1,720,965 research outputs found
Inferring the Weight of Evidence from two-person mixtures when explored by Y-chromosome haplotypes
Full text linkIn recent decades, the improvement in the sensitivity of commercial kits used for the amplification of genetic markers in forensic work, together with the increase in the complexity of the cases dealt with, has led to an increase in the number of mixed traces submitted to the forensic expert for analysis as a model of evidence in molecular investigations aimed at criminal identification.
The interpretation of mixed traces analyzed by autosomal markers has been an intensively studied field, and at least two computational methods are now available to the expert: qualitative (semi-continuous) and quantitative Bayesian (continuous). A good assortment of application software inspired by these principles is also available today, with products that can be purchased commercially or acquired as free shareware (for example, LRmix Studio, EuroForMix, CaseSolver, etc.). Some of these software are surveyed and, to some extent, approved by the International Society of Forensic Genetics.
However, what still makes the theoretical and application landscape on the subject of mixed traces unsatisfactory is the almost total absence of principles and analysis methods that can be applied to the field of markers located on the Y chromosome (Y-Chr).
In this context, the main problems that make theoretical elaboration and interpretative progress complex are as follows:
• The Y-Chr is theoretically inherited en bloc, and the presence of haplotypes makes extrapolating population frequency data that can be integrated into individualization calculations challenging;
• A unique haplotype frequency calculation model does not yet exist;
• The approach to the identification of all possible combinations resulting from a mixed profile has to deal with the construction of pairs, triplets, quadruplets, etc. (in the case of mixtures with two, three, and four contributors, respectively) of haplotypes (and not of single genotypes);
• Many haplotypes generated by an albeit correct haplotype combinatorial process may never have been detected in the population surveys carried out by the laboratories; therefore, their existence may legitimately be questioned;
• Solutions for the deconvolution of Y-STRs (Short Tandem Repeats) mixtures are still practically non-existent.
This work aims to illustrate a computational procedure to extract and evaluate the Power of Evidence (WoE) in biological mixtures corresponding to the two contributors' model, studied employing a genetic marker protocol on the Y-Chr.
In this study, the Y-STRs mixtures are represented with genotype permutation universal matrices, which include several columns equivalent to the number of putative contributors and many rows/states comparable to the number of different permutations incorporating the evidence. After the matrices' construction, a calculation method was proposed based on the assumption of measurable quantities, gene frequencies assumed to be all available, and no drop-out. The three independent indices (Peak Height ratio, Mix Ratio, and χ2) were modelled, and a specific description of how they were calculated is given in the manuscript.
The theoretical development of this work was described following the two contributors – ten loci model; practical calculation examples helpful in testing the effectiveness of the method developed were then described using the two contributors – seven loci model, due to the low data processing capacity of the personal computers used in this work.
The spreadsheets developed in Microsoft Excel, relating to matrix construction and calculation of the Likelihood Ratio, are user-friendly and accessible for reference upon explicit request to the Authors
Validation of the investigator argus y-28 qs kit on the seqstudioTM genetic analyzer for hid: a new panel file for genemapper id-x software v1.6
No full textBackground: The Investigator Argus Y-28 QS Kit is a 27-locus, six-dye multiplex, which includes six rapidly mutating Short Tandem Repeats (RM Y-STRs). Methods: A new text file containing the optimized panel and bin sets for GeneMapper ID-X Software v1.6 has been prepared. In addition, an internal validation study was conducted on the Investigator Argus Y-28 QS kit using the SeqStudioTM Genetic Analyzer for HID. Results: The full results of that study are presented here, including data on precision, sensitivity, reproducibility, stutter determination, and reduction volume analysis. A concordance study and three case reports are documented. Finally, the kit was successfully used to conduct a proficiency test. Conclusions: The obtained findings achieved a satisfactory performance of the Investigator Argus Y-28 QS Kit on the SeqStudioTM Genetic Analyzer for HID
Trisomy 21 disclosure using STR and SNP markers typed by MiSeq FGxTM Forensic Genomics System
No full textThe presence of a tri-allelic pattern at a single locus in a multiplex short tandem repeat (STR) profile is a rarely observable event. Generally, based on peak height measured by the capillary electrophoresis (CE) method and combination of alleles, the tri-allelic pattern is distinguishable into two predominant types: type 1 and 2, which are caused, respectively, by somatic mutations and chromosomal rearrangements. When tri-allelic patterns at more than one STR located on the same chromosome are detected, there is a reasonable suspicion of a trisomy due to an extra copy of a chromosome. Therefore, information on the type of three-band pattern is usually limited to STRs localized on the same chromosome included in the forensic kit in use and sometimes in insufficient numbers to classify this event correctly. The opportunity to extend this evaluation to additional markers, such as SNPs detectable using NGS, has not yet been explored. In this study, using the ForenSeqTM DNA Signature Prep kit, two cases of autosomal aneuploidy were revealed on chromosome 21, relying not only on STRs assessment but also extending the analysis to the five identity-informative single nucleotide polymorphisms (iiSNPs) localized on chromosome 21
Correction: Concordance study on Y-STRs typing between SeqStudioTM genetic analyzer for HID and MiSeqTM FGx forensic genomics system
No full textNo abstract availabl
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Unveiling STRs instability in a colorectal cancer FFPE sample: a case report
Full text link: In forensic genetics, sometimes formalin-fixed paraffin-embedded (FFPE) biopsy material taken during life is the only biological sample available for individual identification or paternity testing. In most cases, this biological tissue is characterized by the presence of tumor cells characterized by instability and loss of heterozygosity of microsatellites (MSI/LOH) compared to the DNA present in cells of normal tissue.In this case report, two FFPE samples from the same male subject were available for genetic investigation: one sample with colorectal cancer tissue and the other with normal tissue (no cancerous histopathological features). The comparison of the genetic profiles obtained from DNA extracted from the two tissues showed in the tumor tissue the presence of three genomic instability phenomena affecting FGA, CSF1P0, D21S2055 loci, located on three distinct autosomal chromosomes, and one duplication phenomenon affecting the DYS438. Therefore, due to the MSI/LOH phenomena, the genetic profile acquired from the tumor tissue was distorted and thus generated a fictitious genetic profile, not corresponding to the subject's real one (normal tissue free of tumor cells)
Can tissue deparaffinization influence the extracted DNA for forensic purposes?
No full textIn forensic genetics, sometimes the biological specimen available for DNA extraction is biopsy tissue taken in life from deceased subjects and then fixed in formalin and embedded in paraffin (FFPE). Degradation and chemical alteration of DNA caused by treatment of tissue with formalin and paraffin is an event reported in the literature, even if the influence of exposure time and intensity of the phenomenon are still uncertain. This results in obtaining DNA of degraded quality, the quantity of which is for sure affected by paraffin hindering its release from the tissues in the lysis step. Therefore, pretreatment of the biological sample, i.e. deparaffinization, may assume a relevant role in the subsequent DNA extraction and amplification steps. In this study, five different tissue deparaffinization protocols were compared to determine which was the most appropriate for the aim, exploiting two tissue samples (lung and kidney), FFPE over the next 24 h, taken during autopsies on two male cadavers. The deparaffinization protocols involved the use of the standard procedure with xylene and 100% ethanol and four methods in which paraffin solubilizing solvents were used, i.e. chloroform and white mineral oil. Then, DNA extraction was performed by employing the QIAamp DNA FFPE Tissue Kit, modifying the procedure only in the post-lysis step, in which the provided treatment at 90°C for 1 h was omitted, proceeding with incubation at 70°C for 24 h, after addition of Tris 1M to the lysate. Extracted DNA was quantified and normalized to 1 ng/μl and then submitted for amplification with two forensic kits. Amplicons were genotyped in capillary electrophoresis and fragment analysis was conducted with the GeneMapper ID-X v1.6 software. The two panels of Short Tandem Repeats yielded reproducible, albeit partial, genetic profiles, referable to 12/13 loci (molecular weight <300 bp), and showed no significant differences correlated with the adopted deparaffinization procedure. Therefore, while being aware that the study needs to implement the number of samples, it seems reasonable to assume that deparaffinization can also be carried out by procedures other than the standard one, using solvents with low toxic characteristics
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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