The 2018 California Wildfires: Integration of Rapid DNA to Dramatically Accelerate Victim Identification

In November 2018, Butte County, California, was decimated by the Camp Fire, the deadliest wildfire in state history. Over 150,000 acres were destroyed, and at its peak, the fire consumed eighty acres per minute. The speed and intensity of the oncoming flames killed scores of people, and weeks before the fire was contained, first responders began searching through the rubble of 18,804 residences and commercial buildings. As with most mass disasters, conventional identification modalities (e.g., fingerprints, odontology, hardware) were utilized to identify victims. The intensity and duration of the fire severely degraded most of the remains, and these approaches were useful in only 22 of 84 cases. In the past, the remaining cases would have been subjected to conventional DNA analysis, which may have required months to years. Instead, Rapid DNA technology was utilized (in a rented recreational vehicle outside the Sacramento morgue) in the victim identification effort. Sixty-nine sets of remains were subjected to Rapid DNA Identification and, of these, 62 (89.9%) generated short tandem repeat profiles that were subjected to familial searching; essentially all these profiles were produced within hours of sample receipt. Samples successfully utilized for DNA identification included blood, bone, liver, muscle, soft tissue of unknown origin, and brain. In tandem with processing of 255 family reference samples, 58 victims were identified. This work represents the first use of Rapid DNA Identification in a mass casualty event, and the results support the use of Rapid DNA as an integrated tool with conventional disaster victim identification modalities.     

Developmental Validation of the ANDE 6C System for Rapid DNA Analysis of Forensic Casework and DVI Samples

A developmental validation was performed to demonstrate reliability, reproducibility, and robustness of the ANDE Rapid DNA Identification System for processing of crime scene and disaster victim identification (DVI) samples. A total of 1705 samples were evaluated, including blood, oral epithelial samples from drinking containers, samples on FTA and untreated paper, semen, bone, and soft tissues. This study was conducted to address the FBI’s Quality Assurance Standards on developmental validation and to accumulate data from a sufficient number of unique donors and sample types to meet NDIS submission requirements for acceptance of the ANDE Expert System for casework use. To date, no Expert System has been approved for such samples, but the results of this study demonstrated that the automated Expert System performs similarly to conventional laboratory data analysis. Furthermore, Rapid DNA analysis demonstrated accuracy, precision, resolution, concordance, and reproducibility that were comparable to conventional processing along with appropriate species specificity, limit of detection, performance in the presence of inhibitors. No lane-to-lane or run-to-run contamination was observed, and the system correctly identified the presence of mixtures. Taken together, the ANDE instrument, I-Chip consumable, FlexPlex chemistry (a 27-locus STR assay compatible with all widely used global loci, including the CODIS core 20 loci), and automated Expert System successfully processed and interpreted more than 1200 unique samples with over 99.99% concordant CODIS alleles. This extensive developmental validation data provides support for broad use of the system by agencies and accredited forensic laboratories in single-source suspect-evidence comparisons, local database searches, and DVI.     

Internal Validation of RapidHIT®ID ACE Sample Cartridge and Assessment of the EXT Sample Cartridge*†

A new rapid DNA solution, the RapidHIT^®ID, can accommodate two different sample cartridges, ACE, for the analysis of a single swab and EXT, for the analysis of DNA extracts. An efficient internal validation designed for low‐throughput rapid DNA is described. An evaluation of the EXT sample cartridge is also described. Each cartridge generated profiles with sufficient data quality to meet CODIS eligibility in fewer than 120 min. The results exhibited 100% correlation when compared to conventional DNA typing methods. Precision, reproducibility, stochastic, mixture, and contamination experiments produced expected results. Sensitivity of the ACE sample cartridge was acceptable for buccal swab analysis. The sensitivity of the EXT sample cartridge is discussed. The ACE validation and the EXT evaluation utilized a minimalist, cost‐saving, efficient design to generate a validated RapidHIT^®ID instrument capable of producing genetic profiles from both extracted forensic DNA samples and buccal swab samples within 120 min.     

Automated DNA casework workflow: A retrospective study of the first implementation of FIDL at the Netherlands Forensic Institute

FIDL is a fast and automated DNA identification line which represents a series of software solutions automating the process from raw capillary electrophoresis data to reporting. This retrospective study provides insight in the numbers of cases, turnaround time, results compared to the standard workflow and the benefits automation has in a large volume workflow.     

Y-STR analysis on DNA mixture samples—Results of a collaborative project of the ENFSI DNA Working Group

The ENFSI (European Network of Forensic Science Institutes) DNA Working Group undertook a collaborative project on Y-STR typing of DNA mixture samples that were centrally prepared and thoroughly tested prior to the shipment. Four commercial Y-STR typing kits (Y-Filer, Applied Biosystems, Foster City, CA, USA; Argus Y Nonaplex, Biotype, Dresden, Germany; Powerplex Y, Promega, Madison, WI, USA; and DYSplex-3, SERAC, Bad Homburg, Germany) were used for the amplification of the mixture samples. The results of the study showed a striking inter-laboratory difference of kit performance as determined from the peak heights of the obtained Y-STR genotypes. Variation in quantity and quality of the shipped DNA can be excluded as reason for the observed differences because both samples and shipping conditions were found to be reproducible in an earlier study. The results suggest that in some cases a laboratory-specific optimization process is indicated to reach a comparable sensitivity for the analysis of minute amounts of DNA.     

Investigative studies into the recovery of DNA from improvised explosive device containers

Apprehending those who utilize improvised explosive devices (IEDs) is a national priority owing to their use both domestically and abroad. IEDs are often concealed in bags, boxes, or backpacks to prevent their detection. Given this, the goal of the research presented was to identify IED handlers through postblast DNA recovery from IED containers. Study participants were asked to use backpacks for 11 days, after which they served as containers for pipe bombs. Eleven postdeflagration backpack regions likely to be handled were swabbed and analyzed via mini-short tandem repeats (miniSTRs) and alleles were called blind. An experimental consensus method was examined in which profiles from all regions were considered, to help identify spurious drop-in/out. Results were correct for all loci, except one that remained ambiguous. The results show that recovering DNA from IED containers is a viable approach for aiding in the identification of those who may have been involved in an IED event.     

Decision support for using mobile Rapid DNA analysis at the crime scene

Mobile Rapid DNA technology is close to being incorporated into crime scene investigations, with the potential to identify a perpetrator within hours. However, the use of these techniques entails the risk of losing the sample and potential evidence, because the device not only consumes the inserted sample, it is also is less sensitive than traditional technologies used in forensic laboratories. Scene of Crime Officers (SoCOs) therefore will face a ‘time/success rate trade-off’ issue when making a decision to apply this technology.In this study we designed and experimentally tested a Decision Support System (DSS) for the use of Rapid DNA technologies based on Rational Decision Theory (RDT). In a vignette study, where SoCOs had to decide on the use of a Rapid DNA analysis device, participating SoCOs were assigned to either the control group (making decisions under standard conditions), the Success Rate (SR) group (making decisions with additional information on DNA success rates of traces), or the DSS group (making decisions supported by introduction to RDT, including information on DNA success rates of traces).This study provides positive evidence that a systematic approach for decision-making on using Rapid DNA analysis assists SoCOs in the decision to use the rapid device. The results demonstrated that participants using a DSS made different and more transparent decisions on the use of Rapid DNA analysis when different case characteristics were explicitly considered. In the DSS group the decision to apply Rapid DNA analysis was influenced by the factors “time pressure” and “trace characteristics” like DNA success rates. In the SR group, the decisions depended solely on the trace characteristics and in the control group the decisions did not show any systematic differences on crime type or trace characteristic.Guiding complex decisions on the use of Rapid DNA analyses with a DSS could be an important step towards the use of these devices at the crime scene.     

Developmental Validation of the PrepFiler™ Forensic DNA Extraction Kit for Extraction of Genomic DNA from Biological Samples*

Abstract: The PrepFiler? Forensic DNA Extraction Kit enables isolation of genomic DNA from a variety of biological samples. The kit facilitates reversible binding of DNA with magnetic particles resulting in high DNA recovery from samples with very low and high quantities of biological materials: 0.1 and 40 μL of human blood (donor 2) provided 14 and 2883 ng of DNA, respectively. Following the revised SWGDAM guidelines, performance of the developed method was investigated using different sample types including saliva on swabs, semen stains on cotton fabric, samples exposed to environment, samples with polymerase chain reaction (PCR) inhibitors, blood stains (on denim, cotton cloth, and FTA^® paper), and touch evidence‐type samples. DNA yields for all samples tested were equal or better than those obtained by both phenol–chloroform extraction and commercial kits tested. DNA obtained from these samples was free of detectable PCR inhibitors. Short tandem repeat profiles were complete, conclusive, and devoid of PCR artifacts.     

Bounding the number of contributors to mixed DNA stains

We derive a simple inequality for the probability of observing a given DNA profile when assuming a fixed number of unknown persons have contributed to the mixed stain. We then show how this inequality can be used to obtain an upper bound for the number of unknown contributors needed to be considered.     

RNA/DNA co-analysis from blood stains—Results of a second collaborative EDNAP exercise

A second collaborative exercise on RNA/DNA co-analysis for body fluid identification and STR profiling was organized by the European DNA Profiling Group (EDNAP). Six human blood stains, two blood dilution series (5-0.001 μl blood) and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by the participating laboratories using a RNA/DNA co-extraction or solely RNA extraction method. Two novel mRNA multiplexes were used for the identification of blood: a highly sensitive duplex (HBA, HBB) and a moderately sensitive pentaplex (ALAS2, CD3G, ANK1, SPTB and PBGD). The laboratories used different chemistries and instrumentation. All of the 18 participating laboratories were able to successfully isolate and detect mRNA in dried blood stains. Thirteen laboratories simultaneously extracted RNA and DNA from individual stains and were able to utilize mRNA profiling to confirm the presence of blood and to obtain autosomal STR profiles from the blood stain donors. The positive identification of blood and good quality DNA profiles were also obtained from old and compromised casework samples. The method proved to be reproducible and sensitive using different analysis strategies. The results of this collaborative exercise involving a RNA/DNA co-extraction strategy support the potential use of an mRNA based system for the identification of blood in forensic casework that is compatible with current DNA analysis methodology.     

D5S818 Typing Discrepancy Between PowerPlex® Fusion and Other STR Kits Including GlobalFiler® Caused by a One‐base Deletion in 31 Nucleotides Upstream of the Repeat Region

Short tandem repeat (STR) typing is widely used in forensic investigation. When the same DNA sample is analyzed with different STR typing kits, a typing discrepancy is occasionally observed. In this study, we examined the cause of a typing discrepancy in a sample at D5S818 locus. This sample was designated as 10, 12 using Identifiler^®, Identifiler^® Plus, GlobalFiler^®, PowerPlex^® 16HS, and PowerPlex^® 18D, but as 9.3, 12 using PowerPlex^® Fusion. Sequencing results indicated that the shorter allele in the sample had a deletion (U31Tdel) at 31 nucleotides upstream of the repeat region (AGAT)₁₀. This deletion was located in the binding site of the published D5S818 forward primer in PowerPlex^® 16 and was only 9 and 11 nucleotides downstream of our estimated 5′ end position of D5S818 forward primer in GlobalFiler^® and PowerPlex^® 18D, respectively. We also examined the effect of primer length on the heterozygous peak balance in this sample.     

The NucleoSpin DNA Clean-up XS kit for the concentration and purification of genomic DNA extracts: An alternative to microdialysis filtration

Traditionally, DNA extracts from biological evidence items have been concentrated and rinsed using microdialysis filtration units, including the Centricon^® and Microcon^® centrifugal filter devices. As an alternative to microdialysis filtration, we present an optimized method for using NucleoSpin^® XS silica columns to concentrate and clean-up aqueous extracts from the organic extraction of DNA from biological samples. The method can be used with standard organic extraction and dithiothreitol (DTT)-based differential extraction methods with no modifications to these methods prior to the concentration and clean-up step. Extracts from laboratory-prepared bloodstains, saliva and semen stains have been successfully amplified with both qPCR and STR assays. Finally, the total time to process a set of samples with the NucleoSpin^® XS column is approximately 30 min vs. approximately 1.5 h with the Centricon^® YM-100 filter device.     

DNA Barcoding in Forensic Entomology – Establishing a DNA Reference Library of Potentially Forensic Relevant Arthropod Species,

Throughout the years, DNA barcoding has gained in importance in forensic entomology as it leads to fast and reliable species determination. High‐quality results, however, can only be achieved with a comprehensive DNA barcode reference database at hand. In collaboration with the Bavarian State Criminal Police Office, we have initiated at the Bavarian State Collection of Zoology the establishment of a reference library containing arthropods of potential forensic relevance to be used for DNA barcoding applications. CO1‐5P’ DNA barcode sequences of hundreds of arthropods were obtained via DNA extraction, PCR and Sanger Sequencing, leading to the establishment of a database containing 502 high‐quality sequences which provide coverage for 88 arthropod species. Furthermore, we demonstrate an application example of this library using it as a backbone to a high throughput sequencing analysis of arthropod bulk samples collected from human corpses, which enabled the identification of 31 different arthropod Barcode Index Numbers.     

Chelex法和两种磁珠法提取接触DNA效果的比较

目的比较Chelex法、DNA IQ磁珠法、EQ国产磁珠法对接触DNA的提取效果。方法将稀释为10ng、100ng的标准品DNA,分别采用Chelex法、DNA IQ磁珠法、EQ国产磁珠法处理;对30例烟蒂和30例牙刷分别采用Chelex法、DNA IQ磁珠法和EQ国产磁珠法提取DNA,然后进行PCR定量和STR检测。结果Chelex法对DNA的提取无损失,DNA IQ磁珠法、EQ国产磁珠法对DNA的提取均有不同程度的损失;烟蒂、牙刷等检材采用Chelex法提取的接触DNA量和IPC CT值显著高于IQ磁珠法、EQ国产磁珠法,但STR检验成功率却低于IQ磁珠法、EQ国产磁珠法。2种磁珠法提取的DNA量、IPC CT值和STR检验成功率无显著性差异。结论污染轻、杂质少的接触DNA检材,用Chelex法提取最为方便快捷;IQ磁珠法、EQ国产磁珠法更适合污染接触DNA检材的提取及自动化操作。     

Sequencing of mitochondrial DNA and the problem of human specificity

When analysing trace materials and degraded DNA the issue of human specificity is highly important. Especially when it comes down to the analysis of mitochondrial DNA which is extremely susceptible to contamination authenticity is the main question. Therefore in the presented study mitochondrial primers were tested on their human specificity. In all cases it was possible to amplify DNA of animals with human mt-primers. These unintentional amplifications could only be decreased by choosing austere PCR parameters. The study implies the importance of comprehensive evaluation of primers, chemicals and PCR parameters.     

Developmental Validation of the Quantifiler® Duo DNA Quantification Kit for Simultaneous Quantification of Total Human and Human Male DNA and Detection of PCR Inhibitors in Biological Samples*

Abstract: The Quantifiler^® Duo DNA Quantification kit enables simultaneous quantification of human DNA and human male DNA as well as detection of inhibitors of PCR in a single real-time PCR well. Pooled human male genomic DNA is used to generate standard curves for both human (ribonuclease P RNA component H1) and human male (sex determining region Y) specific targets. A shift in the cycle threshold (C_T) values for the internal positive control monitors the presence of PCR inhibitors in a sample. The assay is human specific and exhibits a high dynamic range from 0.023 to 50 ng/μL. In addition, the multiplex assay can detect as little as 25 pg/μL of human male DNA in the presence of a 1000-fold excess of human female DNA. The multiplex assay provides assessment of the DNA extract and guidance for the selection of the appropriate AmpFℓSTR^® Amplification Kit to obtain interpretable short tandem repeat profiles.     

试论如何正确应用DNA证据

拟构建一套正确应用DNA证据的逻辑框架,以避免DNA证据被错误解读和运用,明确法庭科学家和法庭审判者在DNA证据应用中的权责界限,保障事实认定之准确性和司法审判之公正性。提出了以概率统计学为工具,实现从“匹配”到“来源”之逻辑转化的必要性、合理性以及初步构想,并对当下主要的DNA证据解释方法予以分类和评价。     

DNA on the inside door handles of entrance doors

DNA from door handles on entry doors could provide a clue as to who last left the scene. However, after years of extensive research on DNA transfer and persistence it can be considered common knowledge that general claims like "the last who touched leaves the most DNA" do not hold true. But who's DNA do we find on door handles that are usually used several times per day by the inhabitants? To assess this question, we sampled inside door handles from real-life burglaries and at the same time collected reference samples from all the inhabitants, to determine if we can detect any (major) profiles from non-inhabitants. We also searched to evaluate how often we detect DNA from the person who last touched the door handle as a (major) contributor. Only small amounts of DNA were recovered from the handles, originating most often, but not always, from inhabitants or even the last inhabitant touching the handle.     

Results of the 2008 Colombian paternity testing quality control exercise

The Reference National Laboratory, Genes Ltda, designated by the Commission of Accreditation and Alertness created by Law 721 of 2001 of Republic of Colombia, organized and coordinated the Quality Control Exercise of 2008 for laboratories undertaking paternity and maternity tests with DNA markers. The Quality Control Exercise included both practical and theoretical exercises. For the practical exercise, three blood samples in FTA Classic Card were sent to each participating laboratory to be genotyped for DNA markers using the routine methodologies in their laboratories. For the theoretical exercise, it was asked to the participating laboratories to calculate the partial and final paternity indexes based on two genetic profiles of an alleged biological father and his son. Allele frequencies were made available to the participants, as well as Y chromosome haplotype database. A total of 12 laboratories have participated with data from 57 STRs, including autosomal and sex chromosome markers. Consensus was found in 37 STRs, 21 in autosomes and 16 Y chromosome linked. The rate of reporting errors was 3.1% (concentrated in just one laboratory). The theoretical exercise had consensus.