Investigative genetics最新文献

{"title":"The iceman cometh.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-3-8","DOIUrl":"https://doi.org/10.1186/2041-2223-3-8","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2012-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30578237","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":"Understanding human evolutionary history: a meeting report of the Swedish Royal Academy of Sciences symposium of modern human genetic variation.","authors":"Joshua M Akey","doi":"10.1186/2041-2223-3-7","DOIUrl":"https://doi.org/10.1186/2041-2223-3-7","url":null,"abstract":"<p><p> A report on the Swedish Royal Academy of Sciences Symposium on Modern Human Genetic Variation. Stockholm, Sweden. January 19-20, 2012.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 ","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2012-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30525368","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":"Development of a fast PCR protocol enabling rapid generation of AmpFℓSTR® Identifiler® profiles for genotyping of human DNA.","authors":"Amanda Foster,&nbsp;Nancy Laurin","doi":"10.1186/2041-2223-3-6","DOIUrl":"https://doi.org/10.1186/2041-2223-3-6","url":null,"abstract":"<p><strong>Background: </strong>Traditional PCR methods for forensic STR genotyping require approximately 2.5 to 4 hours to complete, contributing a significant portion of the time required to process forensic DNA samples. The purpose of this study was to develop and validate a fast PCR protocol that enabled amplification of the 16 loci targeted by the AmpFℓSTR® Identifiler® primer set, allowing decreased cycling times.</p><p><strong>Methods: </strong>Fast PCR conditions were achieved by substituting the traditional Taq polymerase for SpeedSTAR™ HS DNA polymerase which is designed for fast PCR, by upgrading to a thermal cycler with faster temperature ramping rates and by modifying cycling parameters (less time at each temperature) and adopting a two-step PCR approach.</p><p><strong>Results: </strong>The total time required for the optimized protocol is 26 min. A total of 147 forensically relevant DNA samples were amplified using the fast PCR protocol for Identifiler. Heterozygote peak height ratios were not affected by fast PCR conditions, and full profiles were generated for single-source DNA amounts between 0.125 ng and 2.0 ng. Individual loci in profiles produced with the fast PCR protocol exhibited average n-4 stutter percentages ranging from 2.5 ± 0.9% (THO1) to 9.9 ± 2.7% (D2S1338). No increase in non-adenylation or other amplification artefacts was observed. Minor contributor alleles in two-person DNA mixtures were reliably discerned. Low level cross-reactivity (monomorphic peaks) was observed with some domestic animal DNA.</p><p><strong>Conclusions: </strong>The fast PCR protocol presented offers a feasible alternative to current amplification methods and could aid in reducing the overall time in STR profile production or could be incorporated into a fast STR genotyping procedure for time-sensitive situations.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":" ","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2012-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40144317","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 unexpected always happens.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-3-5","DOIUrl":"10.1186/2041-2223-3-5","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 ","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2012-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3298498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30479752","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: of horses and genes'.","authors":"Manfred Kayser","doi":"10.1186/2041-2223-3-4","DOIUrl":"https://doi.org/10.1186/2041-2223-3-4","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 ","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2012-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30464843","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":"Response to: Use of prior odds for missing persons identifications - authors' reply.","authors":"Bruce Budowle,&nbsp;Jianye Ge,&nbsp;Ranajit Chakraborty,&nbsp;Harrell Gill-King","doi":"10.1186/2041-2223-3-3","DOIUrl":"https://doi.org/10.1186/2041-2223-3-3","url":null,"abstract":"<p><p> Please see related article: http://www.investigativegenetics.com/content/3/1/2.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2012-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30425965","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":"Reply to Budowle, Ge, Chakraborty and Gill-King: use of prior odds for missing persons identifications.","authors":"Alex Biedermann,&nbsp;Franco Taroni,&nbsp;Pierre Margot","doi":"10.1186/2041-2223-3-2","DOIUrl":"https://doi.org/10.1186/2041-2223-3-2","url":null,"abstract":"<p><p> 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., published recently in this journal. Contrary to Budowle et al., 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 guidelines edited by the forensic DNA community--as long as probability is properly considered as an expression of personal belief.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2012-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30425616","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":"Developing criteria and data to determine best options for expanding the core CODIS loci.","authors":"Jianye Ge,&nbsp;Arthur Eisenberg,&nbsp;Bruce Budowle","doi":"10.1186/2041-2223-3-1","DOIUrl":"https://doi.org/10.1186/2041-2223-3-1","url":null,"abstract":"<p><strong>Background: </strong>Recently, the Combined DNA Index System (CODIS) Core Loci Working Group established by the US Federal Bureau of Investigation (FBI) reviewed and recommended changes to the CODIS core loci. The Working Group identified 20 short tandem repeat (STR) loci (composed of the original CODIS core set loci (minus TPOX), four European recommended loci, PentaE, and DYS391) plus the Amelogenin marker as the new core set. Before selecting and finalizing the core loci, some evaluations are needed to provide guidance for the best options of core selection.</p><p><strong>Method: </strong>The performance of current and newly proposed CODIS core loci sets were evaluated with simplified analyses for adventitious hit rates in reasonably large datasets under single-source profile comparisons, mixture comparisons and kinship searches, and for international data sharing. Informativeness (for example, match probability, average kinship index (AKI)) and mutation rates of each locus were some of the criteria to consider for loci selection. However, the primary factor was performance with challenged forensic samples.</p><p><strong>Results: </strong>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 perform better. Y-chromosome STR (Y-STR) loci are very useful to trace paternal lineage, deconvolve female and male mixtures, and resolve inconsistencies with Amelogenin typing. The DYS391 locus is of little theoretical or practical use. Combining five or six Y-chromosome STR loci with existing autosomal STR loci can produce 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.</p><p><strong>Conclusion: </strong>A more comprehensive study should be performed to provide the necessary information to decision makers and stakeholders about the construction of a new set of core loci for CODIS. Finally, selection of loci should be driven by the concept that the needs of casework should be supported by the processes of CODIS (or for that matter any forensic DNA database).</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"3 ","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2012-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-3-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30370940","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":"Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing.","authors":"Johanna Maria de Gruijter,&nbsp;Oscar Lao,&nbsp;Mark Vermeulen,&nbsp;Yali Xue,&nbsp;Cara Woodwark,&nbsp;Christopher J Gillson,&nbsp;Alison J Coffey,&nbsp;Qasim Ayub,&nbsp;S Qasim Mehdi,&nbsp;Manfred Kayser,&nbsp;Chris Tyler-Smith","doi":"10.1186/2041-2223-2-24","DOIUrl":"https://doi.org/10.1186/2041-2223-2-24","url":null,"abstract":"<p><strong>Background: </strong>Numerous genome-wide scans conducted by genotyping previously ascertained single-nucleotide polymorphisms (SNPs) have provided candidate signatures for 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 resequencing data. Four genes (oculocutaneous albinism II (OCA2), tyrosinase-related protein 1 (TYRP1), dopachrome tautomerase (DCT), and KIT ligand (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 to 6.7 kb of DNA from each of these genes in Africans, Europeans, East Asians, and South Asians.</p><p><strong>Results: </strong>Applying all commonly used neutrality-test statistics for allele frequency distribution to the newly generated sequence data provided conflicting results regarding evidence for positive selection. Previous haplotype-based findings could not be clearly confirmed. Although some tests were marginally significant for some populations and genes, none of them were significant after multiple-testing correction. Combined P values for each gene-population pair did not improve these results. Application of Approximate Bayesian Computation Markov chain Monte Carlo based 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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 1","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-24","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30296308","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":"Appy christmas.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-2-25","DOIUrl":"https://doi.org/10.1186/2041-2223-2-25","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"2 ","pages":"25"},"PeriodicalIF":0.0,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-2-25","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30296065","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}