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PubMed | University of Porto, King Abdulaziz University, Humboldt University of Berlin, Copenhagen University and 11 more.
Type: | Journal: Forensic science international. Genetics | Year: 2016

The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that provide a precise description of the repeat allele structure of a STR marker and variants that may reside in the flanking areas of the repeat region. When a STR contains a complex arrangement of repeat motifs, the level of genetic polymorphism revealed by the sequence data can increase substantially. As repeat structures can be complex and include substitutions, insertions, deletions, variable tandem repeat arrangements of multiple nucleotide motifs, and flanking region SNPs, established capillary electrophoresis (CE) allele descriptions must be supplemented by a new system of STR allele nomenclature, which retains backward compatibility with the CE data that currently populate national DNA databases and that will continue to be produced for the coming years. Thus, there is a pressing need to produce a standardized framework for describing complex sequences that enable comparison with currently used repeat allele nomenclature derived from conventional CE systems. It is important to discern three levels of information in hierarchical order (i) the sequence, (ii) the alignment, and (iii) the nomenclature of STR sequence data. We propose a sequence (text) string format the minimal requirement of data storage that laboratories should follow when adopting MPS of STRs. We further discuss the variant annotation and sequence comparison framework necessary to maintain compatibility among established and future data. This system must be easy to use and interpret by the DNA specialist, based on a universally accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established nomenclature for CE-based STR analysis will remain unchanged in the future, the nomenclature of sequence-based STR genotypes will need to follow updated rules and be generated by expert systems that translate MPS sequences to match CE conventions in order to guarantee compatibility between the different generations of STR data.

Moreno L.I.,Florida International University | Moreno L.I.,FBI Laboratory | Mills D.,Florida International University | Fetscher J.,Florida International University | And 3 more authors.
Journal of Microbiological Methods | Year: 2011

The placement of cadavers in shallow, clandestine graves may alter the microbial and geochemical composition of the underlying and adjacent soils. Using amplicon length heterogeneity-PCR (LH-PCR) the microbial community changes in these soils can be assessed. In this investigation, nine different grave sites were examined over a period of 16. weeks. The results indicated that measurable changes occurred in the soil bacterial community during the decomposition process. In this study, amplicons corresponding to anaerobic bacteria, not indigenous to the soil, were shown to produce differences between grave sites and control soils. Among the bacteria linked to these amplicons are those that are most often part of the commensal flora of the intestines, mouth and skin. In addition, over the 16. week sampling interval, the level of indicator organisms (i.e., nitrogen fixing bacteria) dropped as the body decomposed and after four weeks of environmental exposure they began to increase again; thus differences in the abundance of nitrogen fixing bacteria were also found to contribute to the variation between controls and grave soils. These results were verified using primers that specifically targeted the nifH gene coding for nitrogenase reductase. LH-PCR provides a fast, robust and reproducible method to measure microbial changes in soil and could be used to determine potential cadaveric contact in a given area. The results obtained with this method could ultimately provide leads to investigators in criminal or missing person scenarios and allow for further analysis using human specific DNA assays to establish the identity of the buried body. © 2010 Elsevier B.V.

Budowle B.,University of North Texas | Polanskey D.,FBI Laboratory | Fisher C.L.,FBI Laboratory | Den Hartog B.K.,Mitotech LLC | And 2 more authors.
Journal of Forensic Sciences | Year: 2010

Naming mtDNA sequences by listing only those sites that differ from a reference sequence is the standard practice for describing the observed variations. Consistency in nomenclature is desirable so that all sequences in a database that are concordant with an evidentiary sequence will be found for estimating the rarity of that profile. The operational alignment and nomenclature rules, i.e., "Wilson Rules," suggested for this purpose do not always guarantee a single consistent sequence description for all observed polymorphisms. In this work, the operational alignment/nomenclature rules were reconfigured to better reflect traditional user preferences. The rules for selecting alignments are described. In addition, to avoid human error and to more efficiently name mtDNA sequence variants, a computer-facilitated method of aligning mtDNA sample sequences with a reference sequence was developed. There were 33 differences between these hierarchical rules and the data in SWGDAM, which translates into a 99.92% consistency between the new rules and the manual historical nomenclature approach. The data support the reliability of the current SWGDAM database. As the few discrepancies were changed in favor of the new hierarchical rules, the quality of the SWGDAM database is further improved. © 2010 American Academy of Forensic Sciences. Published 2010. This article is a U.S. Government work and is in the public domain in the U.S.A.

Parson W.,Innsbruck Medical University | Parson W.,Pennsylvania State University | Gusmao L.,State University of Rio de Janeiro | Gusmao L.,University of Porto | And 9 more authors.
Forensic Science International: Genetics | Year: 2014

The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the question of human identification. Previous recommendations published in 2000 addressed the analysis and interpretation of mitochondrial DNA (mtDNA) in forensic casework. While the foundations set forth in the earlier recommendations still apply, new approaches to the quality control, alignment and nomenclature of mitochondrial sequences, as well as the establishment of mtDNA reference population databases, have been developed. Here, we describe these developments and discuss their application to both mtDNA casework and mtDNA reference population databasing applications. While the generation of mtDNA for forensic casework has always been guided by specific standards, it is now well-established that data of the same quality are required for the mtDNA reference population data used to assess the statistical weight of the evidence. As a result, we introduce guidelines regarding sequence generation, as well as quality control measures based on the known worldwide mtDNA phylogeny, that can be applied to ensure the highest quality population data possible. For both casework and reference population databasing applications, the alignment and nomenclature of haplotypes is revised here and the phylogenetic alignment proffered as acceptable standard. In addition, the interpretation of heteroplasmy in the forensic context is updated, and the utility of alignment-free database searches for unbiased probability estimates is highlighted. Finally, we discuss statistical issues and define minimal standards for mtDNA database searches. © 2014 Elsevier Ireland Ltd.

Parson W.,Innsbruck Medical University | Parson W.,Pennsylvania State University | Strobl C.,Innsbruck Medical University | Huber G.,Innsbruck Medical University | And 9 more authors.
Forensic Science International: Genetics | Year: 2013

Insights into the human mitochondrial phylogeny have been primarily achieved by sequencing full mitochondrial genomes (mtGenomes). In forensic genetics (partial) mtGenome information can be used to assign haplotypes to their phylogenetic backgrounds, which may, in turn, have characteristic geographic distributions that would offer useful information in a forensic case. In addition and perhaps even more relevant in the forensic context, haplogroup-specific patterns of mutations form the basis for quality control of mtDNA sequences. The current method for establishing (partial) mtDNA haplotypes is Sanger-type sequencing (STS), which is laborious, time-consuming, and expensive. With the emergence of Next Generation Sequencing (NGS) technologies, the body of available mtDNA data can potentially be extended much more quickly and cost-efficiently. Customized chemistries, laboratory workflows and data analysis packages could support the community and increase the utility of mtDNA analysis in forensics. We have evaluated the performance of mtGenome sequencing using the Personal Genome Machine (PGM) and compared the resulting haplotypes directly with conventional Sanger-type sequencing. A total of 64 mtGenomes (>1 million bases) were established that yielded high concordance with the corresponding STS haplotypes (<0.02% differences). About two-thirds of the differences were observed in or around homopolymeric sequence stretches. In addition, the sequence alignment algorithm employed to align NGS reads played a significant role in the analysis of the data and the resulting mtDNA haplotypes. Further development of alignment software would be desirable to facilitate the application of NGS in mtDNA forensic genetics. © 2013 Elsevier Ireland Ltd. All rights reserved.

Gilpin M.,George Mason University | Christensen A.M.,George Mason University | Christensen A.M.,FBI Laboratory
Journal of Forensic Sciences | Year: 2015

Analyzing and identifying skeletal remains becomes increasingly difficult when remains have been cremated, especially in cases where the cremated material may have been intentionally contaminated with nonskeletal material. This study examined the potential of X-ray fluorescence spectrometry (XRF) to detect the presence of nonskeletal contaminants in samples of cremains. Eleven samples of cremains were variably combined with concrete mix and analyzed using XRF. Photon counts of elements in each sample were analyzed, and the coefficient of determination (R2) using unweighted linear regression as a function of percent cremains was calculated. Results showed that with changes in the proportion of skeletal material and contaminant, there were significant (R2 > 0.90) changes in detected levels of phosphorus, potassium, zinc, aluminum, and sulfur. The use of XRF is concluded to be a valid approach in the identification of the presence of nonskeletal material in potentially contaminated cremains. © 2015 American Academy of Forensic Sciences.

PubMed | University of Pretoria, Innsbruck Medical University, Life Technologies, University of Aveiro and 2 more.
Type: | Journal: Forensic science international. Genetics | Year: 2016

The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.fsigen.2013.09.007. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.

News Article | September 6, 2016
Site: www.chromatographytechniques.com

A White House panel of experts, including federal judges, are recommending that some forensic disciplines be thrown out of courtrooms, while some others need further scientific validation. The report, approved last Thursday by the President’s Council of Advisors on Science and Technology, blasts some analyses that have drawn recent scrutiny, including bite marks and hair follicles. But the report also contends that the culture needs to change to focus on fact-finding in the laboratory – and not on-the-job experience during criminal investigations, a Forensic Magazine review of the document found. “Casework is not scientifically valid research, and experience alone cannot establish scientific validity,” the report states. “In particular, one cannot reliably estimate error rates from casework because one typically does not have independent knowledge of the ‘ground truth’ or ‘right answer.’” The group included nine federal judges, a former U.S. Solicitor General, a state supreme court justice, law school deans, and statisticians. Overall, they concluded that forensic science results be “repeatable, reproducible and accurate.” The panel held a massive 2002 FBI study of the hair analysis as a “landmark of forensic science,” due to its scientific standards. That study eventually led to reconsideration of tens of thousands of criminal convictions – but only after more than a decade had elapsed. The group also recommended that the FBI Laboratory assume more of a lead role in the ongoing “overhaul” of the forensic science, through training, research, and validation of existing and future technologies. More government funding should be directed to agencies to further forensic scientific study, they added. “The total level of federal funding by NIJ, NIST and NSF to the academic community for fundamental research in forensic science is extremely small,” they write. “Substantially larger funding will be needed to develop a robust research community and to support the development and evaluation of promising new technologies.” Forensic science, which has captured the imagination of the public in the 21st century with the popularization of TV shows like CSI, first came under widespread scrutiny in 2009, with a report by National Research Council entitled “Strengthening Forensic Science in the United States: A Path Forward.” It called for major reforms to the criminal-justice system – and to establish national forensics scientific standards. The American Association for the Advancement of Science has undertaken what could become a “transformational” reevaluation of American forensic science, in response to the 2009 report. Ten disciplines are going to be subject to investigation. First up is ballistics and tool markers, latent fingerprints and arson investigations. Those are already underway. The next seven are: bloodstain pattern analysis, digital evidence, footwear and tire tracks, bitemark analysis, fiber trace evidence, hair trace evidence, and trace evidence of paint and other coatings,according to the AAAS.

Just R.S.,Armed Forces DNA Identification Laboratory | Irwin J.A.,FBI Laboratory | Parson W.,Innsbruck Medical University | Parson W.,Pennsylvania State University
Forensic Science International: Genetics | Year: 2015

Abstract 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. Well vetted 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. © 2015 The Authors.

Diegoli T.M.,413 Research Blvd | Farr M.,National Laboratory Center | Cromartie C.,National Laboratory Center | Cromartie C.,FBI Laboratory | And 3 more authors.
Forensic Science International: Genetics | Year: 2012

Damage to the DNA molecule can occur through exposure to environmental conditions such as ultraviolet light, heat and humidity. Forensic samples are particularly prone to such damage due to their prolonged exposure after deposition at crime scenes or mass disasters. Current methods for typing such samples rely heavily on the intact DNA template, and can be adversely affected by damage that is present. Proposed solutions center around increased access to the smaller remaining fragments and/or increased sensitivity. However, all rely on the polymerase chain reaction to copy the starting material; the required polymerase can be impeded by certain types of damage such as dimer-formation after ultraviolet light exposure, resulting in stochastic effects that can complicate interpretation. In vitro repair of such damage offers the ability to generate high quality profiles using traditional methods without changes to the current amplification reagents or conditions. Typically, repair reactions required large quantities of starting material and a separate repair reaction. Forensic samples, however, usually consist of small quantities, and quality control measures necessitate laboratory procedures that minimize sample manipulation. Here, an optimized protocol for forensic application of the PreCR™ Repair Mix to current typing methods is demonstrated for samples damaged by ultraviolet light exposure. © 2011 Published by Elsevier Ireland Ltd.

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