Investigative genetics最新文献

{"title":"Detecting individual ancestry in the human genome.","authors":"Andreas Wollstein,&nbsp;Oscar Lao","doi":"10.1186/s13323-015-0019-x","DOIUrl":"https://doi.org/10.1186/s13323-015-0019-x","url":null,"abstract":"<p><p>Detecting and quantifying the population substructure present in a sample of individuals are of main interest in the fields of genetic epidemiology, population genetics, and forensics among others. To date, several algorithms have been proposed for estimating the amount of genetic ancestry within an individual. In the present review, we introduce the most widely used methods in population genetics for detecting individual genetic ancestry. We further show, by means of simulations, the performance of popular algorithms for detecting individual ancestry in various controlled demographic scenarios. Finally, we provide some hints on how to interpret the results from these algorithms. </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2015-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0019-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33272124","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":"Inferring positive selection in humans from genomic data.","authors":"Andreas Wollstein,&nbsp;Wolfgang Stephan","doi":"10.1186/s13323-015-0023-1","DOIUrl":"https://doi.org/10.1186/s13323-015-0023-1","url":null,"abstract":"<p><p>Adaptation can be described as an evolutionary process that leads to an adjustment of the phenotypes of a population to their environment. In the classical view, new mutations can introduce novel phenotypic features into a population that leave footprints in the genome after fixation, such as selective sweeps. Alternatively, existing genetic variants may become beneficial after an environmental change and increase in frequency. Although they may not reach fixation, they may cause a shift of the optimum of a phenotypic trait controlled by multiple loci. With the availability of polymorphism data from various organisms, including humans and chimpanzees, it has become possible to detect molecular evidence of adaptation and to estimate the strength and target of positive selection. In this review, we discuss the two competing models of adaptation and suitable approaches for detecting the footprints of positive selection on the molecular level. </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2015-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0023-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33183091","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":"Genome-wide insights into the genetic history of human populations.","authors":"Irina Pugach,&nbsp;Mark Stoneking","doi":"10.1186/s13323-015-0024-0","DOIUrl":"https://doi.org/10.1186/s13323-015-0024-0","url":null,"abstract":"<p><p>Although mtDNA and the non-recombining Y chromosome (NRY) studies continue to provide valuable insights into the genetic history of human populations, recent technical, methodological and computational advances and the increasing availability of large-scale, genome-wide data from contemporary human populations around the world promise to reveal new aspects, resolve finer points, and provide a more detailed look at our past demographic history. Genome-wide data are particularly useful for inferring migrations, admixture, and fine structure, as well as for estimating population divergence and admixture times and fluctuations in effective population sizes. In this review, we highlight some of the stories that have emerged from the analyses of genome-wide SNP genotyping data concerning the human history of Southern Africa, India, Oceania, Island South East Asia, Europe and the Americas and comment on possible future study directions. We also discuss advantages and drawbacks of using SNP-arrays, with a particular focus on the ascertainment bias, and ways to circumvent it. </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2015-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0024-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33183092","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":"Maternal ancestry and population history from whole mitochondrial genomes.","authors":"Toomas Kivisild","doi":"10.1186/s13323-015-0022-2","DOIUrl":"https://doi.org/10.1186/s13323-015-0022-2","url":null,"abstract":"<p><p>MtDNA has been a widely used tool in human evolutionary and population genetic studies over the past three decades. Its maternal inheritance and lack of recombination have offered the opportunity to explore genealogical relationships among individuals and to study the frequency differences of matrilineal clades among human populations at continental and regional scales. The whole mtDNA genome sequencing delivers molecular resolution that is sufficient to distinguish patterns that have arisen over thousands of years. However, mutation rate is highly variable among the functional and non-coding domains of mtDNA which makes it challenging to obtain accurate split dates of the mitochondrial clades. Due to the shallow coalescent time of mitochondrial TMRCA at approximately 100 to 200 thousand years (ky), mtDNA data have only limited power to inform us about the more distant past and the early stages of human evolutionary history. The variation shared by mitochondrial genomes of individuals drawn from different continents outside Africa has been used to illuminate the details of the colonization process of the Old World, whereas regional patterns of variation have been at the focus of studies addressing questions of a more recent time scale. In the era of whole nuclear genome sequencing, mitochondrial genomes are continuing to be informative as a unique tool for the assessment of female-specific aspects of the demographic history of human populations. </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2015-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0022-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33151693","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":"On the nose: genetic and evolutionary aspects of smell.","authors":"Mark A Jobling","doi":"10.1186/s13323-015-0021-3","DOIUrl":"https://doi.org/10.1186/s13323-015-0021-3","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2015-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0021-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33063315","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":"Criteria for selecting microhaplotypes: mixture detection and deconvolution.","authors":"Kenneth K Kidd,&nbsp;William C Speed","doi":"10.1186/s13323-014-0018-3","DOIUrl":"https://doi.org/10.1186/s13323-014-0018-3","url":null,"abstract":"<p><strong>Background: </strong>DNA sequencing is likely to become a standard typing method in forensics in the near future. We define a microhaplotype to be a locus with two or more single nucleotide polymorphisms (SNPs) that occur within a short segment of DNA (e.g., 200 bp) that can be covered by a single sequence run and collectively define a multiallelic locus. Microhaplotypes can be highly informative for many forensic questions, including detection of mixtures of two or more sources in a DNA sample, a common problem in forensic practice.</p><p><strong>Results: </strong>When all alleles are equally frequent, the probability of detecting three or more alleles in a mixture is at maximum. The classical population genetics concept of effective number of alleles at a locus, termed Ae, converts the unequal allele frequencies at a locus into a value that is equivalent to some number of equally frequent alleles, allowing microhaplotype loci to be ranked. The expectations for the ability to qualitatively detect mixtures are given for different integer values of Ae, and the cumulative probabilities of detecting mixtures based on testing multiple microhaps are shown to exceed 95% with as few as five loci with average Ae values of even slightly greater than 3.0.</p><p><strong>Conclusions: </strong>Microhaplotypes with Ae values of >3 will be exceedingly useful in ordinary forensic practice. Based on our studies, 3-SNP microhaplotypes will sometimes meet this criterion, but 4-SNP microhaplotypes can even exceed this criterion and have values >4.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2015-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-014-0018-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33113132","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: Contamination has always been the issue!","authors":"Antti Sajantila","doi":"10.1186/s13323-014-0017-4","DOIUrl":"https://doi.org/10.1186/s13323-014-0017-4","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 1","pages":"106"},"PeriodicalIF":0.0,"publicationDate":"2014-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-014-0017-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32943576","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":"Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science.","authors":"Silvana R Tridico, Dáithí C Murray, Jayne Addison, Kenneth P Kirkbride, Michael Bunce","doi":"10.1186/s13323-014-0016-5","DOIUrl":"10.1186/s13323-014-0016-5","url":null,"abstract":"<p><strong>Background: </strong>Mammalian hairs are one of the most ubiquitous types of trace evidence collected in the course of forensic investigations. However, hairs that are naturally shed or that lack roots are problematic substrates for DNA profiling; these hair types often contain insufficient nuclear DNA to yield short tandem repeat (STR) profiles. Whilst there have been a number of initial investigations evaluating the value of metagenomics analyses for forensic applications (e.g. examination of computer keyboards), there have been no metagenomic evaluations of human hairs-a substrate commonly encountered during forensic practice. This present study attempts to address this forensic capability gap, by conducting a qualitative assessment into the applicability of metagenomic analyses of human scalp and pubic hair.</p><p><strong>Results: </strong>Forty-two DNA extracts obtained from human scalp and pubic hairs generated a total of 79,766 reads, yielding 39,814 reads post control and abundance filtering. The results revealed the presence of unique combinations of microbial taxa that can enable discrimination between individuals and signature taxa indigenous to female pubic hairs. Microbial data from a single co-habiting couple added an extra dimension to the study by suggesting that metagenomic analyses might be of evidentiary value in sexual assault cases when other associative evidence is not present.</p><p><strong>Conclusions: </strong>Of all the data generated in this study, the next-generation sequencing (NGS) data generated from pubic hair held the most potential for forensic applications. Metagenomic analyses of human hairs may provide independent data to augment other forensic results and possibly provide association between victims of sexual assault and offender when other associative evidence is absent. Based on results garnered in the present study, we believe that with further development, bacterial profiling of hair will become a valuable addition to the forensic toolkit.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 1","pages":"16"},"PeriodicalIF":0.0,"publicationDate":"2014-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32913790","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":"Different waves and directions of Neolithic migrations in the Armenian Highland.","authors":"Anahit Hovhannisyan,&nbsp;Zaruhi Khachatryan,&nbsp;Marc Haber,&nbsp;Peter Hrechdakian,&nbsp;Tatiana Karafet,&nbsp;Pierre Zalloua,&nbsp;Levon Yepiskoposyan","doi":"10.1186/s13323-014-0015-6","DOIUrl":"https://doi.org/10.1186/s13323-014-0015-6","url":null,"abstract":"<p><strong>Background: </strong>The peopling of Europe and the nature of the Neolithic agricultural migration as a primary issue in the modern human colonization of the globe is still widely debated. At present, much uncertainty is associated with the reconstruction of the routes of migration for the first farmers from the Near East. In this context, hospitable climatic conditions and the key geographic position of the Armenian Highland suggest that it may have served as a conduit for several waves of expansion of the first agriculturalists from the Near East to Europe and the North Caucasus.</p><p><strong>Results: </strong>Here, we assess Y-chromosomal distribution in six geographically distinct populations of Armenians that roughly represent the extent of historical Armenia. Using the general haplogroup structure and the specific lineages representing putative genetic markers of the Neolithic Revolution, haplogroups R1b1a2, J2, and G, we identify distinct patterns of genetic affinity between the populations of the Armenian Highland and the neighboring ones north and west from this area.</p><p><strong>Conclusions: </strong>Based on the results obtained, we suggest a new insight on the different routes and waves of Neolithic expansion of the first farmers through the Armenian Highland. We detected at least two principle migratory directions: (1) westward alongside the coastline of the Mediterranean Sea and (2) northward to the North Caucasus.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 1","pages":"15"},"PeriodicalIF":0.0,"publicationDate":"2014-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-014-0015-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32862431","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":"Trouble at the races.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-5-14","DOIUrl":"https://doi.org/10.1186/2041-2223-5-14","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 ","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2014-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-5-14","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32775706","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}