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Investigative Genetics

Rosemary S Turingan, Sameer Vasantgadkar, Luke Palombo, Catherine Hogan, Hua Jiang, Eugene Tan, Richard F Selden
BACKGROUND: Short tandem repeat (STR) analysis of casework samples with low DNA content include those resulting from the transfer of epithelial cells from the skin to an object (e.g., cells on a water bottle, or brim of a cap), blood spatter stains, and small bone and tissue fragments. Low DNA content (LDC) samples are important in a wide range of settings, including disaster response teams to assist in victim identification and family reunification, military operations to identify friend or foe, criminal forensics to identify suspects and exonerate the innocent, and medical examiner and coroner offices to identify missing persons...
2016: Investigative Genetics
Konstantinos Voskarides, Stéphane Mazières, Despina Hadjipanagi, Julie Di Cristofaro, Anastasia Ignatiou, Charalambos Stefanou, Roy J King, Peter A Underhill, Jacques Chiaroni, Constantinos Deltas
BACKGROUND: The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization. RESULTS: Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA)...
2016: Investigative Genetics
Daisuke Miyamori, Noboru Ishikawa, Nozomi Idota, Yasuhiro Kakiuchi, Stuart McLean, Tadaichi Kitamura, Hiroshi Ikegaya
BACKGROUND: According to the dual structure model, the modern Japanese ethnic population consists of a mixture of the Jomon people, who have existed in Japan since at least the New Stone Age, and the Yayoi people, who migrated to western Japan from China around the year 300 bc Some reports show that the Yayoi are linked to a mutation of the aldehyde dehydrogenase 2 gene (ALDH2). Recent viral studies indicate two major groups found in the Japanese population: a group with the CY genotype JC virus (JCV) and a group with the MY genotype JCV...
2015: Investigative Genetics
Francesca Tassi, Silvia Ghirotto, Massimo Mezzavilla, Sibelle Torres Vilaça, Lisa De Santi, Guido Barbujani
BACKGROUND: 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. RESULTS: 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...
2015: Investigative Genetics
Miles C Benton, Shani Stuart, Claire Bellis, Donia Macartney-Coxson, David Eccles, Joanne E Curran, Geoff Chambers, John Blangero, Rod A Lea, Lyn R Griffiths
[This corrects the article DOI: 10.1186/s13323-015-0028-9.].
2015: Investigative Genetics
Miles C Benton, Shani Stuart, Claire Bellis, Donia Macartney-Coxson, David Eccles, Joanne E Curran, Geoff Chambers, John Blangero, Rod A Lea, Lyn R Grffiths
BACKGROUND: 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...
2015: Investigative Genetics
James Chun-I Lee, Bill Tseng, Bing-Ching Ho, Adrian Linacre
BACKGROUND: 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...
2015: Investigative Genetics
Li Li, Yuan Lin, Yan Liu, Ruxin Zhu, Zhenmin Zhao, Tingzhi Que
BACKGROUND: 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...
2015: Investigative Genetics
Chuan-Chao Wang, Hui Li
BACKGROUND: 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. FINDINGS: We used two deep-rooting pedigrees with full records and reliable dates to directly evaluate the Y chromosomal STR mutation rates and dating methods...
2015: Investigative Genetics
Andreas Wollstein, Oscar Lao
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...
2015: Investigative Genetics
Michael Knapp, Carles Lalueza-Fox, Michael Hofreiter
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...
2015: Investigative Genetics
Irina Pugach, Mark Stoneking
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...
2015: Investigative Genetics
Andreas Wollstein, Wolfgang Stephan
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...
2015: Investigative Genetics
Toomas Kivisild
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...
2015: Investigative Genetics
Kenneth K Kidd, William C Speed
BACKGROUND: 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...
2015: Investigative Genetics
Mark A Jobling
No abstract text is available yet for this article.
2015: Investigative Genetics
Mark A Jobling
No abstract text is available yet for this article.
January 22, 2014: Investigative Genetics
Antti Sajantila
No abstract text is available yet for this article.
2014: Investigative Genetics
Silvana R Tridico, Dáithí C Murray, Jayne Addison, Kenneth P Kirkbride, Michael Bunce
BACKGROUND: 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...
2014: Investigative Genetics
Anahit Hovhannisyan, Zaruhi Khachatryan, Marc Haber, Peter Hrechdakian, Tatiana Karafet, Pierre Zalloua, Levon Yepiskoposyan
BACKGROUND: 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...
2014: Investigative Genetics
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