http://www.investigativegenetics.com The latest research articles published by Investigative Genetics 2012-02-01T00:00:00Z Please see related article: http://www.investigativegenetics.com/content/3/1/2 Bruce Budowle Jianye Ge Ranajit Chakraborty Harrell Gill-King Investigative Genetics 2012, null:3 2012-02-01T00:00:00Z ${item.identifier} /content/figures/2041-2223-3-3-toc.gif Investigative Genetics 2041-2223 ${item.volume} 3 2012-02-01T00:00:00Z PDF Prior probabilities represent a core element of the Bayesian probabilistic approach to relatedness testing. This letter opinions on the commentary 'Use of prior odds for missing persons identifications' by Budowle et al. (2011), published recently in this journal. Contrary to Budowle et al. (2011), we argue that the concept of prior probabilities (i) is not endowed with the notion of objectivity, (ii) is not a case for computation and (iii) does not require new guidelinesedited by the forensic DNA community - as long as probability is properly considered as an expression ofpersonal belief.Please see related article: http://www.investigativegenetics.com/content/3/1/3 http://www.investigativegenetics.com/content/3/1/2 Alex Biedermann Franco Taroni Pierre Margot Investigative Genetics 2012, null:2 2012-01-31T00:00:00Z doi:10.1186/2041-2223-3-2 /content/figures/2041-2223-3-2-toc.gif Investigative Genetics 2041-2223 ${item.volume} 2 2012-01-31T00:00:00Z PDF 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). http://www.investigativegenetics.com/content/3/1/1 Jianye Ge Arthur Eisenberg Bruce Budowle Investigative Genetics 2012, null:1 2012-01-06T00:00:00Z doi:10.1186/2041-2223-3-1 How to expand a DNA database The rapid expansion of DNA databases over the past few years has lead to numerous problems associated with their use. In order to increase the efficiency of the Combined DNA Index System, expansions to the core loci have been suggested. Budowle et al evaluate these proposed expansions and consider the consequences of the selection of core genetic markers for forensic DNA databases. /content/figures/2041-2223-3-1-toc.gif Investigative Genetics 2041-2223 ${item.volume} 1 2012-01-06T00:00:00Z PDF Commissioned column http://www.investigativegenetics.com/content/2/1/25 Mark Jobling Investigative Genetics 2011, null:25 2011-12-01T00:00:00Z doi:10.1186/2041-2223-2-25 With Christmas just around the corner, a seasonal theme is expected of this month's column. In an appropriately festive way, Mark discusses the related topic of the virgin birth- or parthenogenesis. /content/figures/2041-2223-2-25-toc.gif Investigative Genetics 2041-2223 ${item.volume} 25 2011-12-01T00:00:00Z XML 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. http://www.investigativegenetics.com/content/2/1/24 Johanna Maria de Gruijter Oscar Lao Mark Vermeulen Yali Xue Cara Woodwark Christopher Gillson Alison Coffey Qasim Ayub S Mehdi Manfred Kayser Chris Tyler-Smith Investigative Genetics 2011, null:24 2011-12-01T00:00:00Z doi:10.1186/2041-2223-2-24 /content/figures/2041-2223-2-24-toc.gif Investigative Genetics 2041-2223 ${item.volume} 24 2011-12-01T00:00:00Z PDF 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. http://www.investigativegenetics.com/content/2/1/23 Eva Berglund Anna Kiialainen Ann-Christine Syvanen Investigative Genetics 2011, null:23 2011-11-24T00:00:00Z doi:10.1186/2041-2223-2-23 /content/figures/2041-2223-2-23-toc.gif Investigative Genetics 2041-2223 ${item.volume} 23 2011-11-24T00:00:00Z XML 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. http://www.investigativegenetics.com/content/2/1/22 Joyce Kim Danny Mammo Marni Siegel Sara Katsanis Investigative Genetics 2011, null:22 2011-11-01T00:00:00Z doi:10.1186/2041-2223-2-22 Policy implications for familial searching Advances in technology make familial searching a valuable tool, enabling new leads to be developed in criminal investigations and revitalizing cold cases. The difficulties faced in policy making stem from the need to balance crime fighting against potential impacts on society, taking into account logistical, social, ethical, legal and economic implications. /content/figures/2041-2223-2-22-toc.gif Investigative Genetics 2041-2223 ${item.volume} 22 2011-11-01T00:00:00Z XML - http://www.investigativegenetics.com/content/2/1/21 Mark Jobling Investigative Genetics 2011, null:21 2011-10-06T00:00:00Z doi:10.1186/2041-2223-2-21 Mark discusses the use of Y-chromosome testing to establish relatedness, with the case study of Thomas Jefferson and his alleged illegitimate children. /content/figures/2041-2223-2-21-toc.gif Investigative Genetics 2041-2223 ${item.volume} 21 2011-10-06T00:00:00Z XML 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. http://www.investigativegenetics.com/content/2/1/20 Michael Coble Investigative Genetics 2011, null:20 2011-09-26T00:00:00Z doi:10.1186/2041-2223-2-20 /content/figures/2041-2223-2-20-toc.gif Investigative Genetics 2041-2223 ${item.volume} 20 2011-09-26T00:00:00Z XML Krishna Dronamraju was the legendary population geneticist JBS Haldane's last student, at the end of Haldane's life when he was working and teaching in India. Since then Dronamraju has made something of a career as a Haldane biographer, historian, and nostalgist. He has written articles and books on Haldane's work and career, mixing the professional with the personal. This is another of that kind. It is a short, clearly written, and interesting read. http://www.investigativegenetics.com/content/2/1/19 Ken Weiss Investigative Genetics 2011, null:19 2011-09-19T00:00:00Z doi:10.1186/2041-2223-2-19 /content/figures/2041-2223-2-19-toc.gif Investigative Genetics 2041-2223 ${item.volume} 19 2011-09-19T00:00:00Z XML