scholarly journals Exploring STR sequencing for forensic DNA intelligence databasing using the Austrian National DNA Database as an example

2021 ◽  
Author(s):  
Petra Hölzl-Müller ◽  
Martin Bodner ◽  
Burkhard Berger ◽  
Walther Parson
Keyword(s):  
Tandem Repeats ◽  
Massively Parallel Sequencing ◽  
Population Data ◽  
The Body ◽  
Backward Compatibility ◽  
Dna Database ◽  
Autosomal Str ◽  
Online Catalogue ◽  
Austrian Population ◽  
High Degree

AbstractHere, we present the results from a population study that evaluated the performance of massively parallel sequencing (MPS) of short tandem repeats (STRs) with a particular focus on DNA intelligence databasing purposes. To meet this objective, 247 randomly selected reference samples, earlier being processed with conventional capillary electrophoretic (CE) STR sizing from the Austrian National DNA Database, were reanalyzed with the PowerSeq 46Y kit (Promega). This sample set provides MPS-based population data valid for the Austrian population to increase the body of sequence-based STR variation. The study addressed forensically relevant parameters, such as concordance and backward compatibility to extant amplicon-based genotypes, sequence-based stutter ratios, and relative marker performance. Of the 22 autosomal STR loci included in the PowerSeq 46GY panel, 99.98% of the allele calls were concordant between MPS and CE. Moreover, 25 new sequence variants from 15 markers were found in the Austrian dataset that are yet undescribed in the STRSeq online catalogue and were submitted for inclusion. Despite the high degree of concordance between MPS and CE derived genotypes, our results demonstrate the need for a harmonized allele nomenclature system that is equally applicable to both technologies, but at the same time can take advantage of the increased information content of MPS. This appears to be particularly important with regard to database applications in order to prevent false exclusions due to varying allele naming based on different analysis platforms and ensures backward compatibility.

scholarly journals Massively parallel sequencing of short tandem repeats—Population data and mixture analysis results for the PowerSeq™ system

2016 ◽  
Vol 24 ◽  
pp. 86-96 ◽  
Author(s):  
Kristiaan J. van der Gaag ◽  
Rick H. de Leeuw ◽  
Jerry Hoogenboom ◽  
Jaynish Patel ◽  
Douglas R. Storts ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Massively Parallel Sequencing ◽  
Population Data ◽  
Massively Parallel ◽  
Mixture Analysis ◽  
Parallel Sequencing ◽  
Short Tandem

scholarly journals Massively parallel sequencing of 25 autosomal STRs including SE33 in four population groups for forensic applications

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ye-Lim Kwon ◽  
Bo Min Kim ◽  
Eun Young Lee ◽  
Kyoung-Jin Shin
Keyword(s):  
Large Scale ◽  
Tandem Repeats ◽  
Massively Parallel Sequencing ◽  
Sequence Data ◽  
Population Data ◽  
Massively Parallel ◽  
Autosomal Strs ◽  
Data Set ◽  
Parallel Sequencing ◽  
Sequence Variations

AbstractThe introduction of massively parallel sequencing (MPS) in forensic investigation enables sequence-based large-scale multiplexing beyond size-based analysis using capillary electrophoresis (CE). For the practical application of MPS to forensic casework, many population studies have provided sequence data for autosomal short tandem repeats (STRs). However, SE33, a highly polymorphic STR marker, has little sequence-based data because of difficulties in analysis. In this study, 25 autosomal STRs were analyzed, including SE33, using an in-house MPS panel for 350 samples from four populations (African–American, Caucasian, Hispanic, and Korean). The barcoded MPS library was generated using a two-step PCR method and sequenced using a MiSeq System. As a result, 99.88% genotype concordance was obtained between length- and sequence-based analyses. In SE33, the most discordances (eight samples, 0.08%) were observed because of the 4 bp deletion between the CE and MPS primer binding sites. Compared with the length-based CE method, the number of alleles increased from 332 to 725 (2.18-fold) for 25 autosomal STRs in the sequence-based MPS method. Notably, additional 129 unique alleles, a 4.15-fold increase, were detected in SE33 by identifying sequence variations. This population data set provides sequence variations and sequence-based allele frequencies for 25 autosomal STRs.

scholarly journals Analysis of allele frequencies of the selected 15 autosomal STR markers in Tikrit population – Iraq with comparison to Middle Eastern, African, and Europeans

2021 ◽  
pp. 75-84
Author(s):  
Maan Hasan Salih ◽  
Akeel Hussain Ali Al-Assie ◽  
Majeed Arsheed Sabbah
Keyword(s):  
Tandem Repeats ◽  
Human Genetics ◽  
Forensic Genetics ◽  
Middle Eastern ◽  
Allele Frequencies ◽  
Match Probability ◽  
Discrimination Power ◽  
Str Loci ◽  
Dna Database ◽  
Autosomal Str

Short tandem repeats (STRs) have been recommended as the highest polymorphic loci among the humana DNA regions. Therefore, STRs are agreeable to many genetic fields like forensic, population genetics and anthropological studies. The main aim of this research is to evaluate the autosomal STRs in Tikrit city-Iraq, to expand the human genetics database and forensic genetics analysis. The DNA database was obtained from 306 unrelated volunteers from native Tikrit population-Iraq, using 15 autosomal STR loci. The current study determined the allele frequencies in the Tikrit population and then compared them with other national Iraqi populations as well as with populations in the Middle East, Africa, and Europe. The highest level of heterozygosity was observed in D8S1179 and TH01 loci (0.797), while the less level was shown by CSF1PO (0.48). The departure from HWE Equilibrium was recorded in only 3 STR loci from a total of 15 loci analyzed (p<0.003). The Combined Match Probability (CMP) for 15 autosomal STR was 1 in 7.89208×10-19 and the Combined Discrimination Power (CDP) was 0.9999999997. The discrimination power (DP) was especially high in D2S1338, D18S51, D19S433 and D21S11. Based on the results observed in a Dendrogram, Tikrit population was clustered with other populations, likely reflecting the historical and geographical factors. D2S1338, D18S51, D19S433 and D21S11 markers were recognized as suitable for forensic genetics analysis in Tikrit population. Also, the 15 STRs markers provide information for the studies of genetic distances between the current study and other included populations to be compared with this study.

scholarly journals Overview of European population clustering based on 23 Y-STR loci

Genetika ◽  
2015 ◽  
Vol 47 (3) ◽  
pp. 901-908 ◽  
Author(s):  
Serkan Dogan ◽  
Adna Asic ◽  
Sanida Buljubasic ◽  
Larisa Besic ◽  
Monia Avdic ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Tandem Repeats ◽  
Population Data ◽  
European Population ◽  
Human Populations ◽  
Str Loci ◽  
Autosomal Str ◽  
Haplotype Data ◽  
Study Population ◽  
Regional Clustering

Short tandem repeats (STRs) located on the Y-chromosome are a useful tool for various scientific fields, such as forensic investigation, but also for the investigation of population structure and molecular history. In this study, population data based on 23 Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) from 23 European human populations were compared. All haplotype data for this research were gathered from previously published articles. Arlequin v3.5.1.2, POPTREE2, and MEGA 5.1 software packages were used for the calculation of allelic frequencies and genetic distance, and the construction of the European, as well as worldwide phylogenetic trees. Obtained results indicate a formation of several distinct sub-clusters within European population cluster. Observed sub-clusters were mostly recognized within geographically closer populations, meaning that neighboring populations were a part of the same sub-cluster in most of the cases. Compared with the previously published results obtained using autosomal STR markers, a significant level of concordance was detected. However, it seems that Y-STRs analyzed in this study are more informative since they enabled regional clustering in addition to continental clustering. Also, the use of a larger number of loci yielded clustering that is more specific than what has been calculated to date. Finally, it can be concluded that this study has shown that the application of a larger number of loci enables the more detailed insight into the relationships between European populations, compared to what has been published before.

The First Autosomal STR Population Data of Kinh Ethinic Group in Vietnam by Using Massively Parallel Sequencing

2021 ◽  
Vol 57 (8) ◽  
pp. 985-988
Author(s):  
N. S. Pham ◽  
H. L. Tran ◽  
T. H. T. Nguyen ◽  
V. H. Nguyen ◽  
H. Hoang ◽  
...  
Keyword(s):  
Massively Parallel Sequencing ◽  
Population Data ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Autosomal Str

scholarly journals Assessment of QIAGEN™ Investigator® 24plex GO! kit workflow for autosomal STR profiling of forensic reference samples

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hashom Mohd Hakim ◽  
Hussein Omar Khan ◽  
Siti Afifah Ismail ◽  
Nurul Hazirah Mat Lazim ◽  
Japareng Lalung ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Dna Profiling ◽  
Buccal Swab ◽  
Forensic Dna ◽  
Str Typing ◽  
Str Analysis ◽  
Dna Database ◽  
Autosomal Str ◽  
Dna Template ◽  
Reference Samples

Abstract Background DNA profiling has proven to be a valuable technique for identification of individuals in crime. Currently, the technique targets several short tandem repeat (STR) regions in human genome. However, increasing number of samples submitted for STR analysis may lead to delays due to the limited number of experienced analysts who might be available at any given moment and the time taken to complete lengthy DNA profiling procedures. This study was conducted to test the specificity, repeatability, reproducibility and robustness of Investigator® 24plex GO! kit for genotyping of reference samples submitted to the Royal Malaysian Police Forensic DNA Laboratory for DNA database. Material and methods In this study, Investigator® 24plex GO! kit was used to directly amplify STR loci from buccal swab cell of reference samples that had previously been STR typed using GlobalFiler™ Express kit. Capillary electrophoresis was carried out on a 3500xL Genetic Analyser using POP-4® Polymer. Amplified products were assigned to particular STR alleles using the GeneMapper ID-X version 1.4 software. Results Our study shows that STR profiles generated using Investigator® 24plex GO! gave concordance results with those previously obtained using the GlobalFiler™ Express kit. In addition, quality sensors included in the kit are of particular importance for determining the effectiveness of the PCR reaction and help to indicate the nature and quantity of DNA template for PCR amplification. Conclusion The Investigator® 24plex GO! kit is reliable for STR typing of reference samples.

scholarly journals mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Bing Song ◽  
August E. Woerner ◽  
John Planz
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Genetic Markers ◽  
Software Package ◽  
Tandem Repeats ◽  
Population Data ◽  
Real Data ◽  
R Package ◽  
Nucleotide Polymorphisms ◽  
Mutual Independence

Abstract Background Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly software is necessary for testing and assessing the global linkage disequilibrium among mixed genetic data. Results This study describes a software package for testing the mutual independence of mixed genetic datasets. Mutual independence is defined as no non-random associations among all subsets of the tested panel. The new R package “mixIndependR” calculates basic genetic parameters like allele frequency, genotype frequency, heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium (LD) by mutual independence from population data, regardless of the type of markers, such as simple nucleotide polymorphisms, short tandem repeats, insertions and deletions, and any other genetic markers. A novel method of assessing the dependence of mixed genetic panels is developed in this study and functionally analyzed in the software package. By comparing the observed distribution of two common summary statistics (the number of heterozygous loci [K] and the number of share alleles [X]) with their expected distributions under the assumption of mutual independence, the overall independence is tested. Conclusion The package “mixIndependR” is compatible to all categories of genetic markers and detects the overall non-random associations. Compared to pairwise disequilibrium, the approach described herein tends to have higher power, especially when number of markers is large. With this package, more multi-functional or stronger genetic panels can be developed, like mixed panels with different kinds of markers. In population genetics, the package “mixIndependR” makes it possible to discover more about admixture of populations, natural selection, genetic drift, and population demographics, as a more powerful method of detecting LD. Moreover, this new approach can optimize variants selection in disease studies and contribute to panel combination for treatments in multimorbidity. Application of this approach in real data is expected in the future, and this might bring a leap in the field of genetic technology. Availability The R package mixIndependR, is available on the Comprehensive R Archive Network (CRAN) at: https://cran.r-project.org/web/packages/mixIndependR/index.html.

The Shroud of Turin

1997 ◽  
Vol 9 (1) ◽  
pp. 121-140
Author(s):  
Thaddeus J. Trenn ◽  
Keyword(s):  
Body Image ◽  
Scientific Evidence ◽  
The Body ◽  
Religious Art ◽  
Satisfactory Explanation ◽  
Marshall Mcluhan ◽  
Modern Age ◽  
Shroud Of Turin ◽  
High Degree ◽  
As If

The Shroud of Turin, a linen cloth with but a faint image, continues to capture the interest of many people of diverse beliefs. Although the measured age of the cloth is relatively recent, other scientific findings indicate an earlier provenance. Any firm conclusions regarding the cloth's history remain premature. No satisfactory explanation has been found as yet for how the image on the cloth was produced structurally or stylistically. Iconographic evidence suggests that the image was the source of facial peculiarities found in early works of religious art. The body image bears a striking yet preternatural correlation with Scriptural accounts of wounds. Curiously, the image on the cloth functions as a photographic negative, exhibiting a high degree of resolution, as if the original were produced in pixels. Despite serious efforts to discover some artistic origin md medium, scientific evidence points in the direction that it was not produced by hands. If it is tme that the medium is the message, as Marshall McLuhan wrote, then the Turin Shroud may be a parable for the modern age.

scholarly journals Large elastic deformations of isotropic materials. I. Fundamental concepts

1948 ◽  
Vol 240 (822) ◽  
pp. 459-490 ◽  
Keyword(s):  
The Body ◽  
Elastic Behaviour ◽  
Stress And Strain ◽  
Elastic Deformations ◽  
Hooke’S Law ◽  
Widespread Agreement ◽  
Wide Range ◽  
Hooke's Law ◽  
High Degree

The mathematical theory of small elastic deformations has been developed to a high degree of sophistication on certain fundamental assumptions regarding the stress-strain relationships which are obeyed by the materials considered. The relationships taken are, in effect, a generalization of Hooke’s law— ut tensio, sic vis . The justification for these assumptions lies in the widespread agreement of experiment with the predictions of the theory and in the interpretation of the elastic behaviour of the materials in terms of their known structure. The same factors have contributed to our appreciation of the limitations of these assumptions. The principal problems, which the theory seeks to solve, are the determination of the deformation which a body undergoes and the distribution of stresses in it, when certain forces are applied to it, and when certain points of the body are subjected to specified displacements. These problems are always dealt with on the assumption that the generalization of Hooke’s law is obeyed by the material of the body and that the deformation is small, i.e. the change of length, in any linear element in the material, is small compared with the length of the element in the undeformed state. Apart from the fact that the generalization of Hooke’s law is obeyed accurately by a very wide range of materials, under a considerable variety of stress and strain conditions, it has the further advantage that it leads to a mathematically tractable theory.

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