Investigative Genetics - Most accessed articles

Forensic trace DNA: a review

Roland van Oorschot — 2010-12-01T00:00:00Z

DNA analysis is frequently used to acquire information from biological material to aid enquiries associated with criminal offences, disaster victim identification and missing persons investigations. As the relevance and value of DNA profiling to forensic investigations has increased, so too has the desire to generate this information from smaller amounts of DNA. Trace DNA samples may be defined as any sample which falls below recommended thresholds at any stage of the analysis, from sample detection through to profile interpretation, and can not be defined by a precise picogram amount. Here we review aspects associated with the collection, DNA extraction, amplification, profiling and interpretation of trace DNA samples. Contamination and transfer issues are also briefly discussed within the context of trace DNA analysis. Whilst several methodological changes have facilitated profiling from trace samples in recent years it is also clear that many opportunities exist for further improvements.

Developing criteria and data to determine best options for expanding the core CODIS loci

Jianye Ge — 2012-01-06T00:00:00Z

Background: Recently, the CODIS Core Loci Working Group established by the FBI reviewed and recommended changes for the CODIS core loci. The Working Group identified 20 STR loci comprised of the original CODIS core set loci (minus TPOX), four European recommended loci, Penta E, and DYS391 plus the Amelogenin marker as the new core set. Before selecting and finalizing the core loci some evaluations are in order which could provide guidance for best options of core selection.MethodThe performance of current and newly proposed CODIS core loci sets were evaluated with simplified analyses for adventitious hit rates in reasonably large data sets under single source profile comparisons, mixture comparisons, kinship searches, and for international data sharing. Informativeness (e.g., Match Probability, Average Kinship Index) and mutation rates of each locus are some criteria to consider for loci selection. However, a primary factor should be performance with challenged forensic samples. Results: The current battery of loci provided in already validated commercial kits meet the needs for single source profile comparisons and international data sharing, even with relatively large databases. However, the 13 CODIS core loci are not sufficiently powerful for kinship analyses and searching potential contributors of mixtures in larger databases; 19 or more autosomal STR loci do perform better. Y chromosome STR loci are very useful to trace paternal lineage, deconvolve female and male mixtures, and resolve inconsistencies with Amelogenin typing. The selection by the CODIS Working Group of the DYS391 locus makes little sense theoretically or practically. Combining five or six Y-STR loci with existing autosomal STR loci can have better performance than the same number of autosomal loci for kinship analysis and still yield a sufficiently low match probability for single source profile comparisons. Conclusion: A more comprehensive study should be sought to provide necessary information to decision makers and stakeholders about constructing a new set of core loci for CODIS. Finally, as food for thought, selection of loci should be driven by the concept that the needs of casework should be supported by CODIS (or for that matter any forensic DNA database).

Next generation sequencing technologies and applications for human Genetic History and Forensics

Eva Berglund — 2011-11-24T00:00:00Z

Rapid advances in the development of sequencing technologies in recent years have enabled an increasing number of applications in biology and medicine. Here, we review key technical aspects of the preparation of DNA templates for sequencing, the biochemical reaction principles and assay formats underlying next-generation sequencing systems, methods for imaging and base calling, quality control, and bioinformatic approaches for sequence alignment, variant calling and assembly. We also discuss some of the most important advances that the new sequencing technologies have brought to the fields of human population genetics, human genetic history and forensic genetics.

The Identification of the Romanovs: Can we (finally) put the controversies to rest?

Michael Coble — 2011-09-26T00:00:00Z

For much of the 20th century the fate of the last Imperial family of Russia, the Romanovs, was a mystery after their execution in 1918. In the mid 1970s the mass grave of the Romanov family (minus two of the children) was discovered and officially exhumed after the fall of the Soviet Union. Forensic DNA testing of the remains in the early 1990s was used to identify the family. Despite the overwhelming evidence for establishing the identity of the Romanov family, a small but vocal number of scientists have tried to raise doubt about the DNA testing during the late 1990s and early 2000s. With the discovery of the two missing Romanov children in 2007, there was an opportunity to re-analyze all of the evidence associated with the case which confirmed the initial DNA testing and brought finality to the mystery. This article will discuss the controversies associated with the Romanov identification and reflect upon the importance of the case to the field of forensic DNA typing over the last 20 years.

Genetic variation and population structure among Sudanese populations as indicated by the 15 Identifiler STR loci

Hiba Babiker — 2011-05-04T00:00:00Z

Background: There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.ResultWe report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia. Conclusion: We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea

Soon-Hee Kim — 2011-04-04T00:00:00Z

Background: Koreans are generally considered a Northeast Asian group, thought to be related to Altaic-language-speaking populations. However, recent findings have indicated that the peopling of Korea might have been more complex, involving dual origins from both southern and northern parts of East Asia. To understand the male lineage history of Korea, more data from informative genetic markers from Korea and its surrounding regions are necessary. In this study, 25 Y-chromosome single nucleotide polymorphism markers and 17 Y-chromosome short tandem repeat (Y-STR) loci were genotyped in 1,108 males from several populations in East Asia. Results: In general, we found East Asian populations to be characterized by male haplogroup homogeneity, showing major Y-chromosomal expansions of haplogroup O-M175 lineages. Interestingly, a high frequency (31.4%) of haplogroup O2b-SRY465 (and its sublineage) is characteristic of male Koreans, whereas the haplogroup distribution elsewhere in East Asian populations is patchy. The ages of the haplogroup O2b-SRY465 lineages (~9,900 years) and the pattern of variation within the lineages suggested an ancient origin in a nearby part of northeastern Asia, followed by an expansion in the vicinity of the Korean Peninsula. In addition, the coalescence time (~4,400 years) for the age of haplogroup O2b1-47z, and its Y-STR diversity, suggest that this lineage probably originated in Korea. Further studies with sufficiently large sample sizes to cover the vast East Asian region and using genomewide genotyping should provide further insights. Conclusions: These findings are consistent with linguistic, archaeological and historical evidence, which suggest that the direct ancestors of Koreans were proto-Koreans who inhabited the northeastern region of China and the Korean Peninsula during the Neolithic (8,000-1,000 BC) and Bronze (1,500-400 BC) Ages.

A rare variant of the mtDNA HVS1 sequence in the hairs of Napoleon's family

Gerard Lucotte — 2010-10-04T00:00:00Z

This paper describes the finding of a rare variant in the sequence of the hypervariable segment (HVS1) of mitochondrial (mtDNA) extracted from two preserved hairs, authenticated as belonging to the French Emperor Napoléon I (Napoléon Bonaparte). This rare variant is a mutation that changes the base C to T at position 16,184 (16184C→T), and it constitutes the only mutation found in this HVS1 sequence. This mutation is rare, because it was not found in a reference database (P < 0.05). In a personal database (M. Pala) comprising 37,000 different sequences, the 16184C→T mutation was found in only three samples, thus in this database the mutation frequency was 0.00008%. This mutation 16184C→T was also the only variant found subsequently in the HVS1 sequences of mtDNAs extracted from Napoléon's mother (Letizia) and from his youngest sister (Caroline), confirming that this mutation is maternally inherited. This 16184C→T variant could be used for genetic verification to authenticate any doubtful material and determine whether it should indeed be attributed to Napoléon.

Contrasting signals of positive selection in genes involved in human skin color variation from tests based on SNP scans and resequencing

Johanna Maria de Gruijter — 2011-12-01T00:00:00Z

Background: Numerous genome-wide scans conducted by genotyping previously-ascertained single nucleotide polymorphisms (SNPs) have provided candidate signatures of positive selection in various regions of the human genome, including in genes involved in pigmentation traits. However, it is unclear how well the signatures discovered by such haplotype-based test statistics can be reproduced in tests based on full resequence data. Four genes, OCA2, TYRP1, DCT and KITLG, implicated in human skin color variation, have shown evidence for positive selection in Europeans and East Asians in previous SNP-scan data. In the current study, we resequenced 4.7-6.7 kb of DNA from each of these genes in Africans, Europeans, East Asians and South Asians. Results: Applying all commonly-used allele frequency distribution neutrality test statistics to the newly generated sequence data provided conflicting results in respect of evidence for positive selection. Previous haplotype-based findings could not be clearly confirmed. The application of Markov Chain Monte Carlo Approximate Bayesian Computation to these sequence data using a simple forward simulator revealed broad posterior distributions of the selective parameters for all four genes providing no support for positive selection. However, when we applied this approach to published sequence data on SLC45A2, another human pigmentation candidate gene, we could readily confirm evidence for positive selection as previously detected with sequence-based and some haplotype-based tests. Conclusions: Overall, our data indicate that even genes that are strong biological candidates for positive selection and show reproducible signatures of positive selection in SNP scans do not always show the same replicability of selection signals in other tests, which should be considered in future studies on detecting positive selection in genetic data.

Policy implications for familial searching

Joyce Kim — 2011-11-01T00:00:00Z

In the United States, several states have made policy decisions regarding whether and how to use familial searching of the Combined DNA Index System (CODIS) database in criminal investigations. Familial searching pushes DNA typing beyond merely identifying individuals to detecting genetic relatedness, an application previously reserved for missing persons identifications and custody battles. The intentional search of CODIS for partial matches to an item of evidence offers law enforcement agencies a powerful tool for developing investigative leads, apprehending criminals, revitalizing cold cases and exonerating wrongfully convicted individuals. As familial searching involves a range of logistical, social, ethical and legal considerations, states are now grappling with policy options for implementing familial searching to balance crime fighting with its potential impact on society. When developing policies for familial searching, legislators should take into account the impact of familial searching on select populations and the need to minimize personal intrusion on relatives of individuals in the DNA database. This review describes the approaches used to narrow a suspect pool from a partial match search of CODIS and summarizes the economic, ethical, logistical and political challenges of implementing familial searching. We examine particular US state policies and the policy options adopted to address these issues. The aim of this review is to provide objective background information on the controversial approach of familial searching to inform policy decisions in this area. Herein we highlight key policy options and recommendations regarding effective utilization of familial searching that minimize harm to and afford maximum protection of US citizens.

An overview to the investigative approach to species testing in wildlife forensic science

Adrian Linacre — 2011-01-13T00:00:00Z

The extent of wildlife crime is unknown but it is on the increase and has observable effects with the dramatic decline in many species of flora and fauna. The growing awareness of this area of criminal activity is reflected in the increase in research papers on animal DNA testing, either for the identification of species or for the genetic linkage of a sample to a particular organism. This review focuses on the use of species testing in wildlife crime investigations. Species identification relies primarily on genetic loci within the mitochondrial genome; focusing on the cytochrome b and cytochrome oxidase 1 genes. The use of cytochrome b gained early prominence in species identification through its use in taxonomic and phylogenetic studies, while the gene sequence for cytochrome oxidase was adopted by the Barcode for Life research group. This review compares how these two loci are used in species identification with respect to wildlife crime investigations. As more forensic science laboratories undertake work in the wildlife area, it is important that the quality of work is of the highest standard and that the conclusions reached are based on scientific principles. A key issue in reporting on the identification of a particular species is a knowledge of both the intraspecies variation and the possible overlap of sequence variation from one species to that of a closely related species. Recent data showing this degree of genetic separation in mammalian species will allow greater confidence when preparing a report on an alleged event where the identification of the species is of prime importance. The aim of this review is to illustrate aspects of species testing in wildlife forensic science and to explain how a knowledge of genetic variation at the genus and species level can aid in the reporting of results.