Investigative genetics最新文献

{"title":"Next-generation sequencing technologies and applications for human genetic history and forensics.","authors":"Eva C Berglund,&nbsp;Anna Kiialainen,&nbsp;Ann-Christine Syvänen","doi":"10.1186/2041-2223-2-23","DOIUrl":"10.1186/2041-2223-2-23","url":null,"abstract":"<p><p> 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.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 ","pages":"23"},"PeriodicalIF":0.0,"publicationDate":"2011-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-23","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30279309","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":"Policy implications for familial searching.","authors":"Joyce Kim,&nbsp;Danny Mammo,&nbsp;Marni B Siegel,&nbsp;Sara H Katsanis","doi":"10.1186/2041-2223-2-22","DOIUrl":"https://doi.org/10.1186/2041-2223-2-22","url":null,"abstract":"<p><p> 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.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":" ","pages":"22"},"PeriodicalIF":0.0,"publicationDate":"2011-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-22","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40117188","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":"Father figures.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-2-21","DOIUrl":"https://doi.org/10.1186/2041-2223-2-21","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 ","pages":"21"},"PeriodicalIF":0.0,"publicationDate":"2011-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-21","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30192031","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 identification of the Romanovs: Can we (finally) put the controversies to rest?","authors":"Michael D Coble","doi":"10.1186/2041-2223-2-20","DOIUrl":"https://doi.org/10.1186/2041-2223-2-20","url":null,"abstract":"<p><p> 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.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 1","pages":"20"},"PeriodicalIF":0.0,"publicationDate":"2011-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-20","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30016946","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":"Review of \"Haldane, Mayr, and Beanbag Genetics\" by Krishna Dronamraju","authors":"Ken Weiss","doi":"10.1186/2041-2223-2-19","DOIUrl":"https://doi.org/10.1186/2041-2223-2-19","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 1","pages":"19 - 19"},"PeriodicalIF":0.0,"publicationDate":"2011-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-19","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65700179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Baron's complaint.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-2-18","DOIUrl":"https://doi.org/10.1186/2041-2223-2-18","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 ","pages":"18"},"PeriodicalIF":0.0,"publicationDate":"2011-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-18","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30085772","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":"Long-term room temperature preservation of corpse soft tissue: an approach for tissue sample storage.","authors":"Mariela Caputo,&nbsp;Luis A Bosio,&nbsp;Daniel Corach","doi":"10.1186/2041-2223-2-17","DOIUrl":"https://doi.org/10.1186/2041-2223-2-17","url":null,"abstract":"<p><strong>Background: </strong>Disaster victim identification (DVI) represents one of the most difficult challenges in forensic sciences, and subsequent DNA typing is essential. Collected samples for DNA-based human identification are usually stored at low temperature to halt the degradation processes of human remains. We have developed a simple and reliable procedure for soft tissue storage and preservation for DNA extraction. It ensures high quality DNA suitable for PCR-based DNA typing after at least 1 year of room temperature storage.</p><p><strong>Methods: </strong>Fragments of human psoas muscle were exposed to three different environmental conditions for diverse time periods at room temperature. Storage conditions included: (a) a preserving medium consisting of solid sodium chloride (salt), (b) no additional substances and (c) garden soil. DNA was extracted with proteinase K/SDS followed by organic solvent treatment and concentration by centrifugal filter devices. Quantification was carried out by real-time PCR using commercial kits. Short tandem repeat (STR) typing profiles were analysed with 'expert software'.</p><p><strong>Results: </strong>DNA quantities recovered from samples stored in salt were similar up to the complete storage time and underscored the effectiveness of the preservation method. It was possible to reliably and accurately type different genetic systems including autosomal STRs and mitochondrial and Y-chromosome haplogroups. Autosomal STR typing quality was evaluated by expert software, denoting high quality profiles from DNA samples obtained from corpse tissue stored in salt for up to 365 days.</p><p><strong>Conclusions: </strong>The procedure proposed herein is a cost efficient alternative for storage of human remains in challenging environmental areas, such as mass disaster locations, mass graves and exhumations. This technique should be considered as an additional method for sample storage when preservation of DNA integrity is required for PCR-based DNA typing.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 ","pages":"17"},"PeriodicalIF":0.0,"publicationDate":"2011-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-17","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30080619","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":"Feather barbs as a good source of mtDNA for bird species identification in forensic wildlife investigations.","authors":"Camilla F Speller,&nbsp;George P Nicholas,&nbsp;Dongya Y Yang","doi":"10.1186/2041-2223-2-16","DOIUrl":"https://doi.org/10.1186/2041-2223-2-16","url":null,"abstract":"<p><strong>Background: </strong>The ability to accurately identify bird species is crucial for wildlife law enforcement and bird-strike investigations. However, such identifications may be challenging when only partial or damaged feathers are available for analysis.</p><p><strong>Results: </strong>By applying vigorous contamination controls and sensitive PCR amplification protocols, we found that it was feasible to obtain accurate mitochondrial (mt)DNA-based species identification with as few as two feather barbs. This minimally destructive DNA approach was successfully used and tested on a variety of bird species, including North American wild turkey (Meleagris gallopavo), Canada goose (Branta canadensis), blue heron (Ardea herodias) and pygmy owl (Glaucidium californicum). The mtDNA was successfully obtained from 'fresh' feathers, historic museum specimens and archaeological samples, demonstrating the sensitivity and versatility of this technique.</p><p><strong>Conclusions: </strong>By applying appropriate contamination controls, sufficient quantities of mtDNA can be reliably recovered and analyzed from feather barbs. This previously overlooked substrate provides new opportunities for accurate DNA species identification when minimal feather samples are available for forensic analysis.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 ","pages":"16"},"PeriodicalIF":0.0,"publicationDate":"2011-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-16","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30035742","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":"Use of prior odds for missing persons identifications.","authors":"Bruce Budowle,&nbsp;Jianye Ge,&nbsp;Ranajit Chakraborty,&nbsp;Harrell Gill-King","doi":"10.1186/2041-2223-2-15","DOIUrl":"https://doi.org/10.1186/2041-2223-2-15","url":null,"abstract":"<p><p> Identification of missing persons from mass disasters is based on evaluation of a number of variables and observations regarding the combination of features derived from these variables. DNA typing now is playing a more prominent role in the identification of human remains, and particularly so for highly decomposed and fragmented remains. The strength of genetic associations, by either direct or kinship analyses, is often quantified by calculating a likelihood ratio. The likelihood ratio can be multiplied by prior odds based on nongenetic evidence to calculate the posterior odds, that is, by applying Bayes' Theorem, to arrive at a probability of identity. For the identification of human remains, the path creating the set and intersection of variables that contribute to the prior odds needs to be appreciated and well defined. Other than considering the total number of missing persons, the forensic DNA community has been silent on specifying the elements of prior odds computations. The variables include the number of missing individuals, eyewitness accounts, anthropological features, demographics and other identifying characteristics. The assumptions, supporting data and reasoning that are used to establish a prior probability that will be combined with the genetic data need to be considered and justified. Otherwise, data may be unintentionally or intentionally manipulated to achieve a probability of identity that cannot be supported and can thus misrepresent the uncertainty with associations. The forensic DNA community needs to develop guidelines for objectively computing prior odds.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 1","pages":"15"},"PeriodicalIF":0.0,"publicationDate":"2011-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-15","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30270127","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":"Genes and queens.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-2-14","DOIUrl":"https://doi.org/10.1186/2041-2223-2-14","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 1","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2011-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-14","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30209861","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}