International Commission on Missing Persons

Sarajevo, Bosnia and Herzegovina

International Commission on Missing Persons

Sarajevo, Bosnia and Herzegovina
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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.


Irwin J.A.,413 Research Blvd | Saunier J.,413 Research Blvd | Bodner M.,Innsbruck Medical University | Amory S.,International Commission on Missing Persons | And 5 more authors.
International Journal of Legal Medicine | Year: 2010

In order to better characterize and understand the mtDNA population genetics of Central Asia, the mtDNA control regions of over 1,500 individuals from Uzbekistan have been sequenced. Although all samples were obtained from individuals residing in Uzbekistan, individuals with direct ancestry from neighboring Central Asian countries are included. Individuals of Uzbek ancestry represent five distinct geographic regions of Uzbekistan: Fergana, Karakalpakstan, Khorezm, Qashkadarya, and Tashkent. Individuals with direct ancestry in nearby countries originate from Kazakhstan, Kyrgyzstan, Russia, Afghanistan, Turkmenistan, and Tajikistan. Our data reinforce the evidence of distinct clinal patterns that have been described among Central Asian populations with classical, mtDNA, and Y-chromosomal markers. Our data also reveal hallmarks of recent demographic events. Despite their current close geographic proximity, the populations with ancestry in neighboring countries show little sign of admixture and retain the primary mtDNA patterns of their source populations. The genetic distances and haplogroup distributions among the ethnic populations are more indicative of a broad east-west cline among their source populations than of their relatively small geographic distances from one another in Uzbekistan. Given the significant mtDNA heterogeneity detected, our results emphasize the need for heightened caution in the forensic interpretation of mtDNA data in regions as historically rich and genetically diverse as Central Asia. © Springer-Verlag 2010.


Pitterl F.,Innsbruck Medical University | Schmidt K.,Innsbruck Medical University | Huber G.,Innsbruck Medical University | Zimmermann B.,Innsbruck Medical University | And 7 more authors.
International Journal of Legal Medicine | Year: 2010

Short tandem repeat (STR) typing has become the standard technique in forensic methodology for the identification of unknown samples. National DNA databases have been established that contain STR genotypes for intelligence purposes. Due to their success, national DNA databases have been growing so fast that the number of advantageous matches may become a logistic problem for the analysts. This is especially true for partial STR profiles as they display reduced discrimination power. To overcome this drawback, modified versions (so-called mini-STRs) of existing loci were introduced as well as new loci to improve the information content of (partial) STR profiles. We pursue an alternative approach that makes use of nucleotide variation within the amplified STR fragments, which can be discerned by mass spectrometry. We have developed an assay that determines molecular masses from crude STR amplicons which were purified and separated by a liquid chromatographic system directly hyphenated to an electrospray ionization mass spectrometer. We present here new population data of forensically relevant STRs in Khoisan and Yakut populations. These autochthonous groups were selected as they may harbor additional STR alleles that are rare or unobserved in modern humans from cosmopolitan areas, especially for the Khoisan, which are known to represent a very ancient human population. The analysis of the molecular mass of STRs offered a widened spectrum of allele variability escorted by enhanced forensic use. Thus, established STR data derived from fragment size analysis can still be used in casework or in the context of intelligence databasing. © Springer-Verlag 2010.


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.


Zukowski L.A.,University of Florida | Falsetti A.B.,International Commission on Missing Persons | Tillman M.D.,University of Florida
Journal of Anatomy | Year: 2012

Previous research on lumbar spine osteophyte formation has focused on patterned development and the relation of age and sex to degeneration within the vertebral bodies. The inclusion of osteophytes originating on the laminae and body mass index (BMI) may result in a more complete evaluation. This study investigates lumbar osteophyte development on the laminae and vertebral bodies to determine whether osteophyte development: (i) is related bilaterally, at different lumbar levels, and superior and inferior margins; (ii) on the laminae and vertebral bodies are reciprocally dependent responses; (iii) is correlated with sex, age and/or BMI. Seventy-six individuals (39 females, 37 males) were randomly selected from a modern skeletal collection (Bass Donated Collection). Osteophyte development was scored in eight regions on each vertebra at all five lumbar levels. A factor analysis considered all 40 scoring regions and Pearson's correlation analyses assessed the relatedness of age and BMI with the consequent factors. The factor analysis separated the variables into two similar factors for males and females defined as: (i) superior and inferior vertebral body scores and (ii) superior laminar scores at higher lumbar levels. The factor analysis also determined a third factor for females defined as: (iii) inferior laminar scores at lower lumbar levels. The severity of vertebral body osteophytes increased with age for both sexes. Additionally for females, as BMI increased, osteophyte severity increased for both the superior laminar margins higher in the column and the vertebral bodies. Dissimilarities between the factors in males and females and the correlation of BMI to osteophyte severity exclusively in females provide evidence for different biomechanical processes influencing osteophyte development. © 2011 The Authors. Journal of Anatomy © 2011 Anatomical Society of Great Britain and Ireland.


News Article | January 13, 2016
Site: www.nature.com

Digging foundations for temples or schools, harvesting rice in paddy fields: these are some of the ways that the decaying remains of Vietnam War victims still turn up, 40 years after the conflict ended. Now an effort has begun that will use smart DNA technologies to identify the bones of the half a million or more Vietnamese soldiers and civilians who are thought still to be missing. It is the largest ever systematic identification effort; only the identification of more than 20,000 victims of armed conflicts in Bosnia and Herzegovina during the 1990s comes close. “When I was a 21-year-old in the medical corps there, I never imagined that such a project could ever become possible,” says Vietnam veteran and genomics pioneer Craig Venter, head of the J. Craig Venter Institute in La Jolla, California. “We thought of body counts as statistics — now, decades later, it may be possible to put names to them.” Although the United States has repatriated and identified most of its war dead, Vietnam has so far identified just a few hundred people, using outdated techniques. Yet people in Vietnam remain desperate to acquire the remains of family members. A few years ago, the government responded to their plight and asked the Advanced International Joint Stock Company (AIC) in Hanoi to investigate how best to proceed. The AIC consulted medical-diagnostics company Bioglobe in Hamburg, Germany, on how to equip the Vietnamese labs and train their scientists. In 2014, the Vietnamese government announced an investment of 500 billion dong (US$25 million) in the project and said that it would upgrade its three existing DNA-testing centres. This was great news, says Truong Nam Hai, head of the Institute of Biotechnology at the Vietnam Academy of Science and Technology, which hosts the first DNA-testing laboratory to be upgraded. In the 1990s, his institute proposed plans for identifying the missing, he says. However, “due to difficult circumstances at the time”, these did not take off. Last month, the government signed a training and consultancy contract with Bioglobe, which will allow the sequencing effort to start. “The technical challenges are considerable but tractable,” says Bioglobe’s chief executive, Wolfgang Höppner, who crafted the proposal for Vietnam. In the country’s hot and humid climate, DNA in bones that have lain in shallow graves for decades is likely to have degraded extensively. Moreover, contaminants from soil microbes can inhibit the enzymes that scientists use to amplify what little DNA remains to levels that can be analysed. And because of the large numbers of bones involved, the work needs to be done efficiently, adds Höppner. Höppner’s proposal makes use of kits from Germany-based biotech company Qiagen, which have been designed to protect and reveal as much DNA as possible when dealing with difficult sources such as old, buried bones, and are also amenable to automated, ‘high throughput’ processes. The identification process involves powdering bone samples and chemically breaking down their cells. Before amplification, the DNA is extracted in sealed Qiagen cartridges that contain chemicals to wash away substances that could inhibit the process. Another Qiagen kit then checks the amplified DNA against a large set of genomic markers to create a DNA profile of the sample. The kit can also detect whether inhibitors are still present. In cases in which inhibitors prove stubborn, samples will be analysed manually by slower, more complex methods that have been optimized by an experienced forensic laboratory run by the International Commission on Missing Persons (ICMP). That lab, in Bosnia and Herzegovina’s capital Sarajevo, led the effort to identify people killed during the 1990s conflict, including nearly all of the 8,000 or so who were massacred in 1995 in Srebrenica. The ICMP will also have a role in training Vietnamese scientists. Truong’s lab will next month send six scientists on a three-month programme. They will spend most of their time in Hamburg focusing on DNA tests, but they will also have a stint at the ICMP to learn other critical aspects of identification: how to avoid jumbling bones from different skeletons when exhuming them from mass graves, or how to look for clues in bones that might aid identification, such as pointers to height or gender. It was possible to extract useful levels of DNA from around 80% of the bones from the Srebrenica victims, says Thomas Parsons, head of the ICMP lab. The Vietnamese bones have been in the ground for longer and in a more damaging climate, but highly optimized methods and careful selection of skeletal samples will help, he says. The Vietnam project will also need reference DNA from family members to compare with the bone DNA from victims. It plans to have an outreach programme calling for people to donate saliva samples to create a reference data bank — but this will not be easy. Many war victims may have died too young to have had children, and their parents may also be dead, so reference samples will have to come from more distant relatives whose DNA is less similar. “That is why it is particularly important to do the DNA analysis with a larger than normal set of markers,” says Höppner. The outreach programme will also call for people to come forward with information on where bones might be buried. Unlike in Bosnia, where investigators could in some cases use satellite imagery to identify mass graves, the Vietnamese effort will rely on witness reports, as well as on common and military knowledge. Once all three government DNA-testing centres are upgraded, probably by 2017, they will together be able to identify between 8,000 and 10,000 people a year, says Truong. He also anticipates that the DNA project will improve Vietnam’s scientific culture.


PubMed | University of Porto, International Commission on Missing Persons, Copenhagen University, University of Santiago de Compostela and 5 more.
Type: | Journal: 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.


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.


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

Degraded skeletal remains generally contain limited quantities of genetic material and thus DNA-based identification efforts often target the mitochondrial DNA (mtDNA) control region due to the relative abundance of intact mtDNA as compared to nuclear DNA. In many missing person cases, however, the discriminatory power of mtDNA is inadequate to permit identification when associated anthropological, odontological, or contextual evidence is also limited, and/or the event involves a large number of individuals. In situations such as these, more aggressive amplification protocols which can permit recovery of STR data are badly needed as they may represent the last hope for conclusive identification. We have previously demonstrated the potential of a modified Promega PowerPlex 16 amplification strategy for the recovery of autosomal STR data from severely degraded skeletal elements. Here, we further characterize the results obtained under these modified parameters on a variety of sample types including pristine control DNA and representative case work specimens. Not only is the amplification approach evaluated here sensitive to extremely low authentic DNA input quantities (6 pg), but when the method was applied to thirty-one challenging casework specimens, nine or more alleles were reproducibly recovered from 69% of the samples tested. Moreover, when we independently considered bone samples extracted with a protocol that includes complete demineralization of the bone matrix, the percentage of samples yielding nine or more reproducible alleles increased to 95% with the modified amplification parameters. Overall, direct comparisons between the modified amplification protocol and the standard amplification protocol demonstrated that allele recovery was significantly greater using the aggressive parameters, with only a minimal associated increase in artifactual data.

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