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Voskoboinik L.,Hebrew University of Jerusalem | Voskoboinik L.,Forensic Biology Laboratory | Ayers S.B.,Cellmark Forensics | Lefebvre A.K.,Cellmark Forensics | Darvasi A.,Hebrew University of Jerusalem
Forensic Science International: Genetics | Year: 2015

Common forensic and mass disaster scenarios present DNA evidence that comprises a mixture of several contributors. Identifying the presence of an individual in such mixtures has proven difficult. In the current study, we evaluate the practical usefulness of currently available "off-the-shelf" SNP microarrays for such purposes. We found that a set of 3000 SNPs specifically selected for this purpose can accurately identify the presence of an individual in complex DNA mixtures of various compositions. For example, individuals contributing as little as 5% to a complex DNA mixture can be robustly identified even if the starting DNA amount was as little as 5.0 ng and had undergone whole-genome amplification (WGA) prior to SNP analysis. The work presented in this study represents proof-of-principle that our previously proposed approach, can work with real "forensic-type" samples. Furthermore, in the absence of a low-density focused forensic SNP microarray, the use of standard, currently available high-density SNP microarrays can be similarly used and even increase statistical power due to the larger amount of available information. © 2015 Published by Elsevier Ireland Ltd.


Pasternak Z.,Hebrew University of Jerusalem | Al-Ashhab A.,Ben - Gurion University of the Negev | Gatica J.,Hebrew University of Jerusalem | Gafny R.,Forensic Biology Laboratory | And 4 more authors.
PLoS ONE | Year: 2013

Microbial communities in soils may change in accordance with distance, season, climate, soil texture and other environmental parameters. Microbial diversity patterns have been extensively surveyed in temperate regions, but few such studies attempted to address them with respect to spatial and temporal scales and their correlations to environmental factors, especially in arid ecosystems. In order to fill this gap on a regional scale, the molecular fingerprints and abundance of three taxonomic groups - Bacteria, α-Proteobacteria and Actinobacteria - were sampled from soils 0.5-100 km apart in arid, semi-arid, dry Mediterranean and shoreline Mediterranean regions in Israel. Additionally, on a local scale, the molecular fingerprints of three taxonomic groups - Bacteria, Archaea and Fungi - were sampled from soils 1 cm-500 m apart in the semi-arid region, in both summer and winter. Fingerprints of the Bacteria differentiated between all regions (P<0.02), while those of the α-Proteobacteria differentiated between some of the regions (0.010.05). Locally, fingerprints of archaea and fungi did not display distance-decay relationships (P>0.13), that is, the dissimilarity between communities did not increase with geographic distance. Neither was this phenomenon evident in bacterial samples in summer (P>0.24); in winter, however, differences between bacterial communities significantly increased as the geographic distances between them grew (P<0.01). Microbial community structures, as well as microbial abundance, were both significantly correlated to precipitation and soil characteristics: texture, organic matter and water content (R2>0.60, P<0.01). We conclude that on the whole, microbial biogeography in arid and semi-arid soils in Israel is determined more by specific environmental factors than geographic distances and spatial distribution patterns. © 2013 Pasternak et al.


Voskoboinik L.,Hebrew University of Jerusalem | Voskoboinik L.,Forensic Biology Laboratory | Darvasi A.,Hebrew University of Jerusalem
Forensic Science International: Genetics | Year: 2011

The identification of a suspect in a complex DNA mixture typed with standard short tandem repeat (STR) kits has proved difficult. In the current study we present the theoretical framework of a method aimed to resolve this problem in forensic cases. The method suggests genotyping a specially designed panel of 1000-3000 single nucleotide polymorphisms (SNPs), each with a relatively low (<0.1) minor allele frequency (MAF). The rationale of this method is that any individual will carry a specific set of dozens of rare alleles and the complex DNA mixture will carry this particular set only if the one individual is represented in the DNA mixture. The efficiency of the method is evaluated by estimating the probability that a random man will not be excluded (RMNE) from the mixture. When this probability, P(RMNE), is low, one can conclude that the suspect's DNA is present in the DNA mixture. Essentially, a P(RMNE) < 10 -9 is considered as proof, whereas a P(RMNE) < 10 -6 is considered strong evidence. For completeness, we also analyzed the method using the likelihood ratio (LR) approach. We have analyzed the method for a variety of conditions and found that generally the method will provide highly significant results even for complex mixtures combining up to 10 individuals. The method performs well even when close relatives (one or two brothers) are present in the complex DNA mixture and when contributors or suspects come from different populations. We have also found that the method can accurately identify the number of contributors to the mixture, something that in some instances has significant forensic value on its own. © 2010 Elsevier Ireland Ltd.


PubMed | University Paul Sabatier, Hebrew University of Jerusalem, CNRS Ampere Laboratory, James Hutton Institute and Forensic Biology Laboratory
Type: | Journal: Forensic science international. Genetics | Year: 2016

The ubiquity and transferability of soil makes it a resource for the forensic investigator, as it can provide a link between agents and scenes. However, the information contained in soils, such as chemical compounds, physical particles or biological entities, is seldom used in forensic investigations; due mainly to the associated costs, lack of available expertise, and the lack of soil databases. The microbial DNA in soil is relatively easy to access and analyse, having thus the potential to provide a powerful means for discriminating soil samples or linking them to a common origin. We compared the effectiveness and reliability of multiple methods and genes for bacterial characterisation in the differentiation of soil samples: ribosomal intergenic spacer analysis (RISA), terminal restriction fragment length polymorphism (TRFLP) of the rpoB gene, and five methods using the 16S rRNA gene: phylogenetic microarrays, TRFLP, and high throughput sequencing with Roche 454, Illumina MiSeq and IonTorrent PGM platforms. All these methods were also compared to long-chain hydrocarbons (n-alkanes) and fatty alcohol profiling of the same soil samples. RISA, 16S TRFLP and MiSeq performed best, reliably and significantly discriminating between adjacent, similar soil types. As TRFLP employs the same capillary electrophoresis equipment and procedures used to analyse human DNA, it is readily available for use in most forensic laboratories. TRFLP was optimized for forensic usage in five parameters: choice of primer pair, fluorescent tagging, concentrating DNA after digestion, number of PCR amplifications per sample and number of capillary electrophoresis runs per PCR amplification. This study shows that molecular microbial ecology methodologies are robust in discriminating between soil samples, illustrating their potential usage as an evaluative forensic tool.


Oz C.,Forensic Biology Laboratory | Einot N.,Forensic Biology Laboratory | Dell'Ariccia-Carmon A.,DNA Database Laboratory | Berlyne S.,Forensic Biology Laboratory | Gafny R.,Forensic Biology Laboratory
Forensic Science International: Genetics | Year: 2013

In an effort to promote European cross-border cooperation in fighting crime and international terrorism the Treaty of Prüm was drafted and accepted within the European forensic community. This move led to the commercial development of new multiplex kits which introduced five new STR loci and promised better performance. Recently the Israel Police DNA Casework and Database laboratories adopted the PowerPlex® ESI kit for routine use in our laboratories. Presented in this paper are examples of three types of ambiguous results encountered during the implementation of the PowerPlex® ESI kit into routine work. These ambiguous products presented themselves in the form of (1) extreme variants outside of loci borders, (2) failure to amplify sister allele pairs or expression of null alleles and (3) episodes of loss of separation of adjacent microvariants primarily in mixture samples. The re-analysis of all these samples using the PowerPlex® ESX kit successfully and rapidly clarified all three categories of anomalies. Spotlighting such events to the forensic community, especially regarding the novel loci introduced in these next generation kits, can aid in raising the analyst's awareness to their future appearances and prevent possible erroneous conclusions. In addition, providing timely DNA results to investigating teams is of great importance and operational forensic laboratories do not have at their immediate disposal methods such as sequencing to elucidate such manifestations. We suggest that the complementary use of the PowerPlex® ESI and PowerPlex® ESX can provide a benefit for clarification purposes in routine casework. © 2013 Elsevier Ireland Ltd.


Barash M.,Forensic Biology Laboratory | Barash M.,Bond University | Reshef A.,Forensic Biology Laboratory | Brauner P.,Forensic Biology Laboratory
Journal of Forensic Sciences | Year: 2010

The selection of the appropriate method of collection of biological material from crime scene items can be crucial to obtaining a DNA profile. The three techniques commonly used for sampling items are: cutting, swabbing, and taping. The tape sampling technique offers an advantage, in that it enables the collection of a potentially highly informative source of DNA, shed epithelial cells, from selected areas on crime scene items (the inside fingers of a glove, for instance). Furthermore, surface collection of biological material by taping reduces co-sampling of known PCR inhibitors such as clothing dyes. The correct choice of tape for crime scene item sampling is important. Not all tapes are suitable for biological trace evidence collection as well as DNA extraction. We report on one tape that met both these criteria. Three different cases are presented which demonstrate the usefulness of adhesive tape sampling of crime items. Finally, the advantages of the tape collection technique are discussed and guidelines for preferred areas of tape sampling on various casework items are presented. © 2010 American Academy of Forensic Sciences.


Avraham S.,Forensic Biology Laboratory | Berlyne S.,Forensic Biology Laboratory | Gafny R.,Forensic Biology Laboratory | Hazan-Eitan Z.,Mobile Laboratory for Serious Crimes | And 2 more authors.
Journal of Forensic Identification | Year: 2015

Rocks, although a problematic substrate for retrieval of DNA profiles, occasionally may be the missing link in providing a solution in specific forensic cases. Presented in this article is a developed protocol for approaching and analyzing such crime scene evidence, using moistened swabs for DNA collection. Results from real cases where this procedure was utilized on rocks were examined to determine the protocol's effectiveness.


Barash M.,Forensic Biology Laboratory | Shpitzen M.,Forensic Biology Laboratory | Gafny R.,Forensic Biology Laboratory | Zamir A.,Forensic Biology Laboratory
Journal of Forensic Identification | Year: 2015

FTA cards are regarded as a method of choice for the preservation and storage of blood and saliva prior to genetic testing. In this study, we compared the recommended protocol of DNA purification and amplification from FTA cards to a method we developed in the laboratory. Our simplified method was tailored for amplification using the AmpFLSTR SGM Plus kit. The modified method proved to decrease artifacts in DNA profiles and was more time- and cost-effective than the manufacturer's protocol.


Gefrides L.A.,Forensic Biology Laboratory | Powell M.C.,Forensic Biology Laboratory | Donley M.A.,Forensic Biology Laboratory | Kahn R.,Forensic Biology Laboratory
Forensic Science International: Genetics | Year: 2010

Laboratories employ various approaches to ensure that their consumables are free of DNA contamination. They may purchase pre-treated consumables, perform quality control checks prior to casework, and use in-house profile databases for contamination detection. It is better to prevent contamination prior to DNA typing than identify it after samples are processed. To this end, laboratories may UV irradiate or autoclave consumables prior to use but treatment procedures are typically based on killing microorganisms and not on the elimination of DNA. We report a systematic study of UV and autoclave treatments on the persistence of DNA from saliva. This study was undertaken to determine the best decontamination strategy for the removal of DNA from laboratory consumables. We have identified autoclave and UV irradiation procedures that can eliminate nanogram quantities of contaminating DNA contained within cellular material. Autoclaving is more effective than UV irradiation because it can eliminate short fragments of contaminating DNA more effectively. Lengthy autoclave or UV irradiation treatments are required. Depending on bulb power, a UV crosslinker may take a minimum of 2 h to achieve an effective dose for elimination of nanogram quantities of contaminating DNA (>7250 mJ/cm2). Similarly autoclaving may also take 2 h to eliminate similar quantities of contaminating DNA. For this study, we used dried saliva stains to determine the effective dose. Dried saliva stains were chosen because purified DNA as well as fresh saliva are less difficult to eradicate than dried stains and also because consumable contamination is more likely to be in the form of a collection of dry cells. © 2009 Elsevier Ireland Ltd. All rights reserved.


PubMed | Forensic Biology Laboratory
Type: Journal Article | Journal: Forensic science international. Genetics | Year: 2013

In an effort to promote European cross-border cooperation in fighting crime and international terrorism the Treaty of Prm was drafted and accepted within the European forensic community. This move led to the commercial development of new multiplex kits which introduced five new STR loci and promised better performance. Recently the Israel Police DNA Casework and Database laboratories adopted the PowerPlex() ESI kit for routine use in our laboratories. Presented in this paper are examples of three types of ambiguous results encountered during the implementation of the PowerPlex() ESI kit into routine work. These ambiguous products presented themselves in the form of (1) extreme variants outside of loci borders, (2) failure to amplify sister allele pairs or expression of null alleles and (3) episodes of loss of separation of adjacent microvariants primarily in mixture samples. The re-analysis of all these samples using the PowerPlex() ESX kit successfully and rapidly clarified all three categories of anomalies. Spotlighting such events to the forensic community, especially regarding the novel loci introduced in these next generation kits, can aid in raising the analysts awareness to their future appearances and prevent possible erroneous conclusions. In addition, providing timely DNA results to investigating teams is of great importance and operational forensic laboratories do not have at their immediate disposal methods such as sequencing to elucidate such manifestations. We suggest that the complementary use of the PowerPlex() ESI and PowerPlex() ESX can provide a benefit for clarification purposes in routine casework.

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