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Rock A.,University of Innsbruck | Irwin J.,413 Research Blvd | Dur A.,University of Innsbruck | Parsons T.,International Commission on Missing Persons | Parson W.,Innsbruck Medical University
Forensic Science International: Genetics | Year: 2011

The analysis of the haploid mitochondrial (mt) genome has numerous applications in forensic and population genetics, as well as in disease studies. Although mtDNA haplotypes are usually determined by sequencing, they are rarely reported as a nucleotide string. Traditionally they are presented in a difference-coded position-based format relative to the corrected version of the first sequenced mtDNA. This convention requires recommendations for standardized sequence alignment that is known to vary between scientific disciplines, even between laboratories. As a consequence, database searches that are vital for the interpretation of mtDNA data can suffer from biased results when query and database haplotypes are annotated differently. In the forensic context that would usually lead to underestimation of the absolute and relative frequencies. To address this issue we introduce SAM, a string-based search algorithm that converts query and database sequences to position-free nucleotide strings and thus eliminates the possibility that identical sequences will be missed in a database query. The mere application of a BLAST algorithm would not be a sufficient remedy as it uses a heuristic approach and does not address properties specific to mtDNA, such as phylogenetically stable but also rapidly evolving insertion and deletion events. The software presented here provides additional flexibility to incorporate phylogenetic data, site-specific mutation rates, and other biologically relevant information that would refine the interpretation of mitochondrial DNA data. The manuscript is accompanied by freeware and example data sets that can be used to evaluate the new software (http://stringvalidation.org). © 2010 Elsevier Ireland Ltd. Source

Damann F.E.,National Museum of Health and Medicine | Tanittaisong A.,413 Research Blvd | Carter D.O.,University of Nebraska - Lincoln
Forensic Science International | Year: 2012

The University of Tennessee Anthropology Research Facility (ARF) is known for its unique contribution to forensic science as a site of human decomposition research. Studies conducted at ARF are integral in our understanding of the processes of human decomposition. As such, the authors are interested in the long-term effects of continuous human decomposition on the soil environment. Soil samples collected from within and outside the ARF were evaluated for moisture content, pH, organic content, total carbon and nitrogen content, and biomass by lipid-bound phosphorus, and total extracted DNA. Analyses revealed no significant differences (p<0.05) among the sampled areas within the facility, and yet demonstrated a possible trend toward increased levels of total N, Lipid-P, and water, suggesting an influx of high-quality nutrients into the ARF soil. Furthermore, elevated pH readings, presumably resulting from ammonification of the soil, were observed in areas of high decomposition. The negative control samples proved significantly different from nearly all samples collected within the facility, the exceptions being total carbon content and extractable DNA. These findings indicate that while landscape samples inside may be similar to themselves, they are dissimilar to those taken in a similar temperate forest biome with no recorded history of human decomposition. © 2012. Source

Kline M.C.,U.S. National Institute of Standards and Technology | Hill C.R.,U.S. National Institute of Standards and Technology | Decker A.E.,U.S. National Institute of Standards and Technology | Decker A.E.,413 Research Blvd | Butler J.M.,U.S. National Institute of Standards and Technology
Forensic Science International: Genetics | Year: 2011

DNA sequence variation is known to exist in and around the repeat region of short tandem repeat (STR) loci used in human identity testing. While the vast majority of STR alleles measured in forensic DNA laboratories worldwide type as "normal" alleles compared with STR kit allelic ladders, a number of variant alleles have been reported. In addition, a sequence difference at a polymerase chain reaction (PCR) primer binding site in the DNA template can cause allele drop-out (i.e., a "null" or "silent" allele) with one set of primers and not with another. Our group at the National Institute of Standards and Technology (NIST) has been sequencing variant and null alleles supplied by forensic labs and cataloging this information on the NIST STRBase website for the past decade. The PCR primer sequences and strategy used for our STR allele sequencing work involving 23 autosomal STRs and 17 Y-chromosome STRs are described along with the results from 111 variant and 17 null alleles. Source

Amory S.,International Commission on Missing Persons | Huel R.,International Commission on Missing Persons | Bilic A.,International Commission on Missing Persons | Loreille O.,413 Research Blvd | Parsons T.J.,International Commission on Missing Persons
Forensic Science International: Genetics | Year: 2012

During the 7 year period from 2002 to 2009 a high volume, silica-binding DNA extraction protocol for bone, based on modified QIAGEN's Blood Maxi Kit protocol was highly successful permitting the DNA matching of >14,500 missing persons from former Yugoslavia. This method, however, requires large amount of bone material and large volumes of reagents. The logical evolution was to develop a more efficient extraction protocol for bone samples that uses significantly less starting material while increasing the success in obtaining DNA results from smaller, more challenging samples. In this study we compared the performance of ICMP's original protocol against an automatable full demineralization approach. In order to provide reliable results and to simulate a wide variety of cases, we analyzed 40 bone samples in a comparative study based on DNA concentrations and quality of resulting STR profiles. The new protocol results in the dissolution of the entire bone powder sample, thus eliminating the possibility that DNA is left behind, locked in remaining solid bone matrix. For the majority of samples tested, the DNA concentrations obtained from half a gram of fully digested bone material were equivalent to or greater than the ones obtained from 2 g of partially demineralized bone powder. Furthermore, the full demineralization process significantly increases the proportion of full profiles reflecting the correlation with better DNA quality. This method has been adapted for the QIAcube robotic platform. The performance of this automated full demineralization protocol is similar to the manual version and increases overall lab throughput. It also simplifies the process by eliminating quality control procedures that are advisable in manual procedures, and overall reduces the chance of human error. Finally we described a simple and efficient post-extraction clean-up method that can be applied to DNA extracts obtained from different protocols. This protocol has also been adjusted for the QIAcube platform. © 2011 Elsevier Ireland Ltd. All rights reserved. Source

Ramallo V.,Federal University of Rio Grande do Sul | Bisso-Machado R.,Federal University of Rio Grande do Sul | Bravi C.,CONICET | Coble M.D.,413 Research Blvd | And 4 more authors.
American Journal of Physical Anthropology | Year: 2013

Native Americans are characterized by specific and unique patterns of genetic and cultural/linguistic diversities, and this information has been used to understand patterns of geographic dispersion, and the relationship between these peoples. Particularly interesting are the Tupi and Je speaker dispersions. At present, a large number of individuals speak languages of these two stocks; for instance, Tupi-Guarani is one of the official languages in Paraguay, Bolivia, and the Mercosul economic block. Although the Tupi expansion can be compared in importance to the Bantu migration in Africa, little is known about this event relative to others. Equal and even deeper gaps exist concerning the Je-speakers' expansion. This study aims to elucidate some aspects of these successful expansions. To meet this purpose, we analyzed Native American mtDNA complete control region from nine different populations and included HVS-I sequences available in the literature, resulting in a total of 1,176 samples investigated. Evolutionary relationships were explored through median-joining networks and genetic/geographic/linguistic correlations with Mantel tests and spatial autocorrelation analyses. Both Tupi and Je showed general traces of ancient or more recent fission-fusion processes, but a very different pattern of demographic expansion. Tupi populations displayed a classical isolation-by-distance pattern, while Je groups presented an intricate and nonlinear mode of dispersion. We suggest that the collective memory and other cultural processes could be important factors influencing the fission-fusion events, which likely contributed to the genetic structure, evolution, and dispersion of Native American populations. Copyright © 2013 Wiley Periodicals, Inc. Source

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