Spuren und tatverdächtigen Personen erfasst und verglichen. Eine Übereinstimmung der DNA-Profile ist ein belastendes Beweisstück gegen den Tatverdächtigen, muss aber vom Gericht zusammen mit anderen Untersuchungsergebnissen abschliessend beurteilt werden. Conventional methods to examine the biological origin of a stain are enzymatic or immunological tests, which are not very specific. mRNA profiling is a promising new method for the identification of body fl uids (especially blood, saliva, semen, vaginal secretions and menstrual blood), that relies on the differential expression of mRNAs in different tissues. An RNA/DNA Co-analysis from the same stain allows simultaneous forensic tissue identification and human individual identification. These methods and results are explained by means of a criminal case. In the Swiss DNA database the DNA profiles of stains and suspects are collected and compared. A match of a stain DNA profile with a person DNA profile is incriminating evidence against the perpetrator. The court has to evaluate the RNA and DNA results in the context of other findings and bring everything into an overall conclusion

19th century family saga re-told by DNA recovered from postcard stamps

Old postcards with stamps might help unravelling historical family stories and relationships. By employing ancient DNA recovered from world war I postage stamps, we disprove a family saga of an illegitimate child born in 1887. We developed a protocol to collect DNA from saliva, trapped and protected on the backside of postage stamps glued on postcards. With replicate STR analyses we were able to assemble almost full autosomal and Y-STR profiles of three male, deceased family members. The illegitimate child turned out to be a legitimate child of a later married couple

Postmortem stability of DNA

High-molecular-weight DNA was recovered postmortem in sufficient quantities from various human organ tissues as well as from blood, although not all organs were equally well suitable. Good DNA stability was found in brain cortex, lymph nodes and psoas muscle over a period of three weeks postmortem. Spleen and kidney showed good DNA stability up to five days postmortem but after longer periods, rapid degradation was observed. Yields of DNA from blood were not consistent because of the non homogeneity of samples. Blood clots were rich with DNA. Generally, the amount of degraded DNA correlated directly with the duration of the postmortem period. However in some cases, DNA degradation was already prominent after a short period. However in some cases, DNA degradation was already prominent after a short period. Case histories showed that high environmental temperature at the site of death and/or infectious diseases prior to death were the main factors for rapid autolysis. Gradual disappearance to complete loss of the long fragments (15-23 kb) was observed in DNA fingerprinting using the minisatellite probe 33.15. No extra-bands were noted, thus excluding erroneous conclusions. However, evidentiary value of older samples was lower