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Forensic genetics

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https://www.readbyqxmd.com/read/28088090/degradation-in-forensic-trace-dna-samples-explored-by-massively-parallel-sequencing
#1
Eirik Nataas Hanssen, Robert Lyle, Thore Egeland, Peter Gill
Routine forensic analysis using STRs will fail if the DNA is too degraded. The DNA degradation process in biological stain material is not well understood. In this study we sequenced old semen and blood stains by massively parallel sequencing. The sequence data coverage was used to measure degradation across the genome. The results supported the contention that degradation is uniform across the genome, showing no evidence of regions with increased or decreased resistance towards degradation. Thus the lack of genetic regions robust to degradation removes the possibility of using such regions to further optimize analysis performance for degraded DNA...
January 3, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28087155/population-genetic-data-of-38-insertion-deletion-markers-in-six-populations-of-the-northern-fringe-of-the-iberian-peninsula
#2
Sergio Cardoso, Rubén Sevillano, David Gamarra, Ana Santurtún, Begoña Martínez-Jarreta, Marian M de Pancorbo
Insertion-deletions have been reported very useful markers for forensic purposes. To further deepen in this matter, 38 non-coding bi-allelic autosomal indels were analyzed in 575 individuals representing six populations from the northern fringe of the Iberian Peninsula. Autochthonous populations from the Basque Country, northern Navarre, the Pas Valley in Cantabria and Aragon were analyzed, together with non-autochthonous populations from the Basque Country and northern Navarre. At the intra-population level, all loci analyzed were in Hardy-Weinberg equilibrium except for marker rs33917182 in autochthonous Basques...
January 3, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28078776/performance-of-the-forenseq-tm-dna-signature-prep-kit-on-highly-degraded-samples
#3
Paolo Fattorini, Carlo Previderé, Ilaria Carboni, Giorgio Marrubini, Solange Sorçaburu-Cigliero, Pierangela Grignani, Barbara Bertoglio, Paolo Vatta, Ugo Ricci
Next generation sequencing (NGS) is the emerging technology in forensic genomics laboratories. It offers higher resolution to address most problems of human identification, greater efficiency and potential ability to interrogate very challenging forensic casework samples. In the present study, a trial set of DNA samples was artificially degraded, by progressive aqueous hydrolysis, and analyzed together with the corresponding unmodified DNA sample and control sample 2800M, to test the performance and reliability of the ForenSeq(TM) DNA Signature Prep kit using the MiSeq Sequencer (Illumina)...
January 12, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28078446/detection-of-rage-expression-and-its-application-to-diabetic-wound-age-estimation
#4
Xin-Yi Ji, Yang Chen, Guang-Hua Ye, Miao-Wu Dong, Ke-Zhi Lin, Jun-Ge Han, Xiang-Ping Feng, Xing-Biao Li, Lin-Sheng Yu, Yan-Yan Fan
With the prevalence of diabetes, it is becoming important to analyze the diabetic wound age in forensic practice. The present study investigated the time-dependent expression of receptor for advanced glycation end products (RAGE) during diabetic wound healing in mice and its applicability to wound age determination by immunohistochemistry, double immunofluorescence, and Western blotting. After an incision was created in genetically diabetic db/db mice and control mice, mice were killed at posttraumatic intervals ranging from 6 h to 14 days, followed by the sampling of wound margin...
January 11, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28074886/post-mortem-whole-exome-analysis-in-a-large-sudden-infant-death-syndrome-cohort-with-a-focus-on-cardiovascular-and-metabolic-genetic-diseases
#5
Jacqueline Neubauer, Maria Rita Lecca, Giancarlo Russo, Christine Bartsch, Argelia Medeiros-Domingo, Wolfgang Berger, Cordula Haas
Sudden infant death syndrome (SIDS) is described as the sudden and unexplained death of an apparently healthy infant younger than one year of age. Genetic studies indicate that up to 35% of SIDS cases might be explained by familial or genetic diseases such as cardiomyopathies, ion channelopathies or metabolic disorders that remained undetected during conventional forensic autopsy procedures. Post-mortem genetic testing by using massive parallel sequencing (MPS) approaches represents an efficient and rapid tool to further investigate unexplained death cases and might help to elucidate pathogenic genetic variants and mechanisms in cases without a conclusive cause of death...
January 11, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28073088/characterization-of-the-iberian-y-chromosome-haplogroup-r-df27-in-northern-spain
#6
Patricia Villaescusa, María José Illescas, Laura Valverde, Miriam Baeta, Carolina Nuñez, Begoña Martínez-Jarreta, Maria Teresa Zarrabeitia, Francesc Calafell, Marian M de Pancorbo
The European paternal lineage R-DF27 has been proposed as a haplogroup of Iberian origin due to its maximum frequencies in the Iberian Peninsula. In this study, the distribution and structure of DF27 were characterized in 591 unrelated male individuals from four key populations of the north area of the Iberian Peninsula through the analysis of 12 Y-SNPs that define DF27 main sublineages. Additionally, Y-SNP allele frequencies were also gathered from the reference populations in the 1000 Genomes Project to compare and obtain a better landscape of the distribution of DF27...
December 29, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28073087/a-nearest-neighbour-approach-by-genetic-distance-to-the-assignment-of-individual-trees-to-geographic-origin
#7
Bernd Degen, Céline Blanc-Jolivet, Katrin Stierand, Elizabeth Gillet
During the past decade, the use of DNA for forensic applications has been extensively implemented for plant and animal species, as well as in humans. Tracing back the geographical origin of an individual usually requires genetic assignment analysis. These approaches are based on reference samples that are grouped into populations or other aggregates and intend to identify the most likely group of origin. Often this grouping does not have a biological but rather a historical or political justification, such as "country of origin"...
December 29, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28070706/analysis-of-12-x-str-loci-in-the-population-of-south-croatia
#8
Gordan Mršić, Petar Ozretić, Josip Crnjac, Siniša Merkaš, Ivana Račić, Sara Rožić, Viktorija Sukser, Maja Popović, Marina Korolija
The aim of the study was to assess forensic pertinence of 12 short tandem repeats (STRs) on X-chromosome in south Croatia population. Investigator(®) Argus X-12 kit was used to co-amplify 12 STR loci belonging to four linkage groups (LGs) on X-chromosome in 99 male and 98 female DNA samples of unrelated donors. PCR products were analyzed by capillary electrophoresis. Population genetic and forensic parameters were calculated by the Arlequin and POPTREE2 software, and an on-line tool available at ChrX-STR.org...
January 9, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/28068530/a-new-view-on-the-european-feline-population-from-mtdna-analysis-in-polish-domestic-cats
#9
Iwona Głażewska, Tomasz Kijewski
Domestic cats from Eastern Europe have been poorly represented in studies on mitochondrial DNA diversity for forensic purposes until now. The aim of the present study was to contribute to closing this gap. The genetic structure and the origin of a cat population in Poland were examined against the background of human migrations over the centuries. One hundred and eighty-one cats from animal shelters in seven cities were genotyped. Twenty-one mtDNA haplotypes were found, with only one haplotype present in each of the populations, at an average frequency of 63...
December 29, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28058572/population-genetic-analyses-and-evaluation-of-22-autosomal-strs-in-indian-populations
#10
Mugdha Singh, Madhusudan R Nandineni
The allele frequencies and forensically relevant parameters for the 22 autosomal short tandem repeats (STRs) present in PowerPlex® Fusion (Promega, Madison, WI) were determined for 357 unrelated individuals from 11 states across India. The combined power of discrimination and probability of exclusion were 0.99999999999999999999999999875 and 0.999999997200846, respectively. The panel was found to be informative for Indian populations and generated a total of 275 alleles. Further, analyses with these loci did not show any noticeable clustering among the Indian populations...
January 6, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28057510/investigation-of-extended-y-chromosome-str-haplotypes-in-sardinia
#11
D Lacerenza, S Aneli, C Di Gaetano, R Critelli, A Piazza, G Matullo, C Culigioni, R Robledo, C Robino, C Calò
Y-chromosomal variation of selected single nucleotide polymorphisms (SNPs) and 32 short tandem repeat (STR) loci was evaluated in Sardinia in three open population groups (Northern Sardinia, n=40; Central Sardinia, n=56; Southern Sardinia, n=91) and three isolates (Desulo, n=34; Benetutti, n=45, Carloforte, n=42). The tested Y-STRs consisted of Yfiler(®) Plus markers and the seven rapidly mutating (RM) loci not included in the YFiler(®) Plus kit (DYF399S1, DYF403S1ab, DYF404S1, DYS526ab, DYS547, DYS612, and DYS626)...
December 28, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28032532/the-missing-the-martyred-and-the-disappeared-global-networks-technical-intensification-and-the-end-of-human-rights-genetics
#12
Lindsay A Smith
In 1984, a group of Argentine students, trained by US academics, formed the Argentine Forensic Anthropology Team to apply the latest scientific techniques to the excavation of mass graves and identification of the dead, and to work toward transitional justice. This inaugurated a new era in global forensic science, as groups of scientists in the Global South worked outside of and often against local governments to document war crimes in post-conflict settings. After 2001, however, with the inauguration of the war on terror following the September 11(th) attacks on the World Trade Center in New York, global forensic science was again remade through US and European investment to increase preparedness in the face of potential terrorist attacks...
December 1, 2016: Social Studies of Science
https://www.readbyqxmd.com/read/28032242/molecular-pathological-study-on-lrrc10-in-sudden-unexplained-nocturnal-death-syndrome-in-the-chinese-han-population
#13
Lei Huang, Shuangbo Tang, Yili Chen, Liyong Zhang, Kun Yin, Yeda Wu, Jinxiang Zheng, Qiuping Wu, Jonathan C Makielski, Jianding Cheng
Sudden unexplained nocturnal death syndrome (SUNDS) is a perplexing disorder to both forensic pathologists and clinic physicians. Clinical features of SUNDS survivors suggested that SUNDS is similar to Brugada syndrome (BrS). Leucine-rich repeat containing 10 (LRRC10) gene was a newly identified gene linked to dilated cardiomyopathy, a disease associated with sudden cardiac death. To investigate the prevalence and spectrum of genetic variants of LRRC10 gene in SUNDS and BrS, the coding regions of LRRC10 were genetically screened in 113 sporadic SUNDS victims (from January 2005 to December 2015, 30...
December 28, 2016: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28024238/forensic-application-of-phylogenetic-analyses-exploration-of-suspected-hiv-1-transmission-case
#14
Marina Siljic, Dubravka Salemovic, Valentina Cirkovic, Ivana Pesic-Pavlovic, Jovan Ranin, Marija Todorovic, Slobodan Nikolic, Djordje Jevtovic, Maja Stanojevic
Transmission of human immunodeficiency virus (HIV) between individuals may have important legal implications and therefore may come to require forensic investigation based upon phylogenetic analysis. In criminal trials results of phylogenetic analyses have been used as evidence of responsibility for HIV transmission. In Serbia, as in many countries worldwide, exposure and deliberate transmission of HIV are criminalized. We present the results of applying state of the art phylogenetic analyses, based on pol and env genetic sequences, in exploration of suspected HIV transmission among three subjects: a man and two women, with presumed assumption of transmission direction from one woman to a man...
December 19, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28012376/importance-sampling-allows-hd-true-tests-of-highly-discriminating-dna-profiles
#15
Duncan Taylor, James M Curran, John Buckleton
Hd true testing is a way of assessing the performance of a model, or DNA profile interpretation system. These tests involve simulating DNA profiles of non-donors to a DNA mixture and calculating a likelihood ratio (LR) with one proposition postulating their contribution and the alternative postulating their non-contribution. Following Turing it is possible to predict that "The average LR for the Hd true tests should be one"[1]. This suggests a way of validating softwares. During discussions on the ISFG software validation guidelines [2] it was argued by some that this prediction had not been sufficiently examined experimentally to serve as a criterion for validation...
December 9, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28008628/analysis-of-four-pcr-snapshot-multiplex-assays-analyzing-52-snpforid-markers
#16
Goodwin Will, Alimat Sharizah
The SNPforID consortium identified a panel of 52 SNPs forensic analysis that has been used by several laboratories worldwide. The original analysis of the 52 SNPs was based on a single multiplex reaction followed by two single-base-extension (SBE) reactions each of which was analyzed using capillary electrophoresis. The SBE assays were designed for high throughput genetic analyzers and were difficult to use on the single capillary ABI PRISM 310 Genetic Analyzer and the latest generation 3500 Genetic Analyzer, as sensitivity on the 310 was low and separation of products on the 3500 with POP-7™ was poor...
December 23, 2016: Electrophoresis
https://www.readbyqxmd.com/read/28004788/multi-indel-analysis-for-ancestry-inference-of-sub-populations-in-china
#17
Kuan Sun, Yi Ye, Tao Luo, Yiping Hou
Ancestry inference is of great interest in diverse areas of scientific researches, including the forensic biology, medical genetics and anthropology. Various methods have been published for distinguishing populations. However, few reports refer to sub-populations (like ethnic groups) within Asian populations for the limitation of markers. Several InDel loci located very tightly in physical positions were treated as one marker by us, which is multi-InDel. The multi-InDel shows potential as Ancestry Inference Marker (AIM)...
December 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28000408/ancestral-variations-in-the-shape-and-size-of-the-zygoma
#18
Anna C Oettlé, Fabrice P Demeter, Ericka N L'abbé
The variable development of the zygoma, dictating its shape and size variations among ancestral groups, has important clinical implications and valuable anthropological and evolutionary inferences. The purpose of the study was to review the literature regarding the variations in the zygoma with ancestry. Ancestral variation in the zygoma reflects genetic variations because of genetic drift as well as natural selection and epigenetic changes to adapt to diet and climate variations with possible intensification by isolation...
January 2017: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/27995319/prediction-of-biogeographical-ancestry-from-genotype-a-comparison-of-classifiers
#19
Elaine Y Y Cheung, Michelle Elizabeth Gahan, Dennis McNevin
DNA can provide forensic intelligence regarding a donor's biogeographical ancestry (BGA) and other externally visible characteristics (EVCs). A number of algorithms have been proposed to assign individual human genotypes to a BGA using ancestry informative marker (AIM) panels. This study compares the BGA assignment accuracy of the population clustering program STRUCTURE and three generic classification approaches including a Bayesian algorithm, genetic distance, and multinomial logistic regression (MLR). A selection of 142 ancestry informative single nucleotide polymorphisms (SNPs) were chosen from existing marker panels (SNPforID 34-plex, Eurasiaplex, Seldin, and Kidd's AIM panels) to assess BGA classification at the continental level for Africans, Europeans, East Asians, and Amerindians...
December 20, 2016: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/27992827/development-of-a-snp-based-panel-for-human-identification-for-indian-populations
#20
Anujit Sarkar, Madhusudan R Nandineni
The widely employed short tandem repeat (STR)-based panels for forensic human identification (HID) have limitations while dealing with challenging forensic samples involving DNA degradation, resulting in dropping-out of higher molecular weight alleles/loci. To address this issue, bialleic markers like single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), which can be scored even when the template DNA is heavily degraded (<100bp), have been suggested as alternative markers for HID testing...
December 5, 2016: Forensic Science International. Genetics
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