Back to Amido Black: Uncovering touch DNA in blood-contaminated fingermarks.

Blood-contaminated fingermarks (FMs) found in violent crime scenes may directly connect the suspect to the crime by linking the FM to the suspect and the DNA from the blood to the victim. However, marks that are incomparable are considered "dead-evidence" as the link to the suspect is lost. In this study, a novel approach was attempted to uncover the trace amount of touch DNA of the suspect in such marks. We examined the effect of two enhancement methods, ninhydrin (NIN) and amido black (AB), on DNA recovery from blood-contaminated FMs. A total of 108 fingerprints were deposited in three sets of depleted blood prints, blood-contaminated FMs, and latent FMs. All FMs were developed by either NIN or AB, or left undeveloped as reference followed by the quantification of the total DNA amount. This work shows that while AB had a detrimental effect on the quantity of blood-derived DNA specifically, reducing it by half, no similar effect was observed for touch DNA in latent FMs. This reduction led to the alteration of the major-to-minor DNA profile ratio to 70:30, thus enabling to obtain two distinct DNA profiles of the suspect from the touch DNA as well as the victim's profile from the blood. From an operational perspective, the use of AB in crime scenes may have an added value to retrieve the crucial DNA profile of the suspect, thus resurrecting a "dead-evidence."

"MALDI-CSI": A proposed method for the tandem detection of human blood and DNA typing from enhanced fingermarks.

Matrix Assisted Laser Desorption Ionization Mass Spectrometry Profiling and Imaging (MALDI MSP and MALDI MSI), in combination with bottom up proteomics, have proven to successfully detect and map blood-derived peptide signatures in blood fingermarks, with high specificity and compatibility with a number of blood enhancement techniques (BET). In the present study, the application of MALDI MSP and MSI to blood marks has been investigated further. In particular, the MALDI based detection and visualisation of blood has been explored in tandem with DNA typing. This investigation has been undertaken in a scenario simulating blood fingermarks on painted walls. In the present study, two sets of marks were analysed with each set comprising of a depletion series of four marks deposited on a surface treated to simulate painted walls: Set I - developed with Ninhydrin (NIN) and Set II- developed with Acid Black-1 (AB-1). For both sets, the application of MALDI MSP was successful in detecting haem and human specific haemoglobin peptide markers. MALDI MSI also provided molecular images by visualising haem on the ridge pattern enhanced by BET. The feasibility of successful and subsequent DNA profiling from the recovered fingermarks was also assessed for marks that had undergone enzymatic in situ digestion and MALDI MSI; it was observed that in 73% of the samples analysed, a DNA profile suitable for comparison was obtained. Based on these results, a possible operational workflow has been proposed incorporating the use of a MALDI MS based approach as a confirmatory test for human blood enabling subsequent DNA typing.

Improved amplification results following episodes of failure to amplify at the Amelogenin Locus using PowerPlex® ESI 16 Fast System.

In 2012 the Israel Police DNA Casework laboratory adopted the 16 STR PowerPlex® ESI kit for routine use. The Promega Company updated this kit and developed the PowerPlex® ESI 16 Fast System in which all autosomal primer pairs remained identical to the original set, except at the amelogenin site. The master mix was improved and optimized which allowed for direct, faster and more robust amplification. Prior to implementing the PowerPlex® ESI 16 Fast System in our lab, we conducted a preliminary assay where 213 casework samples were amplified using the new kit. These samples had previously been extracted by one of two extraction kits employed by our lab. (the PrepFiler ExpressTM and PrepFiler BTATM Forensic DNA Extraction Kits). The amplification results from these samples were compared to samples amplified using the original PowerPlex® ESI 16 kit. Multiple incidents of failure to amplify at the amelogenin locus were noted using the new system with the recommended protocol at a rate of 13% (28 of 213 samples). Experiments were performed to understand whether these amplification failures could be a result of primer binding site mutations, extraction method reagents and/or inhibitors. The conclusions reached following these experiments, in conjunction with consultation with the manufacturer, led to the trial of a modified amplification protocol where the suggested annealing temperature was reduced by 2 degrees. To evaluate the efficiency of this altered protocol, a comparison study was undertaken where 88 additional casework samples were chosen and amplified using both the modified 58°C and the recommended 60°C annealing temperatures. We concluded that the most effective method in our laboratory for achieving a consistent and balanced amplification at the amelogenin locus was to reduce the annealing temperature from the manufacturer's recommended 60°C to 58°C. This modification resulted in a reduction of the failure to amplify at the amelogenin locus from 13% (28/213) to 1.1% (1/88) without any observed changes to the autosomal STR amplification results.

Long allele designations at D2S1338 and D19S433 loci as influenced by various multiplex STR kits.

European forensic laboratories are replacing the STR multiplex kits with the new generation 16/17 STR kits. This study examines the influence of the new generation kits and the new Applied Biosystems 3500xL Genetic Analyzer on the designation of long D2S1338 and D19S433 off-ladder alleles. Different allele calls were obtained using the new NGM™ (Applied Biosystems) and PowerPlex(®) ESI™ (Promega) kits compared with AmpFℓSTR(®) SGM Plus™ kit (Applied Biosystems). Sequence analysis was used to determine accurate allele designation. The new multiplex kits and the 3500xL Genetic Analyzer improved accuracy of long allele designations. DNA databases worldwide include countless profiles obtained by previous kits. Discrepancies between the new and former technologies may cause failure to detect hits. Discordance is expected due to primer sequence differences between various kits. An additional discordance, occurring in long alleles, independent of primer sequence is reported in this study.

Recognizing the advantage of employing the PowerPlex(®) ESI and PowerPlex(®) ESX complementary kits for purposes of clarification in routine casework.

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.

Discordance at D3S1358 locus involving SGM Plus™ and the European new generation multiplex kits.

During the course of routine database sample analysis in the Israel Police DNA database, an off-ladder D3S1358 allele, calculated to be >22.1, extending into the adjacent vWA locus was observed using Applied Biosystems SGM Plus™ kit. To verify the size of this D3S1358 long allele and to ensure it was not part of a trialle pattern in the neighboring locus, the sample was amplified using three of the European new generation STR multiplex kits: NGM(TM) (Applied Biosystem), Powerplex™ ESX and ESI (Promega). The results of these amplifications determined the variant to be a 22 allele. Subsequent sequencing confirmed this designation and revealed a nucleotide polymorphism. Ten additional SGM Plus™ profiled samples with D3S1358 alleles larger than 19, were re-analyzed using NGM(TM) and Powerplex™ ESX which also showed discordance in the calculated results between original SGM Plus™ designations and those obtained with the European new generation multiplexes.

The Israel DNA database--the establishment of a rapid, semi-automated analysis system.

The Israel Police DNA database, also known as IPDIS (Israel Police DNA Index System), has been operating since February 2007. During that time more than 135,000 reference samples have been uploaded and more than 2000 hits reported. We have developed an effective semi-automated system that includes two automated punchers, three liquid handler robots and four genetic analyzers. An inhouse LIMS program enables full tracking of every sample through the entire process of registration, pre-PCR handling, analysis of profiles, uploading to the database, hit reports and ultimately storage. The LIMS is also responsible for the future tracking of samples and their profiles to be expunged from the database according to the Israeli DNA legislation. The database is administered by an in-house developed software program, where reference and evidentiary profiles are uploaded, stored, searched and matched. The DNA database has proven to be an effective investigative tool which has gained the confidence of the Israeli public and on which the Israel National Police force has grown to rely.

A Y-chromosome STR marker should be added to commercial multiplex STR kits.

Autosomal short tandem repeat (STR) analysis has become highly relevant in the identification of victims from mass disasters and terrorist attacks. In such events, gender misidentification can be of grave consequences, yet the list reporting amelogenin amplification failure using STR multiplex kits continues to grow. Presented here are three such examples. In the first case, we present two male suspects who demonstrated amelogenin Y-deficient results using two commercial kit procedures. The presence of their Y chromosomes was proven by obtaining a Y-haplotype. The second case demonstrated a profile from a third male suspect where only the Y homolog of the XY pair was amplified. In events such as mass disasters or terrorist attacks, timely and reliable high throughput DNA typing results are essential. As the number of reported cases of amplification failure at the amelogenin gene continues to grow, we suggest that the incorporation of a better gender identification tool in commercial kits is crucial.

A possible source of reference DNA from archived treated adhesive lifters.

During the course of a double murder trial, it became apparent that the two adhesive lifters from the two cadavers had been mislabeled before being presented in court. The question was raised whether DNA testing from the biological material remaining attached to the lifters could resolve this mix-up. In fatal shooting cases where a bullet has been fired through a body surface, an adhesive lifter is applied directly to the entrance wound. The total nitrite residues, as well as biological material surrounding the wound (blood, hair, tissue) are transferred to the adhesive lifter. The nitrite residues are used for estimating firing distance. In a worst-case scenario, the biological material on the lifter may be the only remaining reference material from a victim. In this paper, we examined whether the biological material retrieved from adhesive lifters could be used for DNA typing after the lifters had been treated for GSR pattern. In as much as the biological material found on the lifters can be typed and profiled following physical and chemical treatment, we submit that archived adhesive lifters can be used as a future source of reference DNA from cadavers where no other sample is available.

'The story of Abraham, Isaac and Jacob" or "am I my brother's keeper?".

Presented is a case report of a violent sexual assault where the DNA profile obtained from an item of evidence was compared to a suspect's profile. The profiles did not match, but the sharing of such a large number of alleles raised the suspicion that perhaps the real perpetrator was a blood relative of the suspect. The investigators requested a sample from the suspect's brother, and a match was defined. In an era of technological breakthroughs in the field of forensic DNA analysis, the importance of the scientist's attention to the evidence presented in each case is stressed.

Presentation of a three-banded allele pattern--analysis and interpretation.

The Israel police forensic biology laboratory received as an item of evidence in an attempted murder case, a pair of trousers belonging to a suspect. A bloodstain was observed on the trousers and analyzed by STR typing for nine loci using the Promega GenePrint STR silver stain detection kits. The genetic profile defined was found to be identical to that of the victim's at all nine loci. Within this profile a three-banded allele pattern was observed at the D16S539 locus, both in the bloodstain and in the victim's reference blood sample. Confirmation of this phenomenon was accomplished by amplifying the extracted DNA from both the trousers and the victim's blood sample using the PowerPlex 16 kit by Promega and the AmpFlSTR SGM Plus kit by Perkin Elmer, followed by analysis of the amplification products by capillary electrophoresis on the ABI prism 310 genetic analyzer. The same three-banded allele pattern was observed at the D16S539 locus in both specimen and reference DNA, using each of the three kits. Three additional loci located on chromosome 16 (D16S3407, D16S2617 and D16S3082), not employed for forensic identification, were also analyzed and did not show three-banded allele pattern.

The effect of 1,2-indanedione, a latent fingerprint reagent on subsequent DNA profiling.

The compound 1,2-indanedione was recently introduced in our laboratory as an operational reagent for developing latent fingerprints on porous surfaces. As part of the reagent implementation, a study was carried out in order to determine whether either of the two operational 1,2-indanediones formulations interferes with further DNA profiling. Both formulations are based on HFE7100 solvent. One is acidic and the other neutral. In a controlled experiment, known donors attached stamps to envelopes by licking them. The stamped envelopes were initially treated with either one indanedione formulation or the other, and DNA was then extracted for STR typing. No differences were observed between the STR profiles obtained from treated and untreated stamps and envelopes, indicating that 1,2-indanedione does not adversely affect the extraction and subsequent amplification of the STRs examined. However, preliminary results indicate that potential DNA analysis depends on the time interval between the indanedione treatment and DNA extraction as no DNA can be recovered six days following treatment. For this reason, it is strongly recommended to extract DNA from treated items of evidence as soon as possible after indanedione treatment.