http://www.investigativegenetics.com The latest research articles published by Investigative Genetics 2010-09-01T00:00:00Z This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ Background: The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providing information on the geographic origin of individuals. This has been aided by the development of efficient screening methods and an increased knowledge of geographic distribution. In this study, we describe the development of single base extension assays used to resolve 61 Y chromosome haplogroups, mainly within haplogroups A, B and E, found in Africa. Results: Seven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Y chromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a few Eurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen 683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and South African Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683 samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroups varied appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry. Conclusions: The use of these single base extension assays in screening increased haplogroup resolution and sampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeat markers would considerably improve resolution, thus refining the geographic ancestry of individuals. http://www.investigativegenetics.com/content/1/1/6 Thijessen Naidoo Carina Schlebusch Heeran Makkan Pareen Patel Rajeshree Mahabeer Johannes Erasmus Himla Soodyall Investigative Genetics 2010, 1:6 2010-09-01T00:00:00Z doi:10.1186/2041-2223-1-6 Investigative Genetics 2041-2223 1 6 2010-09-01T00:00:00Z PDF Background: In the event of biocrimes or infectious disease outbreaks, high-resolution genetic characterization for identifying the agent and attributing it to a specific source can be crucial for an effective response. Until recently, in-depth genetic characterization required expensive and time-consuming Sanger sequencing of a few strains, followed by genotyping of a small number of marker loci in a panel of isolates at or by gel-based approaches such as pulsed field gel electrophoresis, which by necessity ignores most of the genome. Next-generation, massively parallel sequencing (MPS) technology (specifically the Applied Biosystems sequencing by oligonucleotide ligation and detection (SOLiDTM) system) is a powerful investigative tool for rapid, cost-effective and parallel microbial whole-genome characterization. Results: To demonstrate the utility of MPS for whole-genome typing of monomorphic pathogens, four Bacillus anthracis and four Yersinia pestis strains were sequenced in parallel. Reads were aligned to complete reference genomes, and genomic variations were identified. Resequencing of the B. anthracis Ames ancestor strain detected no false-positive single-nucleotide polymorphisms (SNPs), and mapping of reads to the Sterne strain correctly identified 98% of the 133 SNPs that are not clustered or associated with repeats. Three geographically distinct B. anthracis strains from the A branch lineage were found to have between 352 and 471 SNPs each, relative to the Ames genome, and one strain harbored a genomic amplification. Sequencing of four Y. pestis strains from the Orientalis lineage identified between 20 and 54 SNPs per strain relative to the CO92 genome, with the single Bolivian isolate having approximately twice as many SNPs as the three more closely related North American strains. Coverage plotting also revealed a common deletion in two strains and an amplification in the Bolivian strain that appear to be due to insertion element-mediated recombination events. Most private SNPs (that is, a, variant found in only one strain in this set) selected for validation by Sanger sequencing were confirmed, although rare false-positive SNPs were associated with variable nucleotide tandem repeats. Conclusions: The high-throughput, multiplexing capability, and accuracy of this system make it suitable for rapid whole-genome typing of microbial pathogens during a forensic or epidemiological investigation. By interrogating nearly every base of the genome, rare polymorphisms can be reliably discovered, thus facilitating high-resolution strain tracking and strengthening forensic attribution. http://www.investigativegenetics.com/content/1/1/5 Craig Cummings Christina Bormann-Chung Rixun Fang Melissa Barker Pius Brzoska Phillip Williamson Jodi Beaudry Molly Matthews James Schupp David Wagner Dawn Birdsell Amy Vogler Manohar Furtado Paul Keim Bruce Budowle Investigative Genetics 2010, 1:5 2010-09-01T00:00:00Z doi:10.1186/2041-2223-1-5 Investigative Genetics 2041-2223 1 5 2010-09-01T00:00:00Z PDF Bacillus anthracis, the causative agent of anthrax, is a proven biological weapon. In order to study this threat, a number of experimental surrogates have been used over the past 70 years. However, not all surrogates are appropriate for B. anthracis, especially when investigating transport, fate and survival. Although B. atrophaeus has been widely used as a B. anthracis surrogate, the two species do not always behave identically in transport and survival models. Therefore, we devised a scheme to identify a more appropriate surrogate for B. anthracis. Our selection criteria included risk of use (pathogenicity), phylogenetic relationship, morphology and comparative survivability when challenged with biocides. Although our knowledge of certain parameters remains incomplete, especially with regards to comparisons of spore longevity under natural conditions, we found that B. thuringiensis provided the best overall fit as a non-pathogenic surrogate for B. anthracis. Thus, we suggest focusing on this surrogate in future experiments of spore fate and transport modelling. http://www.investigativegenetics.com/content/1/1/4 David Greenberg Joseph Busch Paul Keim David Wagner Investigative Genetics 2010, 1:4 2010-09-01T00:00:00Z doi:10.1186/2041-2223-1-4 Investigative Genetics 2041-2223 1 4 2010-09-01T00:00:00Z PDF Through their current policy on data sharing, the National Institutes of Health (NIH) are inadvertently placing a serious and potentially insuperable burden upon non-US researchers who perform patient-based genomics studies in collaboration with US institutions. Because this policy could adversely affect future transnational scientific collaborations, we explore some of its likely consequences and suggest possible courses of remedial action wherever feasible. http://www.investigativegenetics.com/content/1/1/3 Michael Krawczak Jurgen Goebel David Cooper Investigative Genetics 2010, 1:3 2010-09-01T00:00:00Z doi:10.1186/2041-2223-1-3 Investigative Genetics 2041-2223 1 3 2010-09-01T00:00:00Z PDF The first 'Mark my words' column http://www.investigativegenetics.com/content/1/1/2 Mark Jobling Investigative Genetics 2010, 1:2 2010-09-01T00:00:00Z doi:10.1186/2041-2223-1-2 Investigative Genetics 2041-2223 1 2 2010-09-01T00:00:00Z PDF Welcome to Investigative Genetics, a new open access journal concerned with the development and application of molecular genetics within a wide range of science disciplines with societal relevance. http://www.investigativegenetics.com/content/1/1/1 Manfred Kayser Bruce Budowle Antti Sajantila Investigative Genetics 2010, 1:1 2010-09-01T00:00:00Z doi:10.1186/2041-2223-1-1 Investigative Genetics 2041-2223 1 1 2010-09-01T00:00:00Z PDF