Investigative genetics最新文献

{"title":"Rapid DNA analysis for automated processing and interpretation of low DNA content samples","authors":"Rosemary S. Turingan, S. Vasantgadkar, L. Palombo, Catherine Hogan, Hua Jiang, Eugene Tan, R. Selden","doi":"10.1186/s13323-016-0033-7","DOIUrl":"https://doi.org/10.1186/s13323-016-0033-7","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-016-0033-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65844659","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":"Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements","authors":"K. Voskarides, S. Mazières, Despina Hadjipanagi, J. Di Cristofaro, Anastasia Ignatiou, Charalambos Stefanou, Roy J. King, P. Underhill, J. Chiaroni, C. Deltas","doi":"10.1186/s13323-016-0032-8","DOIUrl":"https://doi.org/10.1186/s13323-016-0032-8","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-016-0032-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65844611","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":"Tracing Jomon and Yayoi ancestries in Japan using ALDH2 and JC virus genotype distributions","authors":"Daisuke Miyamori, N. Ishikawa, Nozomi Idota, Yasuhiro Kakiuchi, S. McLean, T. Kitamura, H. Ikegaya","doi":"10.1186/s13323-015-0031-1","DOIUrl":"https://doi.org/10.1186/s13323-015-0031-1","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0031-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65844599","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":"Early modern human dispersal from Africa: genomic evidence for multiple waves of migration.","authors":"Francesca Tassi, Silvia Ghirotto, Massimo Mezzavilla, Sibelle Torres Vilaça, Lisa De Santi, Guido Barbujani","doi":"10.1186/s13323-015-0030-2","DOIUrl":"10.1186/s13323-015-0030-2","url":null,"abstract":"<p><strong>Background: </strong>Anthropological and genetic data agree in indicating the African continent as the main place of origin for anatomically modern humans. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Oceania, and later through a northern route crossing the Levant.</p><p><strong>Results: </strong>Here, we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of either hybridization with archaic human forms in Australo-Melanesia or back migration from Europe into Africa. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes.</p><p><strong>Conclusions: </strong>We conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 1","pages":"13"},"PeriodicalIF":0.0,"publicationDate":"2015-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65844573","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":"Erratum to: 'Mutiny on the Bounty': the genetic history of Norfolk Island reveals extreme gender-biased admixture.","authors":"Miles C Benton,&nbsp;Shani Stuart,&nbsp;Claire Bellis,&nbsp;Donia Macartney-Coxson,&nbsp;David Eccles,&nbsp;Joanne E Curran,&nbsp;Geoff Chambers,&nbsp;John Blangero,&nbsp;Rod A Lea,&nbsp;Lyn R Griffiths","doi":"10.1186/s13323-015-0029-8","DOIUrl":"https://doi.org/10.1186/s13323-015-0029-8","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1186/s13323-015-0028-9.]. </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"12"},"PeriodicalIF":0.0,"publicationDate":"2015-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0029-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34073808","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":"'Mutiny on the Bounty': the genetic history of Norfolk Island reveals extreme gender-biased admixture.","authors":"Miles C Benton,&nbsp;Shani Stuart,&nbsp;Claire Bellis,&nbsp;Donia Macartney-Coxson,&nbsp;David Eccles,&nbsp;Joanne E Curran,&nbsp;Geoff Chambers,&nbsp;John Blangero,&nbsp;Rod A Lea,&nbsp;Lyn R Grffiths","doi":"10.1186/s13323-015-0028-9","DOIUrl":"https://doi.org/10.1186/s13323-015-0028-9","url":null,"abstract":"<p><strong>Background: </strong>The Pacific Oceania region was one of the last regions of the world to be settled via human migration. Here we outline a settlement of this region that has given rise to a uniquely admixed population. The current Norfolk Island population has arisen from a small number of founders with mixed Caucasian and Polynesian ancestry, descendants of a famous historical event. The 'Mutiny on the Bounty' has been told in history books, songs and the big screen, but recently this story can be portrayed through comprehensive molecular genetics. Written history details betrayal and murder leading to the founding of Pitcairn Island by European mutineers and the Polynesian women who left Tahiti with them. Investigation of detailed genealogical records supports historical accounts.</p><p><strong>Findings: </strong>Using genetics, we show distinct maternal Polynesian mitochondrial lineages in the present day population, as well as a European centric Y-chromosome phylogeny. These results comprehensively characterise the unique gender-biased admixture of this genetic isolate and further support the historical records relating to Norfolk Island.</p><p><strong>Conclusions: </strong>Our results significantly refine previous population genetic studies investigating Polynesian versus Caucasian diversity in the Norfolk Island population and add information that is beneficial to future disease and gene mapping studies.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"11"},"PeriodicalIF":0.0,"publicationDate":"2015-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0028-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34044370","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":"pSTR Finder: a rapid method to discover polymorphic short tandem repeat markers from whole-genome sequences.","authors":"James Chun-I Lee,&nbsp;Bill Tseng,&nbsp;Bing-Ching Ho,&nbsp;Adrian Linacre","doi":"10.1186/s13323-015-0027-x","DOIUrl":"https://doi.org/10.1186/s13323-015-0027-x","url":null,"abstract":"<p><strong>Background: </strong>Whole-genome sequencing is performed routinely as a means to identify polymorphic genetic loci such as short tandem repeat loci. We have developed a simple tool, called pSTR Finder, which is freely available as a means of identifying putative polymorphic short tandem repeat (STR) loci from data generated from genome-wide sequences. The program performs cross comparisons on the STR sequences generated using the Tandem Repeats Finder based on multiple-genome samples in a FASTA format. These comparisons generate reports listing identical, polymorphic, and different STR loci when comparing two samples.</p><p><strong>Methods: </strong>The web site http://forensic.mc.ntu.edu.tw:9000/PSTRWeb/Default has been developed as a means to identify polymorphic STR loci within complex mass genome sequences. The program was developed to generate a series of user-friendly reports.</p><p><strong>Results: </strong>As proof of concept for the program, four FASTA genome sequence samples of human chromosome X (AC_000155.1, CM000685.1, NC_018934.2, and CM000274.1) were obtained from GenBank and were analyzed for the presence of putative STR regions. The sequences within AC-000155.1 were used as an initial reference sequence from which there were 5443 identical and 4305 polymorphic STR loci identified using a repeat unit of 1-6 and 10 bp as the flanking sequence either side of the putative STR loci. A reliability test was used to compare five FASTA samples, which had sections of DNA sequence removed to mimic partial or fragmented DNA sequences, to determine whether pSTR Finder can efficiently and consistently find identical, polymorphic, and different STR loci.</p><p><strong>Conclusions: </strong>From the mass of DNA sequence data, the project was found to reproducibly identify polymorphic STR loci and generate user-friendly reports detailing the number and location of these potential polymorphic loci. This freely available program was found to be a useful tool to find polymorphic STR within whole-genome sequence data in forensic genetic studies.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2015-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0027-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34069113","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 case of false mother included with 46 autosomal STR markers.","authors":"Li Li,&nbsp;Yuan Lin,&nbsp;Yan Liu,&nbsp;Ruxin Zhu,&nbsp;Zhenmin Zhao,&nbsp;Tingzhi Que","doi":"10.1186/s13323-015-0026-y","DOIUrl":"https://doi.org/10.1186/s13323-015-0026-y","url":null,"abstract":"<p><strong>Background: </strong>For solving a maternity case, 19 autosomal short tandem repeats (STRs) were amplified using the AmpFℓSTR(®) Sinofiler(TM) kit and PowerPlex(®) 16 System. Additional 27 autosomal STR loci were analyzed using two domestic kits AGCU 21+1 and STRtyper-10G. The combined maternity index (CMI) was calculated to be 3.3 × 10(13), but the putative mother denied that she had given birth to the child. In order to reach an accurate conclusion, further testing of 20 X-chromosomal short tandem repeats (X-STRs), 40 single nucleotide polymorphism (SNP) loci, and mitochondrial DNA (mtDNA) was carried out.</p><p><strong>Findings: </strong>The putative mother and the boy shared at least one allele at all 46 tested autosomal STR loci. But, according to the profile data of 20 X-STR and 40 SNP markers, different genotypes at 13 X-STR loci and five SNP loci excluded maternity. Mitochondrial profiles also clearly excluded the mother as a parent of the son because they have multiple differences. It was finally found that the putative mother is the sister of the biological father.</p><p><strong>Conclusions: </strong>Different kinds of genetic markers needfully supplement the use of autosomal STR loci in case where the putative parent is suspected to be related to the true parent.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0026-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34257139","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":"Evaluating the Y chromosomal STR dating in deep-rooting pedigrees.","authors":"Chuan-Chao Wang,&nbsp;Hui Li","doi":"10.1186/s13323-015-0025-z","DOIUrl":"https://doi.org/10.1186/s13323-015-0025-z","url":null,"abstract":"<p><strong>Background: </strong>Y chromosomal short tandem repeat (STR) has been used in time estimations for single nucleotide polymorphism (SNP) lineages or eminent persons. But to choose which mutation rate and estimation method in the Y chromosome dating is controversial, since different rates and methods can result in several-fold deviation.</p><p><strong>Findings: </strong>We used two deep-rooting pedigrees with full records and reliable dates to directly evaluate the Y chromosomal STR mutation rates and dating methods. We found that the Y chromosomal genealogical mutation rates (OMRB and lmMR) in BATWING method can give the best-fit estimation for historical lineage dating.</p><p><strong>Conclusions: </strong>This study validated a very efficient and reliable way for genealogy and historical anthropology researches.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2015-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0025-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33374539","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":"Re-inventing ancient human DNA.","authors":"Michael Knapp,&nbsp;Carles Lalueza-Fox,&nbsp;Michael Hofreiter","doi":"10.1186/s13323-015-0020-4","DOIUrl":"https://doi.org/10.1186/s13323-015-0020-4","url":null,"abstract":"<p><p>For a long time, the analysis of ancient human DNA represented one of the most controversial disciplines in an already controversial field of research. Scepticism in this field was only matched by the long-lasting controversy over the authenticity of ancient pathogen DNA. This ambiguous view on ancient human DNA had a dichotomous root. On the one hand, the interest in ancient human DNA is great because such studies touch on the history and evolution of our own species. On the other hand, because these studies are dealing with samples from our own species, results are easily compromised by contamination of the experiments with modern human DNA, which is ubiquitous in the environment. Consequently, some of the most disputed studies published - apart maybe from early reports on million year old dinosaur or amber DNA - reported DNA analyses from human subfossil remains. However, the development of so-called next- or second-generation sequencing (SGS) in 2005 and the technological advances associated with it have generated new confidence in the genetic study of ancient human remains. The ability to sequence shorter DNA fragments than with PCR amplification coupled to traditional Sanger sequencing, along with very high sequencing throughput have both reduced the risk of sequencing modern contamination and provided tools to evaluate the authenticity of DNA sequence data. The field is now rapidly developing, providing unprecedented insights into the evolution of our own species and past human population dynamics as well as the evolution and history of human pathogens and epidemics. Here, we review how recent technological improvements have rapidly transformed ancient human DNA research from a highly controversial subject to a central component of modern anthropological research. We also discuss potential future directions of ancient human DNA research. </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"6 ","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2015-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13323-015-0020-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33272125","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}