Analysis of fingerprint samples, testing various conditions, for forensic DNA identification

From dactyloscopy to the Minimum Surface Requirement (MSR): a metric to assess and obtain suitable human STR profiles

Friction skin ridge (Dactyloscopy) and DNA analyses have both played an essential role in forensic investigations for decades. The simultaneous and successful collection of a latent fingermark ridge pattern and the respective isolation of its human DNA can be a challenging task at a crime scene. Maximizing the quantity and quality of genetic information from this type of physical evidence has become one of the objectives of forensic science. Often, friction ridge impressions may lack discriminatory power due to low visual clarity of ridges and/or insufficient pattern area. In such cases, an optimized human DNA collection and extraction becomes crucial for obtaining a genetic identity from an unsuitable fingermark. Recent studies have proven that complete Short Tandem Repeat (STR) profiles can be acquired from touch DNA specimens. Although the impact of fingermark enhancement techniques on DNA recovery has been explored, no research has yet investigated the potential quantity of DNA that could be isolated per area of a ridge pattern. Here, DNA collection and extraction methods to determine the Minimum ridge Surface Requirement (MSR) to extract suitable human STR genotypes have been studied and optimized. Twelve participants, including biological males and females, provided ink prints of their index, middle, and ring fingers from both hands to calculate an average fingertip size to create a "standard" area for analysis across all donors. A standardized cutout template was created to fit every participant's latent fingermarks on pre-cleaned glass surfaces. Two fingermark "recharging-deposition-collecting" methods (i.e., Original Experiment and Optimized Experiment) and two swab types for DNA collection were compared (i.e., cotton swabs from Delta Lab (Spain) and 4N6FLOQSwabs® from Copan (Italy)). Then, ten participants deposited fingermarks for DNA extraction, quantification, STR amplification, and capillary electrophoresis (CE) for STR genotyping. Results showed that flocked swabs were more effective than cotton swabs at collecting DNA and produced suitable STR profiles with the optimized collection method. This research establishes the first MSR surfaces from which meaningful STR profiles can be acquired. These data provide key knowledge that assists crime investigators in prioritizing dactyloscopy, genotyping, or both analyses concurrently when examining latent fingermarks.

Optimization of a DNA extraction protocol from fingerprints for the analysis of nuclear STR and mitochondrial DNA genetic profiles

Most of the cells found in fingerprints belong to the cornified barrier of the epidermis (stratum corneum), lack nuclei and cytoplasmic organelles, and are filled with keratin. Nuclear and mitochondrial DNA is degraded and embedded in the keratin mesh, a very resistant protein that is difficult to remove during DNA extraction. In this work, we studied the possible negative effect of keratin on Polymerase Chain Reaction (PCR) reactions and the influence of keratinase and proteinase K on the extraction of DNA from fingerprints. The role of glycogen in the DNA yield during the precipitation step and the importance of washing the obtained DNA with 70% ethanol were also studied. DNA was extracted from 96 fingerprints corresponding to recent prints and stored for 0, 1, 5, and 18 months from six individuals. No differences were observed in the concentration of extracted DNA or in the number of nuclear Short Tandem Repeat (STR) alleles in the genetic profiles of fingerprints stored during different times. However, sex differences were observed in both the concentration of DNA obtained and the number of nuclear STR alleles detected, being lower in females than in males. In 80% of the fingerprints genetic profiles were obtained with at least half of the STR nuclear markers and, in 50% of the fingerprints genetic profiles were obtained with more than 90% of the markers, which would allow an unambiguous identification of the donor. In all fingerprints where mitochondrial DNA was analyzed, complete sequencing of the HV1 and HV2 regions was possible, which increases the accuracy of the results obtained. The optimized protocol allowed obtaining a complete STR nuclear genetic profile of a 20-year-old palmprint.

Key points

The presence of keratin negatively influences PCR reactions.The addition of keratinase in latent fingerprint DNA extraction protocol improves the yield and quality of the DNA obtained.The use of glycogen for DNA precipitation and 70% ethanol for washing the precipitate influence the yield and quality of the DNA isolated from fingerprint.The DNA obtained is useful for STR marker profiling and HV1 and HV2 hypervariable regions of mitochondrial DNA analysis.The amount of DNA obtained and the number of STR markers detected from fingerprints depend on the sex of the individual, but not on the time elapsed. The optimized protocol is efficient in analysis of a 20-year-old sample.

Microbes in fingerprints: A source for dating crime evidence?

Interest in the human microbiome has grown in recent years because of increasing applications to biomedicine and forensic science. However, the potential for dating evidence at a crime scene based upon time-dependent changes in microbial signatures has not been established, despite a relatively straightforward scientific process for isolating the microbiome. We hypothesize that modifications in microbial diversity, abundance, and succession can provide estimates of the time a surface was touched for investigative purposes. In this proof-of-concept research, the sequencing and analysis of the 16 S rRNA gene from microbes present in fresh and aged latent fingerprints deposited by three donors with pre- and post-washed hands is reported. The stability of major microbial phyla is confirmed while the dynamics of less abundant groups is described up to 21 days post-deposition. Most importantly, a phylum is suggested as the source for possible biological markers to date fingerprints: Deinococcus-Thermus.

Development of Improved DNA Collection and Extraction Methods for Handled Documents

Handwritten documents may contain probative DNA, but most crime laboratories do not process this evidence. DNA recovery should not impair other evidence processing such as latent prints or indented writing. In this study, single fingermarks on paper were sampled with flocked swabs, cutting, and dry vacuuming. In addition, two extraction methods were compared for the sample type. DNA yields were low across all methods; however, this work confirms the ability to recover DNA from paper and the usefulness of the vacuum sampling method combined with the Chelex-Tween method. Stability of touch DNA deposits were compared over an 11-month period to better understand degradation that may occur over time. No significant difference in DNA recovery was observed, suggesting DNA deposits on paper are stable over an 11-month span.

Who touched the document?: A new overall strategy for collection and identification of DNA from the questioned documents as a supportive evidence

The questions on which judges/prosecutors apply for expertise are mostly about by whom a document was drafted/signed. In this study, a new collective strategy was constructed including a collection method, a modified-silica-based DNA isolation method, and a novel purification method on four contact traces formed on four different paper surface during writing, using PCR with AmpFlSTR®GlobalFiler™ STR kit (after experimental comparison between three different kits) and identification using CE. This collective analysis approach is more sensitive and superior to its equivalents on questioned documents in literature because quantifiable amounts of touch DNA and profiles with high loci percentages (100% on day 1, 72.72% after 1 week) were obtained up to 1 week even after the most challenging conditions of sample forming that a forensic scientist can meet; as washing hands just before drafting and using a very low pressure in a shorter time (simulating a simple contact real conditions while drafting), using no visualizing technique that damages the document. Using the strategy, four most commonly used paper types were compared, to see in which of them DNA could be recovered better. The success of this strategy was shown on the 1-day to 10-year-old real samples from a diary and some archive documents from a law office (including the mix-DNA and different ballpoint pens). Thus, it became possible to show if a person had touched the document, in high success rates up to 1 week as a secondary evidence, when primary evidences are insufficient for the detection of document fraud offenses.

Forensic proteomics

Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.

Visualizing shed skin cells in fingerprint residue using dark-field microscopy

This proof-of-concept study shows that dark-field microscopy provides sufficient contrast for cell visualization in fingerprints with high sebum content. Although the application is limited to smooth surfaces that do not scatter light, such as polyethylene terephthalate (PET), it was able to measure the number of cells deposited within a fingerprint residue and the reduction in cell transfer with repeated skin contact. On a PET surface, at roughly 5 N of contact force, a typical finger transfers several hundred cells onto the surface. Over subsequent finger contacts onto a clean PET surface, this number decreased exponentially until a steady state was reached, which is characterized by the transfer of (78 ± 36) cells or (0.46 ± 0.21) cells/mm² when normalized for fingerprint area. High uncertainty in cell transfer was due to: the highly variable nature of a human finger (where the number of loose cells varies from person to person and from day to day depending on what they touch) and difficulties in controlling the contact force and finger movement such as twisting during deposition (where twisting of the finger can expose a new patch of skin to the substrate, increasing the number of cell transfer). Plasma etching was also explored as an effective way to validate dark-field microscopy for cell counting. Although limited to inorganic substrates due to etching effects, exposing the fingerprint for less than 10 min can remove a majority of the sebum while keeping the cells intact for a before-and-after comparison using light microscopy.

Non-destructive DNA recovery from handwritten documents using a dry vacuum technique

Investigations of many crimes such as robberies, kidnappings, and terrorism are often associated with the recovery of a paper document which has been written by the perpetrator. Paper can provide a variety of forensic evidence such as DNA, latent fingermarks, and indented writing. The focus of this study was DNA recovery from handwritten notes through a vacuum suction device while preserving the other evidence types and the integrity of the document. Copy paper was used to create handwritten documents and sheets with deliberate fingerprints, and indentations. The homemade vacuum device consists of a glass pipette blocked with a moistened swab and attached to a vacuum source. The method collected sufficient DNA amounts for DNA typing analysis with 80% of the 11 copy paper samples tested giving probative DNA profiles with five being eligible for DNA database entry. DNA recovery was also tested on other commonly encountered paper types. DNA quantities would have been sufficient for STR typing for approximately 50% of manila envelopes and notebook paper samples, but not for magazine pages and bank deposit slips. Deliberate sebaceous and eccrine latent fingermarks placed onto copy paper and developed with magnetic fingerprint developer or 1,2 indanedione were not affected by the vacuum swabbing technique. Simulated robbery notes with indented writing and processed using an Electrostatic Detection Apparatus (ESDA) demonstrated no interference through the DNA collection. This vacuum-based collection method enables laboratories to reverse the current questioned document workflow and start with DNA collection.

The compatibility of immunolabeling with STR profiling

Immunolabeling is a technique, which has recently been introduced to enhance the quality of developed fingermarks and subsequently strengthen the evidential value. The effect of this method on subsequent DNA analysis, however, has not been explored yet. Therefore, the current pilot study aimed to determine whether STR profiling is possible after immunolabeling. Since immunolabeling involves washing steps which could reduce DNA quantities, the use of different fixatives including methanol, formaldehyde and universal molecular fixative (UMFIX) were investigated. STR profiles from the (immunolabeled) fingermarks were generated after four days and four weeks by a direct PCR method to enable comparison of relatively fresh and old fingermarks. The fingermarks were deposited on diverse forensically relevant substrates, including glass, metal and tile. STR profiles could be recovered for all tested fixatives with no significant difference in performance. However, the mean number of detected alleles was the highest when methanol was used for fixation. Furthermore, immunolabeling on aged fingermarks (4 weeks) was also possible, but the number of detected alleles showed a non-significant decrease. DNA could be recovered from deposits on all substrates, of which glass showed the highest mean number of detected alleles followed by metal and tile.

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.

An efficient and eco-friendly workflow for dual fingermark processing and STR profiling

Since its discovery in 1997, DNA retrieved from touched or handled items (touch DNA) has been increasingly used in criminal casework. Depending on the nature of the substrate examined, numerous techniques are being used for fingermark (FM) collection and development, however, it has been shown that FM processing may impede or even prevent the dual analysis of FMs and DNA. In search for a possible solution, we have recently established a novel workflow for a non-destructive collection and eco-friendly visualization of latent FMs using white BVDA gel-lifters and black Wetwop® solution. In the present study, the scope and limitations of the proposed protocol were thoroughly examined for DNA recovery and genotyping in relation to substrate type (porous and non-porous), time elapsed after the deposition (1, 7 and 14 days) and donor's gender. The study included 120 developed FMs of 20 donors (10 males and 10 females, aged 25-50 years), from which 240 DNA samples were recovered and quantified. The independent analysis of two DNA samples recovered from each FM, one - from the adhesive surface of the gel-lifter and the other - from its imprint on the protecting acetate cover, allowed us not only to increase the total number of the identified donors, but also to achieve a higher level of confidence per FM. Though this approach appeared to be more efficient on non-porous substrates (up to 65% on car tin), it is noteworthy that forensically useful DNA profiles (with at least 8 full STR loci) were generated from poor-quality FMs on the porous substrate, drywall (25% and 15% in males and females, respectively). Finally, the integration of the results of touch DNA analysis and that of FM visual inspection allowed us to increase by more than half the number of personal identifications and to strengthen the chain of forensic evidence.

Evaluation of DNA Extraction Methods for Processing Fingerprint Powder-Coated Forensic Evidence

In unison, fingerprinting and DNA analysis have played a pivotal role in forensic investigations. Fingerprint powders that are available on the market can come in a range of colors and with specific properties. This study evaluated the efficiency of DNA extraction from samples coated with 3 brands of fingerprint powders: Lightning, Sirchie, and SupraNano, covering a range of colors and properties. A total of 23 fingerprint powders were tested using the Chelex, Promega DNA IQ™, and Applied Biosystems™ PrepFiler™ DNA extraction protocols. The DNA IQ™ and PrepFiler™ methods extracted higher yields of DNA in comparison to Chelex, which also accounted for better quality of PowerPlex x00AE; 21 DNA profiles recovered. There were no signs of degradation or inhibition in the quantification data, indicating that samples returning low DNA yield was due to interference during DNA extraction and not PCR inhibition. DNA profiles were recovered from the majority of fingerprint powders with only a single powder, Sirchie Magnetic Silver, failing to produce a profile using any of the methods tested. A link was observed between the DNA extraction chemistry, fingerprint powder property, that is, nonmagnetic, magnetic and aqueous, and the brand of fingerprint powder. Overall, the DNA IQ™ method was favorable for nonmagnetic fingerprint powders, while magnetic fingerprint powders produced more DNA profiles when extracted with the PrepFiler™ chemistry. This study highlights the importance of screening DNA extraction chemistries for the type of fingerprint powder used, as there is not a single DNA extraction method that suits all fingerprint powder brands and properties.

DNA recovery from gelatin fingerprint lifters by direct proteolytic digestion

Fingerprints are a valuable source for DNA profiling in forensic investigations. In practice, the fingerprints are routinely visualized first by powder staining and then often transferred to tapes or gelatin lifters for storage or examination. If at all, fingerprints are usually sampled for DNA in a second step. To target the DNA sampling in an optimal way, it is essential to know how much of the DNA in the sample remains in place and how much is transferred to the lifter. In the present study we addressed this question analyzing 16 pairs of thumb prints and revealed that more than 80% of the DNA from a fingerprint is transferred to the gelatin lifter. Therefore, subsequent DNA sampling of the stored gelatin lifters appears more promising than recovery of the residual DNA from the original fingerprint. Furthermore, as a proof of principle, we developed a protocol for the direct extraction of DNA from gelatin fingerprint lifters by proteolytic digestion of the gelatin matrix followed by organic extraction. We show that DNA recovery from gelatin lifters by this direct extraction protocol is more efficient compared to swabbing the lifter followed by standard magnetic bead extraction of swabs. However, given the more elaborate protocol for direct extraction, we would still recommend the swab technique as the method of choice for forensic routine work.