An innovative transfer DNA experimental design and qPCR assay to identify primary,secondary, and tertiary DNA transfer

“Touch DNA” is a form of trace DNA that is presumed to be deposited when an individual touches something and leaves behind DNA-containing skin cells, sweat, or other fluids. While touch DNA is often the result of direct contact (i.e., primary transfer), it can also be indirectly transferred between surfaces or individuals (e.g., secondary or tertiary transfer). Even experts cannot distinguish between different types of transfer and do not fully understand which variables affect direct versus indirect transfer or how often each type of transfer occurs. In this study, we utilize an innovative protocol that combines a paired male and female transfer DNA experimental design with an Amelogenin qPCR assay to generate data on primary, secondary, and tertiary DNA transfer. We report frequencies of indirect DNA transfer and also investigate the potential effects of participant age, self-identified ethnicity, and skin conditions on DNA transfer. Out of 22 experimental trials, we detected primary transfer (male + female) in 71% of trials, secondary DNA transfer in 50% of trials, and tertiary DNA transfer in 27% of trials. No significant associations were found between primary DNA transfer and age, self-identified ancestry, or skin conditions, however, all individuals with sloughing skin conditions demonstrated primary DNA transfer and we suggest this variable be explored in larger samples. These results contribute to a better understanding of the conditions under which secondary and tertiary DNA transfer occurs and can be used to propose realistic DNA transfer scenarios in court cases.     

Detection of cellular material within handprints

A novel technique for the visualisation of cellular material has been published harnessing an external binding nucleic acid fluorescence dye, Diamond™ dye (DD), in combination with a digital fluorescence microscope. This technique can effectively detect cellular material on an object transferred by touch allowing targeted collection of latent DNA. Previous studies on the visualisation of touch DNA have focussed on transfer from fingertips only.Here we report on the visualisation of cellular material transferred via twenty different positions over the entire handprint. Three volunteers (a heavy, an intermediate and a light shedder) were asked to press their hands onto a plastic surface with medium pressure for 15 s at undefined time points post-handwashing, creating a complete handprint. DD was applied to the entire area and the presence of cellular material was recorded based on cells within 5 separate frames at each of the 20 positions. All tests were performed in triplicate such that the final dataset contained 1,800 observed frames.This extensive study allows accurate monitoring of cellular transfer deposited by different parts of the hand. Our study highlights which areas of an individual’s hand shed the greatest, or least, amount of cellular material. This simple process can act as a guide for DNA collection from items held within the entire hand, rather than only touched by the fingertips only, such as weapons, knives and steering wheels.     

Secondary transfer of organic gunshot residues: Empirical data to assist the evaluation of three scenarios

The present study aimed at providing data to assess the secondary transfer of organic gunshot residues (OGSR). Three scenarios were evaluated in controlled conditions, namely displacing a firearm from point A to point B, a simple handshake and an arrest involving handcuffing on the ground. Specimens were collected from the firearm, the hands of the shooter and the non-shooter undergoing the secondary transfer in order to compare the amounts detected.Secondary transfer was observed for the three scenarios, but to a different extent. It was found that displacing a firearm resulted in secondary transfer in <50% of the experiments. The firearm also had an influence, as contrary to the pistol, no secondary OGSR were detected using the revolver. Shaking the hand of the shooter also transferred OGSR to the non-shooter's hand. In that case, the amount of OGSR was generally higher on the shooter than on the non-shooter. Finally, the largest secondary transfer was observed after the arrest with handcuffing with positive results in all cases using the pistol. In that scenario, the amounts on the shooter and the non-shooter were in the same range.This study highlights that the secondary transfer must be taken into account in the interpretation of OGSR. Indeed, an individual's hands might be contaminated by handling a firearm or having physical contact with a shooter.     

An innovative transfer DNA experimental design and qPCR assay: Protocol and pilot study

Forensic “touch” DNA samples are low-quantity samples that are recovered from surfaces that have been touched by single or multiple individuals. These samples can include DNA from primary contributors who directly touched the surface, as well as secondary contributors whose DNA was transferred to the surface through an intermediary. It is difficult to determine the type of transfer, or how often and under what conditions DNA transfer occurs. In this paper, we present an innovative protocol that combines (1) a paired male and female transfer DNA experimental design in which the presence of male DNA indicates secondary transfer and (2) a cost-effective quantitative PCR (qPCR) assay of a sex-specific region in the Amelogenin gene to detect male and female DNA. We evaluate the ability of the Amelogenin qPCR assay to detect low concentrations of male and female DNA in mixed samples. We also test experimental DNA samples using our transfer DNA protocol to differentiate primary and secondary DNA transfer. Male DNA was detected in the majority of known mixed samples, even in samples with 4× more female DNA—this result demonstrates the ability to detect low concentrations of male DNA and the presence of secondary transfer DNA in our experimental design. Primary DNA transfer was detected in 100% of our experimental trials and secondary DNA transfer was detected in 37.5% of trials. Our innovative protocol mimics realistic case scenarios to establish rates of primary and secondary DNA transfer in an inexpensive and simplified manner.     

Assessing the Risk of Secondary Transfer Via Fingerprint Brush Contamination Using Enhanced Sensitivity DNA Analysis Methods

Experiments were performed to determine the extent of cross‐contamination of DNA resulting from secondary transfer due to fingerprint brushes used on multiple items of evidence. Analysis of both standard and low copy number (LCN) STR was performed. Two different procedures were used to enhance sensitivity, post‐PCR cleanup and increased cycle number. Under standard STR typing procedures, some additional alleles were produced that were not present in the controls or blanks; however, there was insufficient data to include the contaminant donor as a contributor. Inclusion of the contaminant donor did occur for one sample using post‐PCR cleanup. Detection of the contaminant donor occurred for every replicate of the 31 cycle amplifications; however, using LCN interpretation recommendations for consensus profiles, only one sample would include the contaminant donor. Our results indicate that detection of secondary transfer of DNA can occur through fingerprint brush contamination and is enhanced using LCN‐DNA methods.     

DNA transfer during social interactions

Multiple DNA transfer has increasingly been brought up in court as potential means for the presence of the defendants DNA at the crime scene or on a piece of evidence. This has prompted several investigations into DNA transfer under very controlled and semi-controlled conditions, however little is published about DNA transfer in “uncontrolled” or real life situations.Here we examined the effects of multiple direct and indirect transfer of DNA within a small group of people and objects: three individuals participating in a social interaction of having a drink (jug of juice) together for 20 min. At the end of the tests all the surfaces of interest were sampled and analyzed.In many instances the last person or the only person to come in contact with the object was the main or the only depositor of the DNA detected on it. The jug was a clear vector for secondary DNA transfer. Interestingly, in many instances the participants acted as vectors for foreign DNA transfer.     

An investigation on the secondary transfer of organic gunshot residues

Gunshot residues (GSR) are an important forensic trace in firearm-related events. Currently, routine GSR analyses focus on the detection and characterisation of the inorganic components (IGSR). The increasing prevalence of heavy metal-free ammunition challenges these current protocols and there is an increasing interest in how the organic components of GSR (OGSR) can provide complementary information. Similar to the situation with IGSR, OGSR compounds originally deposited on the shooter during the firing process may further be transferred onto another individual or surface. Hence, the aim of this study was to provide additional information regarding the risk of a secondary transfer of OGSR. Two scenarios were investigated, the first one related to the arrest process and the possibilities of a secondary transfer arising between a shooter onto a non-shooter (e.g. between a police officer and a person of interest (POI)). The second scenario concerned the transfer of OGSR onto the non-shooter after handling a firearm for few minutes without discharging it. One calibre was chosen, the .40 S&W calibre, used by several Australian State police forces. A secondary transfer was observed in all cases for the two scenarios investigated, for three compounds of interest: ethylcentralite (EC), diphenylamine (DPA), N-nitrosodiphenylamine (N-nDPA). The firearm handling scenario resulted in a larger secondary transfer to that of the arrest scenario. Overall, the amounts of OGSR detected on the non-shooter were generally lower than that detected on the shooter and controls after the arrest scenario. The results of this study provide complementary knowledge about OGSR, which can be further used to improve the current practice and the interpretation of OGSR evidence. In particular, it highlights that the secondary transfer proposition must be considered during the interpretation of forensic findings, especially when small amounts of OGSR target compounds are detected.     

Transfer of DNA without contact from used clothing,pillowcases and towels by shaking agitation

DNA is frequently retrieved from commonly used objects or surfaces with no apparent biological stains. This DNA may have come from one or more individuals who directly deposited their DNA, or indirectly transferred the DNA of others, when physically contacting the sampled object or surface. Furthermore, contactless indirect DNA transfer of this ‘touch DNA’ from fabric substrates was recently demonstrated to be possible in a controlled laboratory environment. The circumstances and extent to which this form of contactless DNA transfer occurs are largely unknown. This study investigated indirect DNA transfer without contact by applying a gentle shaking agitation to used clothing, pillowcases and towels, with known usage and history, of 10 volunteers above the collection zone of the secondary surface. DNA transfer frequently occurred and was possible from all three investigated items. It occurred at levels that often produced informative profiles where transferred profiles closely resembled the profiles generated from the primary item. The outcomes of this study contribute to expanding the understanding of indirect DNA transfer without contact. However, this field would benefit from investigating a wider range of agitations and/or item types with various histories of use to determine the level of transfer and its detectability under different conditions.     

两种包装方式对小体积生物检材DNA检验的影响

目的探讨一种适用于小体积生物物证检材的包装方式。方法选择M4型螺丝钉作为研究对象,经去污消毒处理,通过手握方式转移人体脱落细胞到其表面,对螺丝钉采用两种不同的包装方式(滤纸包裹和悬空固定),经KingFisher Flex自动提取工作站进行DNA提取,从基因座等位基因检出情况、STR分型谱带峰高、均衡性等方面比较两种包装方式对螺丝钉上DNA检出率的影响。结果悬空固定包装螺丝钉实验组获得的STR分型谱带峰高、均衡性等方面均优于滤纸包裹包装实验组,其在基因座检出数量、分型完全相同样本数及有效分型样本数方面也多于滤纸包裹包装实验组。结论为降低微量生物检材DNA二次转移造成的损耗,提高小体积生物检材DNA的检出率,建议对小体积生物检材采用悬空固定方式进行物证包装。     

鼠抗人转铁蛋白单链抗体基因序列测定及分析

从携带人转铁蛋白单链抗体基因载体转化的大肠杆菌菌株中提取质粒,经电泳分析及筛选、纯化出线状质粒DNA,定量后以载体上人转铁蛋白单链抗体基因插入子两边的已知DNA序列经合成后作为引物进行测序扩增凝胶电泳,将得到的人转铁蛋白单链杭体基因序列重轻链可变区部分同基因库中鼠抗体重轻链进行同源比对,证明人转铁蛋白单链抗体基因确由鼠抗体重轻链可变区基因构成,在此基础上,进一步对基因核苷酸序列的可变区结构特征作推断分析,并推导出其对应的氨基酸序列.     

Investigation into "normal" background DNA on adult necks: implications for DNA profiling of manual strangulation victims

Others have investigated the role that DNA profiling could play as a method for identifying the perpetrator of manual strangulation. These studies have demonstrated that it is possible to collect offender DNA from the skin surface of a victim following physical contact. It is not known whether nonself biological material is normally present on the skin surface due to adventitious transfer occurring during innocent everyday interactions. To test the hypothesis that detectable amounts of nonself DNA are normally present on the skin surface of healthy adult individuals due to the adventitious transfer of DNA occurring during normal day-to-day social interactions, we designed an experiment in three phases. Phase 1 was used to deduce which DNA collection, extraction, and amplification methods were suited to investigating this question. During phase 2, the neck surface of 24 healthy adult volunteers was swabbed. DNA was extracted using the QIAamp DNA mini kit and amplified using the SGM Plus PCR amplification kit, using 28 PCR cycles. The work carried out during phase 3 involved a simulated assault to investigate primary and secondary transfer of DNA during physical contact. It was found that 23% of neck areas swabbed during phase 2 of this investigation showed nondonor alleles in the resulting DNA profile, with 5% of areas showing six or more nondonor alleles. The results of phase 3 showed that primary, secondary, and zero transfer of victim and/or offender DNA could be observed after physical contact and that alleles from an unknown source could still be detected in this more controlled experiment. The data presented in this paper demonstrate that DNA profiles generated after swabbing the skin surface of healthy adults can include components of an unknown source, present due to adventitious transfer. These components, if present in large quantities, have the potential to interfere with DNA profile interpretation of swabs taken for the investigation of physical assault by DNA profiling.     

Analysis of restriction fragment length polymorphisms in deoxyribonucleic acid (DNA) recovered from dried bloodstains

Deoxyribonucleic acid (DNA) was recovered from dried bloodstains aged up to three years and shown to be of high molecular weight. DNA was digested with restriction endonucleases and fractionated by agarose gel electrophoresis. Following transfer to a filter, DNA was hybridized with two different radioactively labeled recombinant probes which recognize highly polymorphic regions in human DNA. The autoradiographic pattern observed was not altered by sample age, and the size of the alleles was consistent with those observed in the general population. Therefore, DNA of high molecular weight prepared from dried blood samples can be used for identification.     

Following the transfer of DNA: How far can it go?

The issue of DNA transfer is becoming increasingly important in crime scene situations, as DNA analytical techniques now detect tiny amounts. Whereas primary and secondary DNA transfers have been well studied, subsequent transfer steps have received much less focus. This study aimed to measure the detectability of a DNA source after multiple transfer events. Transfer of wet blood gave a full genetic profile well beyond the secondary transfer events on both cotton and glass substrates. Dry blood gave a full profile well beyond the secondary transfer events on glass only, but to a lesser extent than wet blood. Touch DNA only produced a full profile on the primary substrate on both cotton and glass, and detectable quantities beyond the secondary transfer event on glass only. Our results will contribute to a better understanding of the tertiary and subsequent transfer of DNA, which will allow for improved evaluation of the likelihood of alternative scenarios explaining why an individual's DNA was found at a crime scene.     

Long PCR for VNTR analysis

The Polymerase Chain Reaction (PCR) has revolutionized the analysis of DNA from a variety of sources. With its sensitivity and ability to amplify degraded DNAs and small quantities of samples, coupled with fast turn-around-time, PCR is often the analytical method of choice for DNA profiling in forensic laboratories. RFLP methods, while requiring larger amounts of high molecular weight DNA and needing approximately 6-8 weeks of analytical time, still provide a higher power of discrimination per locus than that achieved using the loci currently available for PCR. The combination of both RFLP and PCR would be advantageous for some applications. A new technique, Long PCR, allows for the effective amplification of long DNA targets from approximately 0.5 kb to > 20 kb of genomic DNA. Currently, several Long PCR systems are commercially available. Using a Taq/Pyrococcus DNA polymerase enzyme system and DNA isolated from bloodstains, we have successfully amplified 1-20 ng of Chelex-extracted DNA, an amount commonly used in Amp-FLP technology. The robustness of Long PCR in comparison to RFLP was also examined through the use of partially degraded blood samples. Long PCR was then used to amplify both D2S44 and D5S110 RFLP loci. Although all D2 and D5 alleles were detected, the larger alleles were amplified at significantly lower levels than the smaller alleles.     

Increasing Allele Detection by Altering the Quantity of Internal Lane Standard

Electrokinetic injection (EI) is the primary method used in forensic laboratories to load amplified PCR product in capillary electrophoresis for short tandem repeat (STR) fragment separation. Because all samples subjected to capillary electrophoresis use internal lane standard (ILS), this study investigated the consequence of varying the volume of ILS and its effects on allele peak heights and number of alleles detected. Results demonstrated that when the volume of ILS is reduced, the average peak height and number of alleles increased, thereby increasing the sensitivity of the detection method. Sizing anomalies were observed; however, they did not adversely affect accuracy and precision. The method developed in this study offers a simple and universal procedure to increase the alleles detected in forensic STR analysis. Reducing the volume of ILS to achieve greater sensitivity is applicable to all STR amplification kits and capillary electrophoresis instruments currently used in forensic DNA analysis.     

Investigation into the usefulness of DNA profiling of earprints

DNA profiling of biological trace evidence has been used for many years. The application of this technique specifically to the DNA profiling of earprints has not to date been thoroughly investigated. This report presents the results of 60 earprints collected from three healthy adult volunteers under controlled laboratory conditions. DNA profile analysis revealed that high levels of non-donor alleles are observed when earprints are collected for DNA profiling. The source of these non-donor alleles is investigated and the impact that their presence within the profile may have on the use of this technique is discussed.     

Visualising DNA transfer: Latent DNA detection using Diamond Dye

A central question is ‘how did DNA get there’? To help answer this, we visually monitored and recorded DNA transfer from one substrate to another. When an individual touches a substrate, traces of their DNA are transferred (primary/direct) which can then subsequently be transferred to a second substrate (secondary/indirect). Currently DNA transfer and how much remains can only be determined by collecting the biological material from the substrate, isolating the DNA and quantifying the amount recovered. However, Diamond™ Dye (DD) enables such DNA transfer events to be visualised by monitoring the movement of cellular material.We examined primary and secondary DNA transfer using aluminium as a primary substrate with cotton, polyester, aluminium and plastic as secondary substrates and four contact types between two substrates (passive, pressure, friction and friction with pressure). Participants pressed their index finger against the aluminium for 15 s and then DD was applied to the area of contact; cellular material was detected via a fluorescence microscope. Contact between that substrate and a second substrate was performed, using one of the four contact types. After this contact between substrates each was viewed microscopically and transfer of cellular material was recorded.Cellular material could be recorded as having transferred from one substrate to another. Substrate and contact type had an effect on the extent DNA transfers. DNA transferred at a high rate with aluminium as a primary substrate and cotton, polyester and aluminium as secondary substrates when pressure with friction was applied. This information expands our understanding of how DNA transfers and which factors affect it, thus assisting greatly with activity level reporting as to how DNA came to be where it was found.     

The polymerase chain reaction and post-mortem forensic identity testing: application of amplified D1S80 and HLA-DQ alpha loci to the identification of fire victims.

The application of DNA typing methods after amplification by the polymerase chain reaction (PCR) of DNA derived from body tissues from charred fire victims was investigated. A total of 26 different tissue specimens from ten extensively burned individuals were analyzed. The samples included femoral muscle, psoas muscle, bone marrow and blood. The post-mortem period varied from 38 to 183 h. After amplifying the DNA by PCR from the various tissues, the D1S80 locus was analyzed with a high resolution polyacrylamide gel electrophoresis technique followed by silver staining and the alleles of the HLA-DQ alpha locus were detected by using a reverse dot blot format. All samples could be typed for both loci and the genotypes were consistent in the various tissues from each individual. A parentage test was performed in two cases and Mendelian inheritance of the alleles for both loci was observed.     

An investigation into the persistence of textile fibres on buried carcasses

A significant amount of research has been carried out on fibres to aid the forensic scientist in determining the significance of these when found on a victim or suspect. This work has focused on open-air environments, and as such no research has been undertaken to examine the persistence of fibres on bodies in the burial environment.Wool and cotton fibres, known to fluoresce under ultraviolet (UV) light, were transferred onto the skin of four porcine (Sus scrofa) carcasses (two carcasses per fibre type). The number of fibres transferred was recorded from images taken under UV light. The remains were subsequently placed in four burial sites and left interred for 14 days. After this period the carcasses were excavated and lightly brushed down to remove the soil layer that had adhered to the skin. Once again photography under UV light was used to record the number of fibres which persisted on the skin.Results showed that after 14 days, wool and cotton fibres remain on the surface of the buried carcasses. In no circumstance was there a total loss of fibres suggesting that in such scenarios, the likelihood of finding fibres is high but the initial number of fibres transferred would be strongly diminished. This has important implications for both the excavation protocol for buried remains and the subsequent analysis for physical evidence.     

A comparison of the characteristics of profiles produced with the AMPFlSTR SGM Plus multiplex system for both standard and low copy number (LCN) STR DNA analysis.

DNA STR profiles have been generated from 1 ng and low copy number (LCN) templates using 28 and 34 cycles of amplification, respectively. Characteristics which facilitate the interpretation of profiles, such as heterozygous balance, allelic dropout and stutter proportions have been quantified. We demonstrate that a reduction in DNA template coupled with an increase in amplification cycle number produces an increased rate of allelic dropout out which can be correlated to the peak areas of those alleles observed. In addition, the LCN conditions increase the degree of peak area asymmetry observed from heterozygotes and the size range of stutters. Analysis of the data allows us to develop sets of guidelines appropriate for interpreting both single and mixed DNA profiles.