Forensic evaluation of the QIAshredder/QIAamp DNA extraction procedure

Comparison of DNA recovery methods and locations from regularly-worn hooded jumpers before and after use by a second wearer

Items of worn clothing are routinely examined for DNA in forensic casework, commonly with the expectation that at least some of the DNA will come from a wearer of the item, so-called 'wearer DNA'. This study investigated DNA recovered from hooded jumpers that were regularly worn and laundered for four weeks and then subsequently worn by a different individual for four hours. This study also systematically investigated whether using different recovery methods or sampling locations on the jumpers might distinguish between DNA deposited by the regular and most recent wearers of clothing. Four volunteers each wore a new hooded jumper regularly (6 h/day, 2 days/week, washed at weekends) during two 4-week periods. At the end of each month, DNA was first recovered by cutting out and mini-taping the inside left cuff, half-collar, pocket and underarm fabric. The jumpers were then worn by a different individual for four hours, and DNA was again recovered by cutting out and mini-taping, but this time from the inside right cuff, half-collar, pocket and underarm fabric. All DNA samples (n = 128) were quantified and profiled. DNA quantities ranged from 0 to ∼40 ng with an outlier of ∼150 ng, and no significant differences were observed among recovery methods and sampling locations, nor whether one or two wearers had worn the jumpers. However, one volunteer consistently deposited significantly more DNA to their jumpers than two other volunteers, confirming the impact of 'shedder status' on DNA deposition during wearing of clothing. When jumpers were regularly worn by one wearer, the majority (72.7-83.3 %) of the samples for all wearers across both months comprised a major profile of the wearer with a minor profile of non-wearer alleles. When jumpers were then worn by a second wearer, the composition of the profiles obtained were generally reproducible across the recovery methods used, the sampling locations and the two replicates of the experiment for each pairing of wearers. However, profile compositions differed between wearer pairings. Overall, ∼60 % of profiles obtained gave a major profile of the regular wearer, whereas ∼30 % gave a major profile of the second wearer. The remaining profiles comprised other much less frequent observations of single-source profiles of each wearer and equal proportions of DNA from both wearers. Non-wearer DNA was also observed in the majority of samples, both before and after jumpers were worn by a second wearer. For one volunteer's jumpers, a recurring non-wearer DNA profile was observed that could be attributed to their romantic partner, and this DNA persisted on the jumpers even after being worn by the second wearer. This study provides insight on the impact of shedder status, multiple wearers, different recovery methods and sampling locations on the quantities of DNA and compositions of DNA profiles recovered from authentically regularly-worn hooded jumpers. The findings also provide a preliminary dataset that can be used to infer activity level probabilities in casework.

DNA transfer when using gloves in burglary simulations

Several studies have demonstrated that DNA can be indirectly transferred from an individual onto a surface. Therefore, the presence of DNA that is compatible with a given person does not necessarily mean that this person has touched the surface on which the DNA was recovered. The present work simulates cases, where DNA is recovered on a door handle and compared to several reference DNA profiles. The DNA profile of the trace shares DNA components with a person of interest (POI). When asked about the DNA results, the POI says he has nothing to do with the incident and has never been at the scene. However, a possibility would be that the DNA came from his recently stolen gloves. Someone else, the alternative offender (AO), could have opened the door wearing his gloves (POI's gloves), and transferred his DNA (POI's DNA). Based on the above-mentioned scenario, 60 burglary simulations experiments were carried out to generate data to assess DNA results given these allegations. The quantity and quality of DNA profiles (NGM SElect) recovered when the POI opened/closed the door bare-handed or when someone else performed the same activity but using POI's gloves, were compared. The gloves were regularly worn during at least three months by their owner during the winter. On the contrary, the AO wore them only for two minutes. Among the traces collected on the door handles, less than 50% of the traces led to interpretable DNA profiles. In 30% of the cases (3/10), when the door was opened/closed with bare hands, the DNA found on the door handle led to a mixed DNA profile with the POI's DNA aligning with the major contributor. For the experiments where the AO opened/closed the door with the POI's gloves, the POI's DNA was compatible with 22% (11/50) of the mixed DNA profile, aligning with the major in 8% of the cases (4/50). The DNA profiles of the offices' occupants were observed on the door handles, but not the AO's. In addition to the results of the experiments, we show two examples of how one can assess results observed in casework. Given the possibility of indirect transfer of minute DNA quantities, this research emphasizes the need to evaluate DNA results given the activities when the POI has a legitimate reason that can explain the presence of their DNA.

DNA recovery and human identification from semen stains washed at different temperatures

One of the most important pieces of evidence to find the suspect of a sexual assault are semen stains. It has been observed that suspects do not use condoms in many cases and transfer seminal fluids over the body of the victim, to their clothes, to bed linen, or to other objects in the environment. However, in many cases, it has been seen that the suspects or the victims tend to clean their bodies and clothes because of psychological conditions such as fear, panic, and anxiety. This study aims to determine whether human identification can be accomplished from washed semen stains by evaluating the quantity of extracted DNA obtained from washed clothes. In this study, both cotton- and nylon-blended fabrics were stained with semen samples taken from 10 volunteers and washed with detergent at 40 °C, 60 °C, and 90 °C. After stains were made re-visible using an ultraviolet (UV) light source, DNA was extracted using two different extraction methods (phenol-chloroform and spin-column). As a result, DNA extraction methods, washing conditions, and obtained DNA quantity from different washed fabrics were compared. It was shown that DNA could be obtained from all samples and that these DNA amounts could be used to perform identification. This study gives hope to the victims who have not been able to go to the judicial units immediately after the incident for fear or any other reasons and who think that they cannot get results because they have washed the laundry.

Methods for ensuring the highest DNA concentration and yield in future and retrospective trace DNA extracts

In forensic laboratories, increased extraction efficiency of trace evidence is paramount because analytical success is intrinsically dependent on the quantity of DNA recovered. Moreover, highly concentrated nucleic acids are vital for effective downstream analysis and high quality results. This study investigated the efficiency of extraction with the Qiagen® QIAamp® DNA Investigator kit, and explored improvements to the methodology that would maximise the recovery of low concentration forensic samples. Controlled amounts of starting cellular material were used to mimic trace (or low level) DNA deposits prior to DNA extraction with the Investigator kit. Addition of the provided carrier RNA along with conducting two successive elutions of 50 µL improved the net recovery of DNA to 95%. Concentration with centrifugal filters post-extraction were able to concentrate DNA but a large net loss was observed. For the concentration of historic, retrospectively extracted DNA, centrifugal methods are able to concentrate DNA extracts previously too dilute for analysis. These concentrated volumes, however are small, allowing for minimal downstream analysis attempts before the sample is exhausted.

Impact of metal ions on PCR inhibition and RT-PCR efficiency

Inhibition of PCR by metal ions can pose a serious challenge in the process of forensic DNA analysis. Samples contaminated with various types of metal ions encountered at crime scenes include swabs from metal surfaces such as bullets, cartridge casings, weapons (including guns and knives), metal wires and surfaces as well as bone samples which contain calcium. The mechanism behind the impact of metal ions on DNA recovery, extraction and subsequent amplification is not fully understood. In this study, we assessed the inhibitory effects of commonly encountered metals on DNA amplification. Of the nine tested metals, zinc, tin, iron(II) and copper were shown to have the strongest inhibitory properties having IC50 values significantly below 1 mM. In the second part of the study, three commercially available DNA polymerases were tested for their susceptibility to metal inhibition. We found that KOD polymerase was the most resistant to metal inhibition when compared with Q5 and Taq polymerase. We also demonstrate how the calcium chelator ethylene glycol-bis(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA) can be used as an easy and non-destructive method of reversing calcium-induced inhibition of PCR reactions.

The novel use of a spray-on rubber coating to recover cellular material from the surface of bricks

Currently, forensic investigators utilise various types of swabs and tape lifts to recover cellular material from coarse surfaces identified during a criminal investigation. However, a number of challenges prevent successful recovery and therefore warrants the need for an alternative method. Plasti dip® is peel-off rubber coating that can be applied to most surfaces and may have an application in the recovery of DNA from coarse surfaces. The aim of this study was to determine the effectiveness of Plasti dip® to recover DNA from coarse brick surfaces and assess how this method compares to current techniques. Cellular material was deposited onto brick pieces in varying concentrations and recovered with either flocked, foam or rayon swabs, or Plasti dip®. Material recovered, using each technique, was extracted and quantitated for comparison of DNA yields. At low and medium cell concentrations, an observable but not statistically significant difference was observed between the swabbing methods and Plasti dip®. At high cell concentrations Plasti dip® was able to recover a significantly higher DNA concentration than all three swabbing methods. Quantitation results indicated no degradation of DNA. This is a novel approach to the collection of trace DNA from surfaces that have historically proven difficult to sample. While there is further validation required, this landmark study demonstrates the potential that spray-on rubber coatings have for casework involving rough, porous surfaces like bricks, stones or rocks.

Blood-Based Cancer Biomarkers in Liquid Biopsy: A Promising Non-Invasive Alternative to Tissue Biopsy

Cancer is one of the greatest threats facing our society, being the second leading cause of death globally. Currents strategies for cancer diagnosis consist of the extraction of a solid tissue from the affected area. This sample enables the study of specific biomarkers and the genetic nature of the tumor. However, the tissue extraction is risky and painful for the patient and in some cases is unavailable in inaccessible tumors. Moreover, a solid biopsy is expensive and time consuming and cannot be applied repeatedly. New alternatives that overcome these drawbacks are rising up nowadays, such as liquid biopsy. A liquid biopsy is the analysis of biomarkers in a non-solid biological tissue, mainly blood, which has remarkable advantages over the traditional method; it has no risk, it is non-invasive and painless, it does not require surgery and reduces cost and diagnosis time. The most studied cancer non-invasive biomarkers are circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and exosomes. These circulating biomarkers play a key role in the understanding of metastasis and tumorigenesis, which could provide a better insight into the evolution of the tumor dynamics during treatment and disease progression. Improvements in isolation technologies, based on a higher grade of purification of CTCs, exosomes, and ctDNA, will provide a better characterization of biomarkers and give rise to a wide range of clinical applications, such as early detection of diseases, and the prediction of treatment responses due to the discovery of personalized tumor-related biomarkers.

DNA persistence of bite marks on food and its relevance for STR typing

In forensic DNA analysis, salivary traces at crime scenes are a promising way to identify a person. However, crime scenes are oftentimes investigated a while after the crime and recovered samples might have been degraded leading to poor PCR amplification. Probably due to decomposition and negative visual impression of spoiled food, bite mark samples make up only a small part of our casework routine. In this study, bite marks on apples and chocolate bars as well as on an inert surface (microscope slide) were stored up to 3 weeks indoors and outdoors during different seasons and analyzed for amylase activity and DNA quantity and quality. The results underlined the stability of human nuclear DNA not only on inert but also on biological surfaces and their forensic usefulness even when bite marks are stored 21 days under adverse but realistic conditions at a crime scene. Overall, amylase activity as well as DNA quantity decreased over time depending on storage environment with a certain inter- and intrapersonal variation. But amylase activity testing was not found to be an appropriate screening tool for further analysis. Apple bite marks resulted in generally higher DNA amounts than chocolate bars and microscope slides. Although mold reduced the DNA quantity, complete STR profiles could be analyzed. High air humidity and cold temperatures were found to act preservative on raw food with high water content but caused loss of information over time for smooth inert surfaces and hygroscopic foods like sweets. Many factors are involved in the stability of DNA in bite marks and its resulting quality and quantity available for an STR analysis. However, since there was a substantial proportion of informative STR profiles even from bite marks stored for 21 days, the results encourage the analysis of those even if their visual appearance seems unfavorable.

A rapid and efficient DNA extraction protocol from fresh and frozen human blood samples

BACKGROUND

Different methods available for extraction of human genomic DNA suffer from one or more drawbacks including low yield, compromised quality, cost, time consumption, use of toxic organic solvents, and many more. Herein, we aimed to develop a method to extract DNA from 500 μL of fresh or frozen human blood.

METHODS

Five hundred microliters of fresh and frozen human blood samples were used for standardization of the extraction procedure. Absorbance at 260 and 280 nm, respectively, (A₂₆₀ /A₂₈₀ ) were estimated to check the quality and quantity of the extracted DNA sample. Qualitative assessment of the extracted DNA was checked by Polymerase Chain reaction and double digestion of the DNA sample.

RESULTS

Our protocol resulted in average yield of 22±2.97 μg and 20.5±3.97 μg from 500 μL of fresh and frozen blood, respectively, which were comparable to many reference protocols and kits.

CONCLUSION

Besides yielding bulk amount of DNA, our protocol is rapid, economical, and avoids toxic organic solvents such as Phenol. Due to unaffected quality, the DNA is suitable for downstream applications. The protocol may also be useful for pursuing basic molecular researches in laboratories having limited funds.

Assessing DNA recovery from chewing gum

The purpose of this study was to evaluate which DNA extraction method yields the highest quantity of DNA from chewing gum. In this study, several popular extraction methods were tested, including Chelex-100, phenol-chloroform-isoamyl alcohol (PCIA), DNA IQ, PrepFiler, and QIAamp Investigator, and the quantity of DNA recovered from chewing gum was determined using real-time polymerase chain reaction with Quantifiler. Chewed gum control samples were submitted by anonymous healthy adult donors, and discarded environmental chewing gum samples simulating forensic evidence were collected from outside public areas (e.g., campus bus stops, streets, and sidewalks). As expected, results indicate that all methods tested yielded sufficient amplifiable human DNA from chewing gum using the wet-swab method. The QIAamp performed best when DNA was extracted from whole pieces of control gum (142.7 ng on average), and the DNA IQ method performed best on the environmental whole gum samples (29.0 ng on average). On average, the QIAamp kit also recovered the most DNA from saliva swabs. The PCIA method demonstrated the highest yield with wet swabs of the environmental gum (26.4 ng of DNA on average). However, this method should be avoided with whole gum samples (no DNA yield) due to the action of the organic reagents in dissolving and softening the gum and inhibiting DNA recovery during the extraction.

Human mitochondrial DNA and nuclear DNA isolation from food bite marks

OBJECTIVE

Bite mark analysis is used for comparison between bite marks on a bitten object and the suspects' teeth. However, if it is not possible to obtain a correct match, it is important to recover salivary DNA. Previous studies have tried to isolate human nuclear DNA from bitten foods but were not completely successful. In the present work, we studied the efficiency of human nuclear and mitochondrial DNA isolation from bite marks in cheese, a donut and an apple.

DESIGN

Using a double swab technique and silica-based DNA extraction kit, nuclear and mitochondrial DNA were isolated. Human housekeeping genes were amplified to analyse the efficiency of nuclear DNA profiling. mtDNA was sequencing and haplogroup assign.

RESULTS

Although cheese and apple samples showed the highest concentration of DNA, the purity of DNA on the apple was low. Moreover, apple samples failed to amplify the two human housekeeping genes, GAPDH and RPL22. In contrast, cheese samples have high purity and amplification efficiency. Donut samples showed an intermediate value and low amplification efficiency. In spite of these results, isolation and characterization/sequencing of human mitochondrial DNA was completely successful in the three samples, which pointed out the possibility of identification through this type of DNA.

CONCLUSIONS

This research indicated that it is possible to recover and isolate human nuclear and mitochondrial DNA from bitten foods, although the quantity and purity of nuclear DNA depends on the type of food. That is of significance important in forensic sciences for the correct identification of a suspect.

Stabbing simulations and DNA transfer

Technical developments have made it possible to analyze very low amounts of DNA. This has many advantages, but the drawback of this technological progress is that interpretation of the results becomes increasingly complex: the number of mixed DNA profiles increased relatively to single source DNA profiles and stochastic effects in the DNA profile, such as drop-in and drop-out, are more frequently observed. Moreover, the relevance of low template DNA material regarding the activities alleged is not as straightforward as it was a few years ago, when for example large quantities of blood were recovered. The possibility of secondary and tertiary transfer is now becoming an issue. The purpose of this research is twofold: first, to study the transfer of DNA from the handler and secondly, to observe if handlers would transfer DNA from persons closely connected to them. We chose to mimic cases where the offender would attack a person with a knife. As a first approach, we envisaged that the defense would not give an alternative explanation for the origin of the DNA. In our transfer experiments (4 donors, 16 experiments each, 64 traces), 3% of the traces were single DNA profiles. Most of the time, the DNA profile of the person handling the knife was present as the major profile: in 83% of the traces the major contributor profile corresponded to the stabber's DNA profile (in single stains and mixtures). Mixture with no clear major/minor fraction (12%) were observed. 5% of the traces were considered of insufficient quality (more than 3 contributors, presence of a few minor peaks). In that case, we considered that the stabber's DNA was absent. In our experiments, no traces allowed excluding the stabber, however it must be noted that precautions were taken to minimize background DNA as knives were cleaned before the experiments. DNA profiles of the stabber's colleagues were not observed. We hope that this study will allow for a better understanding of the transfer mechanism and of how to assess and describe results given activity level propositions. In this preliminary research, we have focused on the transfer of DNA on the hand of the person. Besides, more research is needed to assign the probability of the results given an alternative activity proposed by the defense, for instance when the source of the DNA is not contested, but that the activities are.

Advantages of using the QIAshredder instead of restriction digestion to prepare DNA for droplet digital PCR

The viscosity of genomic DNA can interfere with digital PCR systems that partition samples into oil droplets or microfluidic wells. Restriction digestion may reduce the viscosity, but the process is labor-intensive, and the buffer can alter the conditions for PCR. DNA fragmentation using the QIAshredder (a biopolymer spin column) is faster, may result in more predictable and uniformly-sized fragments, and avoids the need for restriction buffers that can inhibit downstream PCR. In 10 separate head-to-head experiments comparing aliquots of DNA processed using the QIAshredder to those digested with RsaI or BsaJI prior to droplet digital PCR, we found that the copy numbers measured from the QIAshredded DNA tended to be greater than those measured from the digested DNA (average of 1.35-fold compared with BsaJI; P < 0.0001), even for inputs as high as 1.8 μg or dilution down to the single copy level.

Role of oral fluids in DNA investigations

The assay of oral fluid (OF), a biofluid historically well-studied biochemically and physiologically, is a growing area of research with implications for basic and clinical purposes. In the last decade, it has gained considerable attention and lately, the use of OF has provided a substantial addition as an investigative tool in forensic and/or legal procedures. This article is an appraisal of various applications of OF sourced DNA in the field of forensic analysis. We have discussed the significance of different collection methods and their variations along with the application of specific analytical methods based on the condition of the sample. It is likely that the germaneness of OF assays will continue to expand thus providing a new instrument for investigation in criminal/legal proceedings.

Purification of crime scene DNA extracts using centrifugal filter devices

BACKGROUND

The success of forensic DNA analysis is limited by the size, quality and purity of biological evidence found at crime scenes. Sample impurities can inhibit PCR, resulting in partial or negative DNA profiles. Various DNA purification methods are applied to remove impurities, for example, employing centrifugal filter devices. However, irrespective of method, DNA purification leads to DNA loss. Here we evaluate the filter devices Amicon Ultra 30 K and Microsep 30 K with respect to recovery rate and general performance for various types of PCR-inhibitory crime scene samples.

METHODS

Recovery rates for DNA purification using Amicon Ultra 30 K and Microsep 30 K were gathered using quantitative PCR. Mock crime scene DNA extracts were analyzed using quantitative PCR and short tandem repeat (STR) profiling to test the general performance and inhibitor-removal properties of the two filter devices. Additionally, the outcome of long-term routine casework DNA analysis applying each of the devices was evaluated.

RESULTS

Applying Microsep 30 K, 14 to 32% of the input DNA was recovered, whereas Amicon Ultra 30 K retained 62 to 70% of the DNA. The improved purity following filter purification counteracted some of this DNA loss, leading to slightly increased electropherogram peak heights for blood on denim (Amicon Ultra 30 K and Microsep 30 K) and saliva on envelope (Amicon Ultra 30 K). Comparing Amicon Ultra 30 K and Microsep 30 K for purification of DNA extracts from mock crime scene samples, the former generated significantly higher peak heights for rape case samples (P-values <0.01) and for hairs (P-values <0.036). In long-term routine use of the two filter devices, DNA extracts purified with Amicon Ultra 30 K were considerably less PCR-inhibitory in Quantifiler Human qPCR analysis compared to Microsep 30 K.

CONCLUSIONS

Amicon Ultra 30 K performed better than Microsep 30 K due to higher DNA recovery and more efficient removal of PCR-inhibitory substances. The different performances of the filter devices are likely caused by the quality of the filters and plastic wares, for example, their DNA binding properties. DNA purification using centrifugal filter devices can be necessary for successful DNA profiling of impure crime scene samples and for consistency between different PCR-based analysis systems, such as quantification and STR analysis. In order to maximize the possibility to obtain complete STR DNA profiles and to create an efficient workflow, the level of DNA purification applied should be correlated to the inhibitor-tolerance of the STR analysis system used.

Differential DNA extraction of challenging simulated sexual-assault samples: a Swiss collaborative study

In sexual-assault cases, autosomal DNA analysis of gynecological swabs is a challenge, as the presence of a large quantity of female material may prevent detection of the male DNA. A solution to this problem is differential DNA extraction, but there is no established best practice for this. We decided to test the efficacy of a number of different protocols on simulated casework samples. Four difficult samples were sent to the nine Swiss laboratories active in forensic genetics. In each laboratory, staff used their routine protocols to separate the epithelial-cell fraction, enriched with the non-sperm DNA, from the sperm fraction. DNA extracts were then sent to the organizing laboratory for analysis. Estimates of male:female DNA ratio without differential DNA extraction ranged from 1:38 to 1:339, depending on the semen used to prepare the samples. After differential DNA extraction, most of the ratios ranged from 1:12 to 9:1, allowing detection of the male DNA. Compared with direct DNA extraction, cell separation resulted in losses of 94-98% of the male DNA. As expected, more male DNA was generally present in the sperm than in the epithelial-cell fraction. However, for about 30% of the samples, the reverse trend was seen. The recovery of male and female DNA was highly variable, depending on the laboratory involved. An experimental design similar to the one used in this study may be of assistance for local protocol testing and improvement.

A ranking index for quality assessment of forensic DNA profiles forensic DNA profiles

BACKGROUND

Assessment of DNA profile quality is vital in forensic DNA analysis, both in order to determine the evidentiary value of DNA results and to compare the performance of different DNA analysis protocols. Generally the quality assessment is performed through manual examination of the DNA profiles based on empirical knowledge, or by comparing the intensities (allelic peak heights) of the capillary electrophoresis electropherograms.

RESULTS

We recently developed a ranking index for unbiased and quantitative quality assessment of forensic DNA profiles, the forensic DNA profile index (FI) (Hedman et al. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles, Biotechniques 47 (2009) 951-958). FI uses electropherogram data to combine the intensities of the allelic peaks with the balances within and between loci, using Principal Components Analysis. Here we present the construction of FI. We explain the mathematical and statistical methodologies used and present details about the applied data reduction method. Thereby we show how to adapt the ranking index for any Short Tandem Repeat-based forensic DNA typing system through validation against a manual grading scale and calibration against a specific set of DNA profiles.

CONCLUSIONS

The developed tool provides unbiased quality assessment of forensic DNA profiles. It can be applied for any DNA profiling system based on Short Tandem Repeat markers. Apart from crime related DNA analysis, FI can therefore be used as a quality tool in paternal or familial testing as well as in disaster victim identification.

Molecular confirmation of pathological specimen integrity in Australasia

AIM

Investigations into 14 suspected pathology sample identification errors and mix-ups were performed, as a service for several public hospital and private laboratories, from 2005 to 2007.

METHODS

Analyses were performed with the forensic ABI Identifiler kit of 16 microsatellites (15 autosomal and amelogenin) on DNA from paraffin-embedded tissues or blood specimens and compared to independently verified (single or multiple) patient samples.

RESULTS

Of 23 unique patient specimens referred for sample integrity confirmation because of pathologist, clinician or patient concern, six (26.1%) were demonstrated to be discordant, indicating that specimen identification errors or mix-ups had occurred.

CONCLUSIONS

Due to their great sensitivity and high discrimination power, forensic identity multiplex systems using either microsatellites or single nucleotide polymorphisms (SNPs) can resolve concerns about pathology specimen identity and integrity.

Accurate real-time PCR strategy for monitoring bloodstream parasitic loads in chagas disease patients

BACKGROUND

This report describes a real-time PCR (Q-PCR) strategy to quantify Trypanosoma cruzi (T. cruzi) DNA in peripheral blood samples from Chagas disease patients targeted to conserved motifs within the repetitive satellite sequence.

METHODOLOGY/PRINCIPAL FINDINGS

The Q-PCR has a detection limit of 0.1 and 0.01 parasites/mL, with a dynamic range of 10(6) and 10(7) for Silvio X10 cl1 (T. cruzi I) and Cl Brener stocks (T. cruzi IIe), respectively, an efficiency of 99%, and a coefficient of determination (R(2)) of 0.998. In order to express accurately the parasitic loads: (1) we adapted a commercial kit based on silica-membrane technology to enable efficient processing of Guanidine Hydrochloride-EDTA treated blood samples and minimize PCR inhibition; (2) results were normalized incorporating a linearized plasmid as an internal standard of the whole procedure; and (3) a correction factor according to the representativity of satellite sequences in each parasite lineage group was determined using a modified real-time PCR protocol (Lg-PCR). The Q-PCR strategy was applied (1) to estimate basal parasite loads in 43 pediatric Chagas disease patients, (2) to follow-up 38 of them receiving treatment with benznidazole, and (3) to monitor three chronic Chagas heart disease patients who underwent heart-transplantation and displayed events of clinical reactivation due to immunosupression.

CONCLUSION/SIGNIFICANCE

All together, the high analytical sensitivity of the Q-PCR strategy, the low levels of intra- and inter-assay variations, as well as the accuracy provided by the Lg-PCR based correction factor support this methodology as a key laboratory tool for monitoring clinical reactivation and etiological treatment outcome in Chagas disease patients.

Genetic identification of decomposed cadavers using nails as DNA source

Blood or muscle can be used as a DNA source for the genetic identification of recently deceased persons. If the post mortem interval increases, bones and teeth are used. In this case, collection and DNA isolation will be more difficult and time consuming. The aim of this study was to evaluate the use of nails as an alternative DNA source for the genetic identification of decomposed cadavers. DNA extraction from 5mg of fingernails from 7 volunteers using 1h cell lysis in a standard buffer and a DNA purification on QIAamp DNA mini kit columns allowed to acquire a mean quantity of 100 ng DNA/mg nail. This was unexpected, as blood and muscle contain comparable amounts of DNA. Our protocol allowed to obtain full PowerPlex 16 DNA profiles from 10 cadavers characterized by post mortem intervals ranging from 5 days to more than 6 months. The good quality of these profiles indicated that DNA from nail is well preserved. In conclusion, nails are very easy to collect and contain large amounts of good quality DNA that can be extracted within a few hours. They may therefore represent an attractive DNA source not only for routine, but also for urgent genetic identification of decomposed cadavers.