Category Archives: Forensic DNA

Journal articles relating to forensic DNA including disaster victim identification.

[In Depth] Forensic labs explore blind testing to prevent errors

Science 31 July 2015:  Vol. 349 no. 6247 pp. 462-463
DOI: 10.1126/science.349.6247.462

Last week, at the first International Symposium on Forensic Science Error Management in Arlington, Virginia, nearly 500 forensic scientists, crime lab managers, and other practitioners confronted the factors that have led to unreliable results in the field. A key problem, many said, is that people who evaluate evidence from crime scenes have access to information about a case that could bias their analysis. That subconscious bias could arise from irrelevant contextual information, such as the nature of the crime or police investigators’ beliefs about a suspect’s guilt, or from the physical evidence itself. As forensics struggles to recover from revelations of serious flaws in its methodology and scientific underpinnings, more labs are considering ways to shield their examiners from potential bias.

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Comparison of hard tissues that are useful for DNA analysis in forensic autopsy

Legal Medicine Available online 3 July 2015

Forensic analysis of DNA from hard tissues can be important when investigating a variety of cases resulting from mass disaster or criminal cases. This study was conducted to evaluate the most suitable tissues, method and sample size for processing of hard tissues prior to DNA isolation. We also evaluated the elapsed time after death in relation to the quantity of DNA extracted. Samples of hard tissues (37 teeth, 42 skull, 42 rib, and 39 nails) from 42 individuals aged between 50 and 83 years were used. The samples were taken from remains following forensic autopsy (from 2 days to 2 years after death). To evaluate the integrity of the nuclear DNA isolated, the percentage of allele calls for short tandem repeat profiles were compared between the hard tissues. DNA typing results indicated that until one month after death, any of the four hard tissue samples could be used as an alternative to teeth, allowing analysis of all of the loci. However, in terms of the sampling site, collection method and sample size adjustment, the rib appeared to be the best choice in view of the ease of specimen preparation. Our data suggest that the rib could be an alternative hard tissue sample for DNA analysis of human remains.

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U.S. initiatives to strengthen forensic science & international standards in forensic DNA

Forensic Science International: Genetics  Available online 30 June 2015

A number of initiatives are underway in the United States in response to the 2009 critique of forensic science by a National Academy of Sciences committee. This article provides a broad review of activities including efforts of the White House National Science and Technology Council Subcommittee on Forensic Science and a partnership between the Department of Justice (DOJ) and the National Institute of Standards and Technology (NIST) to create the National Commission on Forensic Science and the Organization of Scientific Area Committees. These initiatives are seeking to improve policies and practices of forensic science. Efforts to fund research activities and aid technology transition and training in forensic science are also covered.

The second portion of the article reviews standards in place or in development around the world for forensic DNA. Documentary standards are used to help define written procedures to perform testing. Physical standards serve as reference materials for calibration and traceability purposes when testing is performed. Both documentary and physical standards enable reliable data comparison, and standard data formats and common markers or testing regions are crucial for effective data sharing. Core DNA markers provide a common framework and currency for constructing DNA databases with compatible data. Recent developments in expanding core DNA markers in Europe and the United States are discussed.

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Secondary and subsequent DNA transfer during criminal investigation

Forensic Science International: Genetics Volume 17, July 2015, Pages 155–162

With the introduction of new multiplex PCR kits and instrumentation such as the Applied Biosystems 3500xl, there has recently been a rapid change in technology that has greatly increased sensitivity of detection so that a DNA profile can routinely be obtained from only a few cells. Research to evaluate the risks of passive transfer has not kept pace with this development; hence the risk of innocent DNA transfer at the crime-scene is currently not properly understood. The purpose of this study was to investigate the possibility of investigator-mediated transfer of DNA traces with disposable nitrile-gloves used during crime-scene examinations. We investigated the primary transfer of freshly deposited DNA from touched plastic, wood or metal substrates and secondary and tertiary transfer by a person wearing disposable nitrile-gloves and onto a third object. We show that with use of the new highly sensitive technologies available in forensic DNA analysis there is an enhanced probability to obtain a DNA-profile which has not been directly deposited on the object but is an outcome of one or more transfer events. The nitrile-gloves used by investigators during exhibit examination can act as a vector for DNA transfer from one item to another. We have shown that the amount of DNA deposited on an object affects the probability of transfer. Secondly, the type of substrate material that DNA is deposited onto has an impact on transfer rates.

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Leading-edge forensic DNA analyses and the necessity of including crime scene investigators, police officers and technicians in a DNA elimination database

Forensic Science International: Genetics Available online 12 June 2015

In recent years, sophisticated technology has significantly increased the sensitivity and analytical power of genetic analyses so that very little starting material may now produce viable genetic profiles. This sensitivity however, has also increased the risk of detecting unknown genetic profiles assumed to be that of the perpetrator, yet originate from extraneous sources such as from crime scene workers. These contaminants may mislead investigations, keeping criminal cases active and unresolved for long spans of time. Voluntary submission of DNA samples from crime scene workers is fairly low, therefore we have created a promotional method for our staff elimination database that has resulted in a significant increase in voluntary samples since 2011. Our database enforces privacy safeguards and allows for optional anonymity to all staff members. We also offer information sessions at various police precincts to advise crime scene workers of the importance and success of our staff elimination database. This study, a pioneer in its field, has obtained 327 voluntary submissions from crime scene workers to date, of which 46 individual profiles (14%) have been matched to 58 criminal cases. By implementing our methods and respect for individual privacy, forensic laboratories everywhere may see similar growth and success in explaining unidentified genetic profiles in stagnate criminal cases.

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New book in the library collection: The murder of Allison Baden-Clay

The Murder of Allison Baden-Clay (2014) / David Murray
The Murder of Allison Baden-Clay is written by the investigative journalist who covered the case from the start. It weaves together exclusive interviews and police and court records to explain how a father with no criminal history came to be on trial for a brutal murder. It’s also a story about everyday choices and their consequences.

If you would like to borrow this item, click on the book title (make sure your details are correct) and click SEND.  If the book is currently on loan, we will add your details to the reservations list.

Forensic Science International: Genetics – recent online articles

Developing a DNA methylation assay for human age prediction in blood and bloodstain Available online 8 May 2015

Age prediction of an individual based on biological traces remained in a crime scene is of ultimate importance for criminal investigation. Growing evidence indicates that some CpG sites may have age-related methylation changes and thus may be a promising tool for age prediction. In this study, we utilized the pyrosequencing approach to screen age-related CpG (AR-CpG) sites for age prediction. Five AR-CpGs were identified as age-related markers from thirty-eight candidates, among which three CpG sites, ITGA2B_1, NPTX2_3, and NPTX2_4 were never reported in previous studies. We fit a linear regression model for age prediction based on methylation assay for 89 blood samples from donors aged 9-75 years old. The model included four AR-CpG markers in three gene fragments ASPA, ITGA2B and NPTX2 and enabled the age prediction with R2=0.819. The mean absolute deviation (MAD) from chronological age of the model was 7.870. We validated the linear regression model with a validation set of 40 blood samples, and the prediction MAD was 7.986. There was no statistically significant difference in age prediction between 20 pairs of blood samples and bloodstains. Six pairs of fresh and old bloodstains were analyzed using our assay. The obtained results showed the assay still performed an effective prediction on bloodstains after four-month storage in room conditions. This study indicates that our DNA methylation assay is a reliable and effective method for age prediction for forensic purposes.
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Evaluation of the RapidHIT™ 200 System: A comparative study of its performance with Maxwell® DNA IQTM/Identifiler® Plus/ABI 3500xL Workflow  Available online 8 May 2015

RapidHITTM System is a rapid DNA instrument that is capable of processing forensic samples from extraction through to capillary electrophoresis and profile generation within two hours. Evaluation of the RapidHITTM 200 System was conducted to examine several key performance indicators of the instrument, including reproducibility, contamination, sensitivity, versatility and the possibility of sample re-extraction. Results indicated that the RapidHITTM 200 System was capable of generating high quality DNA profiles which were comparable to those from the standard protocol comprising of Maxwell® 16 DNA IQTM System, Identifiler® Plus and ABI 3500xL. No contamination was detected during the studies. Results also showed that the instrument was able to generate DNA profiles from samples containing lower amounts of DNA (0.5 μl of blood) albeit with more allele and locus dropouts when compared to the standard protocol. The ability to process blood swabs, blood-stained FTA punches, semen swabs, buccal swabs, product of conception (POC), bone marrow, fingernail clippings and cigarette butts at a good success rate indicated the robustness and versatility of the RapidHITTM 200 System. Furthermore, additional alleles could be recovered via re-analysis of the failed samples using the standard protocol. In summary, our results showed that the RapidHITTM 200 System was able to process casework samples for the purpose of providing rapid intelligence through DNA database searches and reference matching. Confirmative DNA results can be obtained through either concurrent processing of duplicate samples via standard protocol or re-extraction of samples retrieved from the RapidHITTM sample cartridge.
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Allele frequencies of 20 autosomal STR in the population from Rio Grande do Sul Southern Brazil  Available online 7 May 2015

One of the solutions applied by most of the forensic experts – when faced
with unsolved cases of genetic reconstruction of deceased or missing persons
using only recommended loci by CODIS or by any other genetic databases system
– is to include a larger number of DNA regions [1]. When genetic mutations occur
between parents and progeny, by addition or deletion of repeating units in the
regions of occurrence of STR, the occurrence of null alleles or even single-parent
paternity cases, increasing the number of genetic markers, can also assist in
solving cases of paternity/maternity or any genetic link type[2].
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Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing Available online 6 May 2015
Long an important and useful tool in forensic genetic investigations, mitochondrial DNA (mtDNA) typing continues to mature. Research in the last few years has demonstrated both that data from the entire molecule will have practical benefits in forensic DNA casework, and that massively parallel sequencing (MPS) methods will make full mitochondrial genome (mtGenome) sequencing of forensic specimens feasible and cost-effective. A spate of recent studies has employed these new technologies to assess intraindividual mtDNA variation. However, in several instances, contamination and other sources of mixed mtDNA data have been erroneously identified as heteroplasmy. Wellvetted mtGenome datasets based on both Sanger and MPS sequences have found authentic point heteroplasmy in approximately 25% of individuals when minor component detection thresholds are in the range of 10-20%, along with positional distribution patterns in the coding region that differ from patterns of point heteroplasmy in the well-studied control region. A few recent studies that examined very low-level heteroplasmy are concordant with these observations when the data are examined at a common level of resolution. In this review we provide an overview of considerations related to the use of MPS technologies to detect mtDNA heteroplasmy. In addition, we examine published reports on point heteroplasmy to characterize features of the data that will assist in the evaluation of future mtGenome data developed by any typing method.
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Developmental Validation of the ParaDNA® Intelligence System—A novel approach to DNA profiling  Available online 6 May 2015

DNA profiling through the analysis of STRs remains one of the most widely used tools inhuman identification across the world. Current laboratory STR analysis is slow, costly and requiresexpert users and interpretation which can lead to instances of delayed investigations or non-testing of evidence on budget grounds. The ParaDNA® Intelligence System has been designed to provide asimple, fast and robust way to profile DNA samples in a lab or field-deployable manner. The System analyses 5-STRs plus amelogenin to deliver a DNA profile that enables users to gain rapid investigative leads and intelligent prioritisation of samples in human identity testing applications. Utilising an innovative sample collector, minimal training is required to enable both DNA analysts and nonspecialist personnel to analyse biological samples directly, without prior processing, in approximately 75 minutes. The test uses direct PCR with fluorescent HyBeacon® detection of STR allele lengths to provide a DNA profile. The developmental validation study described here followed the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines and tested the sensitivity, reproducibility, accuracy, inhibitor tolerance, and performance of the ParaDNA Intelligence System on a range of mock evidence items. The data collected demonstrate that the ParaDNA Intelligence System displays useful DNA profiles when sampling a variety of evidence items including blood, saliva, semen and touch DNA items indicating the potential to benefit a number of applications in fields such as forensic, military and disaster victim identification (DVI).
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Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application

Routine use of massively parallel sequencing (MPS) for forensic genomics is on the horizon. The last few years, several algorithms and workflows have been developed to analyze forensic MPS data. However, none have yet been tailored to the needs of the forensic analyst who does not possess an extensive bioinformatics background.

We developed our previously published forensic MPS data analysis framework MyFLq (My-Forensic-Loci-queries) into an open-source, user-friendly, web-based application. It can be installed as a standalone web application, or run directly from the Illumina BaseSpace environment. In the former, laboratories can keep their data on-site, while in the latter, data from forensic samples that are sequenced on an Illumina sequencer can be uploaded to Basespace during acquisition, and can subsequently be analyzed using the published MyFLq BaseSpace application. Additional features were implemented such as an interactive graphical report of the results, an interactive threshold selection bar, and an allele length-based analysis in addition to the sequenced-based analysis.
Practical use of the application is demonstrated through the analysis of four 16-plex short tandem repeat (STR) samples, showing the complementarity between the sequence- and length-based analysis of the same MPS data.
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Development of a forensically useful age prediction method based on DNA methylation analysis Available online 5 May 2015
Forensic DNA phenotyping needs to be supplemented with age prediction to become a relevant source of information on human appearance. Recent progress in analysis of the human methylome has enabled selection of multiple candidate loci showing linear correlation with chronological age. Practical application in forensic science depends on successful validation of these potential age predictors. In this study, eight DNA methylation candidate loci were analysed using convenient and reliable pyrosequencing technology. A total number of 41CpG sites was investigated in 420 samples collected from men and women aged from 2 to 75 years. The study confirmed correlation of all the investigated markers with human age. The five most significantly correlated CpG sites in ELOVL2 on 6p24.2, C1orf132 on 1q32.2, TRIM59 on 3q25.33, KLF14 on 7q32.3 and FHL2 on 2q12.2 were chosen to build a prediction model. This restriction allowed the technical analysis to be simplified without lowering the prediction accuracy significantly. Model parameters for a discovery set of 300 samples were R2 = 0.94 and the standard error of the estimate = 4.5 years. An independent set of 120 samples was used to test the model performance. Mean absolute deviation for this testing set was 3.9 years. The number of correct predictions ±5 years achieved a very high level of 86.7% in the age category 2-19 and gradually decreased to 50% in the age category 60-75. The prediction model was deterministic for individuals belonging to these two extreme age categories. The developed method was implemented in a freely available online age prediction calculator.
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Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™  Volume 17, July 2015, Pages 110–121
Next generation sequencing (NGS) offers the opportunity to analyse forensic DNA samples and obtain massively parallel coverage of targeted short sequences with the variants they carry. We evaluated the levels of sequence coverage, genotyping precision, sensitivity and mixed DNA patterns of a prototype version of the first commercial forensic NGS kit: the HID-Ion AmpliSeq™ Identity Panel with 169-markers designed for the Ion PGM™ system. Evaluations were made between three laboratories following closely matched Ion PGM™ protocols and a simple validation framework of shared DNA controls. The sequence coverage obtained was extensive for the bulk of SNPs targeted by the HID-Ion AmpliSeq™ Identity Panel. Sensitivity studies showed 90–95% of SNP genotypes could be obtained from 25 to 100 pg of input DNA. Genotyping concordance tests included Coriell cell-line control DNA analyses checked against whole-genome sequencing data from 1000 Genomes and Complete Genomics, indicating a very high concordance rate of 99.8%. Discordant genotypes detected in rs1979255, rs1004357, rs938283, rs2032597 and rs2399332 indicate these loci should be excluded from the panel. Therefore, the HID-Ion AmpliSeq™ Identity Panel and Ion PGM™ system provide a sensitive and accurate forensic SNP genotyping assay. However, low-level DNA produced much more varied sequence coverage and in forensic use the Ion PGM™ system will require careful calibration of the total samples loaded per chip to preserve the genotyping reliability seen in routine forensic DNA. Furthermore, assessments of mixed DNA indicate the user’s control of sequence analysis parameter settings is necessary to ensure mixtures are detected robustly. Given the sensitivity of Ion PGM™, this aspect of forensic genotyping requires further optimisation before massively parallel sequencing is applied to routine casework.
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Genetic structure and forensic parameters of 38 Indels for human identification purposes in eight Mexican populations  Available online 2 May 2015
Insertion-deletions for human identification purposes (HID-Indels) offer advantages to solve particular forensic situations and complex paternity cases. In Mexico, admixed population known as Mestizos is the largest (∼90 %), plus a number of Amerindian groups (∼ 10%), which have not been studied with HID-Indels. For this reason, allele frequencies and forensic parameters for 38HID-Indels were estimated in 531 unrelated individuals from one Amerindian (Purépecha) and seven Mestizo populations from different regions of the country. Genotype distribution was in agreement with Hardy-Weinberg expectations in almost all loci/populations. The linkage disequilibrium (LD) test did not reveal possible associations between loci pairs in all eight Mexican populations. The combined power of discrimination was high in all populations (PD > 99.99999999998%). However, the power of exclusion of the 38HID-Indel system (PE > 99.6863%) was reduced regarding most of autosomal STR kits. The assessment of genetic structure (AMOVA) and relationships between populations (FST) demonstrated significant differences among Mexican populations, mainly of the Purépecha Amerindian group. Among Mexican-Mestizos, three population clusters consistent with geography were defined: i) North-West region: Chihuahua, Sinaloa, and Jalisco; ii) Central-Southern region: Mexico City, Veracruz and Yucatan; iii) South region: Chiapas. In brief, this report validates the inclusion of the 38HID-Indel system in forensic casework and paternity cases in seven Mexican-Mestizo populations from different regions, and in one Mexican Amerindian group.
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Assessing the impact of common forensic presumptive tests on the ability to obtain results using a novel rapid DNA platform  Volume 17, July 2015, Pages 87–90
The rise of DNA evidence to the forefront of forensic science has led to high sample numbers being submitted for profiling by investigators to casework laboratories: bottleneck effects are often seen resulting in slow turnaround times and sample backlog. The ParaDNA® Screening and Intelligence Tests have been designed to guide investigators on the viability of potential sources of DNA allowing them to determine which samples should be sent for full DNA analysis. Both tests are designed to augment the arsenal of available forensic tests for end users and be used concurrently to those commonly available. Therefore, assessing the impact that common forensic tests have on such novel technology is important to measure. The systems were tested against various potential inhibitors to which samples may be exposed as part of the investigative process. Presumptive test agents for biological materials (blood, semen and saliva) and those used as fingerprint enhancement agents were both used. The Screening Test showed a drop in performance following application of aluminium powder and cyanoacrylate (CNA) on fingerprints samples; however this drop in performance was not replicated with high template DNA. No significant effect was observed for any agent using the Intelligence Test. Therefore, both tests stand up well to the chemical agents applied and can be used by investigators with confidence that system performance will be maintained.
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