Investigative genetics最新文献

{"title":"Introducing the Forensic Research/Reference on Genetics knowledge base, FROG-kb.","authors":"Haseena Rajeevan, Usha Soundararajan, Andrew J Pakstis, Kenneth K Kidd","doi":"10.1186/2041-2223-3-18","DOIUrl":"10.1186/2041-2223-3-18","url":null,"abstract":"<p><strong>Background: </strong>Online tools and databases based on multi-allelic short tandem repeat polymorphisms (STRPs) are actively used in forensic teaching, research, and investigations. The Fst value of each CODIS marker tends to be low across the populations of the world and most populations typically have all the common STRP alleles present diminishing the ability of these systems to discriminate ethnicity. Recently, considerable research is being conducted on single nucleotide polymorphisms (SNPs) to be considered for human identification and description. However, online tools and databases that can be used for forensic research and investigation are limited.</p><p><strong>Methods: </strong>The back end DBMS (Database Management System) for FROG-kb is Oracle version 10. The front end is implemented with specific code using technologies such as Java, Java Servlet, JSP, JQuery, and GoogleCharts.</p><p><strong>Results: </strong>We present an open access web application, FROG-kb (Forensic Research/Reference on Genetics-knowledge base, http://frog.med.yale.edu), that is useful for teaching and research relevant to forensics and can serve as a tool facilitating forensic practice. The underlying data for FROG-kb are provided by the already extensively used and referenced ALlele FREquency Database, ALFRED (http://alfred.med.yale.edu). In addition to displaying data in an organized manner, computational tools that use the underlying allele frequencies with user-provided data are implemented in FROG-kb. These tools are organized by the different published SNP/marker panels available. This web tool currently has implemented general functions possible for two types of SNP panels, individual identification and ancestry inference, and a prediction function specific to a phenotype informative panel for eye color.</p><p><strong>Conclusion: </strong>The current online version of FROG-kb already provides new and useful functionality. We expect FROG-kb to grow and expand in capabilities and welcome input from the forensic community in identifying datasets and functionalities that will be most helpful and useful. Thus, the structure and functionality of FROG-kb will be revised in an ongoing process of improvement. This paper describes the state as of early June 2012.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"18"},"PeriodicalIF":0.0,"publicationDate":"2012-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30873226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Illegal hunting cases detected with molecular forensics in Brazil.","authors":"Alexandra Sanches, Paola M Tokumoto, Wellington Am Peres, Fernando L Nunes, Mariana St Gotardi, Carolina S Carvalho, Cristiane Pelizzon, Tamissa G Godoi, Mauro Galetti","doi":"10.1186/2041-2223-3-17","DOIUrl":"10.1186/2041-2223-3-17","url":null,"abstract":"<p><strong>Background: </strong>Illegal hunting is one of the major threats to vertebrate populations in tropical regions. This unsustainable practice has serious consequences not only for the target populations, but also for the dynamics and structure of tropical ecosystems. Generally, in cases of suspected illegal hunting, the only evidence available is pieces of meat, skin or bone. In these cases, species identification can only be reliably determined using molecular technologies. Here, we reported an investigative study of three cases of suspected wildlife poaching in which molecular biology techniques were employed to identify the hunted species from remains of meat.</p><p><strong>Findings: </strong>By applying cytochrome b (cyt-b) and cytochrome oxidase subunit I (COI) molecular markers, the suspected illegal poaching was confirmed by the identification of three wild species, capybara (Hydrochoerus hydrochaeris), Chaco Chachalaca (Ortalis canicollis) and Pampas deer (Ozotoceros bezoarticus). In Brazil, hunting is a criminal offense, and based on this evidence, the defendants were found guilty and punished with fines; they may still be sentenced to prison for a period of 6 to 12 months.</p><p><strong>Conclusions: </strong>The genetic analysis used in this investigative study was suitable to diagnose the species killed and solve these criminal investigations. Molecular forensic techniques can therefore provide an important tool that enables local law enforcement agencies to apprehend illegal poachers.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"17"},"PeriodicalIF":0.0,"publicationDate":"2012-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30810995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Bayesian network approach to the database search problem in criminal proceedings.","authors":"Alex Biedermann,&nbsp;Joëlle Vuille,&nbsp;Franco Taroni","doi":"10.1186/2041-2223-3-16","DOIUrl":"https://doi.org/10.1186/2041-2223-3-16","url":null,"abstract":"<p><strong>Unlabelled: </strong></p><p><strong>Background: </strong>The 'database search problem', that is, the strengthening of a case - in terms of probative value - against an individual who is found as a result of a database search, has been approached during the last two decades with substantial mathematical analyses, accompanied by lively debate and centrally opposing conclusions. This represents a challenging obstacle in teaching but also hinders a balanced and coherent discussion of the topic within the wider scientific and legal community. This paper revisits and tracks the associated mathematical analyses in terms of Bayesian networks. Their derivation and discussion for capturing probabilistic arguments that explain the database search problem are outlined in detail. The resulting Bayesian networks offer a distinct view on the main debated issues, along with further clarity.</p><p><strong>Methods: </strong>As a general framework for representing and analyzing formal arguments in probabilistic reasoning about uncertain target propositions (that is, whether or not a given individual is the source of a crime stain), this paper relies on graphical probability models, in particular, Bayesian networks. This graphical probability modeling approach is used to capture, within a single model, a series of key variables, such as the number of individuals in a database, the size of the population of potential crime stain sources, and the rarity of the corresponding analytical characteristics in a relevant population.</p><p><strong>Results: </strong>This paper demonstrates the feasibility of deriving Bayesian network structures for analyzing, representing, and tracking the database search problem. The output of the proposed models can be shown to agree with existing but exclusively formulaic approaches.</p><p><strong>Conclusions: </strong>The proposed Bayesian networks allow one to capture and analyze the currently most well-supported but reputedly counter-intuitive and difficult solution to the database search problem in a way that goes beyond the traditional, purely formulaic expressions. The method's graphical environment, along with its computational and probabilistic architectures, represents a rich package that offers analysts and discussants with additional modes of interaction, concise representation, and coherent communication.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"16"},"PeriodicalIF":0.0,"publicationDate":"2012-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-16","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30802497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitochondrial DNA analysis of 114 hairs measuring less than 1 cm from a 19-year-old homicide.","authors":"Terry Melton,&nbsp;Gloria Dimick,&nbsp;Bonnie Higgins,&nbsp;Michele Yon,&nbsp;Charity Holland","doi":"10.1186/2041-2223-3-12","DOIUrl":"https://doi.org/10.1186/2041-2223-3-12","url":null,"abstract":"<p><strong>Background: </strong>Mitochondrial DNA analysis is typically applied to degraded skeletal remains and telogen or rootless hairs. Data on the application of the method to very small hairs less than 0.5 cm from an age-matched and -challenged sample set are lacking.</p><p><strong>Methods: </strong>One hundred fourteen hairs sized less than 1 cm from a 1993 case were analyzed for mitochondrial DNA according to laboratory standard operating procedures. For some hairs, a screening approach was applied, which permitted some samples, such as victim hairs on victim clothing, to be eliminated from the process quickly. Degraded samples were amplified with \"mini-primers,\" and 12S species testing was applied when non-human hairs were encountered.</p><p><strong>Results: </strong>Partial to full control region human mitochondrial DNA profiles or species identifications (non-human species) were obtained from 93% of hairs under 1 cm, 92% of hairs under 5 mm, and 90% of hairs under 3.5 mm. Nineteen of 21 hairs 2 mm or less gave full or partial profiles. Among 128 hairs of all sizes tested in the case, 9 gave no results, 3 were canine in origin, and 73 did not exclude six known individuals tested in the case. Twenty-two hairs had nine additional profiles that were observed two or more times each. Twenty-one hairs showed singleton types not matching each other or any individual.</p><p><strong>Conclusions: </strong>Crime scene hairs that are both aged and small are often judged to be unsuitable for either hair microscopy or DNA analysis. This study of age-matched challenged small hairs indicates that even the smallest probative crime scene hairs are suitable for mitochondrial DNA analysis and can provide useful data.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"12"},"PeriodicalIF":0.0,"publicationDate":"2012-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-12","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30680685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editors' Pick: A real Caucasian and the genetic investigation of Caucasus peoples.","authors":"Manfred Kayser","doi":"10.1186/2041-2223-3-15","DOIUrl":"https://doi.org/10.1186/2041-2223-3-15","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"15"},"PeriodicalIF":0.0,"publicationDate":"2012-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-15","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30751601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of STR profiling from low template DNA extracts with and without the consensus profiling method.","authors":"Kelly S Grisedale,&nbsp;Angela van Daal","doi":"10.1186/2041-2223-3-14","DOIUrl":"https://doi.org/10.1186/2041-2223-3-14","url":null,"abstract":"<p><strong>Background: </strong>The consensus profiling method was introduced to overcome the exaggerated stochastic effects associated with low copy number DNA typing. However, little empirical evidence has been provided which shows that a consensus profile, derived from dividing a sample into separate aliquots and including only alleles seen at least twice, gives the most informative profile, compared to a profile obtained by amplifying the entire low template DNA extract in one reaction. Therefore, this study aimed to investigate the quality of consensus profiles compared to profiles obtained using the whole low template extract for amplification.</p><p><strong>Methods: </strong>A total of 100 pg and 25 pg DNA samples were amplified with the PowerPlex® ESI 16 Kits using 30 or 34 PCR cycles. A total of 100 pg and 25 pg DNA samples were then divided into three aliquots for a 34-cycle PCR and a consensus profile derived that included alleles that appeared in at least two of the replicates. Profiles from the non-split samples were compared to the consensus profiles focusing on peak heights, allele drop out, locus drop out and allele drop in.</p><p><strong>Results: </strong>Performing DNA profiling on non-split extracts produced profiles with a higher percentage of correct loci compared to the consensus profiling technique. Consensus profiling did eliminate any spurious alleles from the final profile. However, there was a notable increase in allele and locus drop out when a LTDNA sample was divided prior to amplification.</p><p><strong>Conclusions: </strong>The loss of information that occurs when a sample is split for amplification indicates that consensus profiling may not be producing the most informative DNA profile for samples where the template amount is limited.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2012-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-14","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30728727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Boys and girls.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-3-13","DOIUrl":"https://doi.org/10.1186/2041-2223-3-13","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"13"},"PeriodicalIF":0.0,"publicationDate":"2012-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30705406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editors' Pick: Normal aging versus Alzheimer's disease - expression patterns may discern the differences.","authors":"Bruce Budowle","doi":"10.1186/2041-2223-3-11","DOIUrl":"https://doi.org/10.1186/2041-2223-3-11","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"11"},"PeriodicalIF":0.0,"publicationDate":"2012-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-11","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30628138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Method: a single nucleotide polymorphism genotyping method for Wheat streak mosaic virus.","authors":"Stephanie M Rogers, Mark Payton, Robert W Allen, Ulrich Melcher, Jesse Carver, Jacqueline Fletcher","doi":"10.1186/2041-2223-3-10","DOIUrl":"10.1186/2041-2223-3-10","url":null,"abstract":"<p><strong>Background: </strong>The September 11, 2001 attacks on the World Trade Center and the Pentagon increased the concern about the potential for terrorist attacks on many vulnerable sectors of the US, including agriculture. The concentrated nature of crops, easily obtainable biological agents, and highly detrimental impacts make agroterrorism a potential threat. Although procedures for an effective criminal investigation and attribution following such an attack are available, important enhancements are still needed, one of which is the capability for fine discrimination among pathogen strains. The purpose of this study was to develop a molecular typing assay for use in a forensic investigation, using Wheat streak mosaic virus (WSMV) as a model plant virus.</p><p><strong>Method: </strong>This genotyping technique utilizes single base primer extension to generate a genetic fingerprint. Fifteen single nucleotide polymorphisms (SNPs) within the coat protein and helper component-protease genes were selected as the genetic markers for this assay. Assay optimization and sensitivity testing was conducted using synthetic targets. WSMV strains and field isolates were collected from regions around the world and used to evaluate the assay for discrimination. The assay specificity was tested against a panel of near-neighbors consisting of genetic and environmental near-neighbors.</p><p><strong>Result: </strong>Each WSMV strain or field isolate tested produced a unique SNP fingerprint, with the exception of three isolates collected within the same geographic location that produced indistinguishable fingerprints. The results were consistent among replicates, demonstrating the reproducibility of the assay. No SNP fingerprints were generated from organisms included in the near-neighbor panel, suggesting the assay is specific for WSMV. Using synthetic targets, a complete profile could be generated from as low as 7.15 fmoles of cDNA.</p><p><strong>Conclusion: </strong>The molecular typing method presented is one tool that could be incorporated into the forensic science tool box after a thorough validation study. This method incorporates molecular biology techniques that are already well established in research and diagnostic laboratories, allowing for an easy introduction of this method into existing laboratories.</p><p><strong>Keywords: </strong>single nucleotide polymorphisms, genotyping, plant pathology, viruses, microbial forensics, Single base primer extension, SNaPshot Multiplex Kit.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2012-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30624667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Y chromosome and the heartache of males.","authors":"Antti Sajantila","doi":"10.1186/2041-2223-3-9","DOIUrl":"https://doi.org/10.1186/2041-2223-3-9","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":" ","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2012-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40170358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}