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"forensic genetic"

Angie D Ambers, Jennifer D Churchill, Jonathan L King, Monika Stoljarova, Harrell Gill-King, Mourad Assidi, Muhammad Abu-Elmagd, Abdelbaset Buhmeida, Bruce Budowle
BACKGROUND: Although the primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for comparison. Massively parallel sequencing (MPS) offers an opportunity to provide biometric data in such cases, and these cases provide valuable data on the feasibility of applying MPS for characterization of modern forensic casework samples. In this study, MPS was used to characterize 140-year-old human skeletal remains discovered at a historical site in Deadwood, South Dakota, United States...
October 17, 2016: BMC Genomics
Humberto Ossa, Juliana Aquino, Rui Pereira, Adriana Ibarra, Rafael H Ossa, Luz Adriana Pérez, Juan David Granda, Maria Claudia Lattig, Helena Groot, Elizeu Fagundes de Carvalho, Leonor Gusmão
The ancestry of the Colombian population comprises a large number of well differentiated Native communities belonging to diverse linguistic groups. In the late fifteenth century, a process of admixture was initiated with the arrival of the Europeans, and several years later, Africans also became part of the Colombian population. Therefore, the genepool of the current Colombian population results from the admixture of Native Americans, Europeans and Africans. This admixture occurred differently in each region of the country, producing a clearly stratified population...
2016: PloS One
Jiří Drábek, Michaela Smolíková, Ruslan Kalendar, Fernando A Lopes Pinto, Pavel Pavloušek, Karel Klepárník, Ivo Frébort
Although the analysis of length polymorphism at short tandem repeat (STR) loci has become a method of choice for grape cultivar identification, the standardization of methods for this purpose lags behind that of methods for DNA profiling in human and animal forensic genetics. The aim of this study was thus to design and validate a grapevine STR protocol with a practically useful level of multiplexing. Using free bioinformatics tools, published primer sequences, and nucleotide databases, we constructed and optimized a primer set for the simultaneous analysis of six STR loci (VVIi51, scu08vv, scu05vv, VVMD17, VrZAG47, and VrZAG83) by multiplex PCR and capillary electrophoresis with laser induced fluorescence, and tested it on 90 grape cultivars...
October 2, 2016: Electrophoresis
R Wojtkiewicz, B Markiewicz, M Jędrzejczyk, R Jacewicz
In this study Polish population data as well as efficiency parameters of 12 STR loci included in the Investigator HDplex set were presented. This set contains 9 systems not available in any other commercial multiplexes, ie.: D2S1360, D3S1744, D4S2366, D5S2500, D6S474, D7S1517, D8S1132, D10S2325 and D21S2055. The evaluation was preformed based on DNA samples derived from 303 unrelated individuals living in Lodz region, central part of Poland. The obtained distribution of the genotypes is consistent with the assumptions of the Hardy and Weinberg equilibrium (HWE)...
2016: Archiwum Medycyny Sa̧dowej i Kryminologii
M D Coble, J Buckleton, J M Butler, T Egeland, R Fimmers, P Gill, L Gusmão, B Guttman, M Krawczak, N Morling, W Parson, N Pinto, P M Schneider, S T Sherry, S Willuweit, M Prinz
The use of biostatistical software programs to assist in data interpretation and calculate likelihood ratios is essential to forensic geneticists and part of the daily case work flow for both kinship and DNA identification laboratories. Previous recommendations issued by the DNA Commission of the International Society for Forensic Genetics (ISFG) covered the application of bio-statistical evaluations for STR typing results in identification and kinship cases, and this is now being expanded to provide best practices regarding validation and verification of the software required for these calculations...
September 4, 2016: Forensic Science International. Genetics
Marie-Louise Kampmann, Anders Buchard, Claus Børsting, Niels Morling
Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory...
2016: BioTechniques
Qiu-Ling Liu, Ye-Fei Chen, Xiao-Ling Huang, Kai-Yan Liu, Hu Zhao, De-Jian Lu
Short tandem repeat (STR) analysis is a primary tool in forensic casework. Population data and mutation rates of STRs are very important for paternity testing and forensic genetics. However, the population data and mutation rates of STRs in Han nationality based on large samples have still not been fully described in China. In this study, the allelic frequencies, forensic parameters, and mutation rate of 19 STR loci (D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSFIPO, PentaD, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, and FGA) based on the Goldeneye™ DNA ID System 20A in Southern China Han nationality among seven provinces were investigated...
September 13, 2016: International Journal of Legal Medicine
Maria-Bernadette Madel, Harald Niederstätter, Walther Parson
Sexing of biological evidence is an important aspect in forensic investigations. A routinely used molecular-genetic approach to this endeavour is the amelogenin sex test, which is integrated in most commercially available polymerase chain reaction (PCR) kits for human identification. However, this assay is not entirely effective in respect to highly degraded DNA samples. This study presents a homogeneous PCR assay for robust sex diagnosis, especially for the analysis of severely fragmented DNA. The introduced triplex for the X and Y chromosome (TriXY) is based on real-time PCR amplification of short intergenic sequences (<50bp) on both gonosomes...
September 3, 2016: Forensic Science International. Genetics
So Yeun Kwon, Hwan Young Lee, Eun Hye Kim, Eun Young Lee, Kyoung-Jin Shin
Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data for many targeted regions with a high depth of coverage, suggesting its successful application to the amplicons of forensic genetic markers. In the present study, we evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR) analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex(®) Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from 85 to 253bp...
August 28, 2016: Forensic Science International. Genetics
Galina Kulstein, Ralf Marienfeld, Erich Miltner, Peter Wiegand
In the last years microRNA (miRNA) analysis came into focus in the field of forensic genetics. Yet, no standardized and recommendable protocols for co-isolation of miRNA and DNA from forensic relevant samples have been developed so far. Hence, this study evaluated the performance of an automated Maxwell(®) 16 System-based strategy (Promega) for co-extraction of DNA and miRNA from forensically relevant (blood and saliva) samples compared to (semi-)manual extraction methods. Three procedures were compared on the basis of recovered quantity of DNA and miRNA (as determined by real-time PCR and Bioanalyzer), miRNA profiling (shown by Cq values and extraction efficiency), STR profiles, duration, contamination risk and handling...
August 19, 2016: Electrophoresis
Vincent Zvénigorosky, Eric Crubézy, Morgane Gibert, Catherine Thèves, Clémence Hollard, Angéla Gonzalez, Sardana A Fedorova, Anatoly N Alexeev, Rozalia I Bravina, Bertrand Ludes, Christine Keyser
For fifteen years, part of the work of our research team has been focused on the study of parental links between individuals living hundreds or thousands of years ago, whose remains have been found in single graves or large funerary complexes. These studies have been undertaken using methods developed by forensic genetics to identify individuals, mainly based on the genotyping of autosomal STR (Short Tandem Repeats). Issues arose from this work, namely the limits of studying small numbers of subjects, originating from groups of finite sizes where kinships cannot be inferred a priori and for which reference allelic frequencies do not exist...
July 28, 2016: Forensic Science International. Genetics
Atif Adnan, Arwin Ralf, Allah Rakha, Nefeli Kousouri, Manfred Kayser
Y-chromosomal short tandem repeat (Y-STR) markers are commonly used in forensic genetics. Male-specific haplotypes provided by commercial Y-STR kits allow discriminating between many - but not all - unrelated men, while they mostly fail to separate related ones. Aiming to improve male relative and paternal lineage differentiation, a set of 13 rapidly-mutating (RM) Y-STRs was previously identified and introduced to forensic Y-chromosome analysis. Recently, their value was highlighted by separating 99% of over 12,200 unrelated men from 111 global populations, as well as 29% of over 2500 male relative pairs, the vast majority were father-sons...
July 9, 2016: Forensic Science International. Genetics
Toni Marie Diegoli, Heinrich Rohde, Stefan Borowski, Michael Krawczak, Michael D Coble, Michael Nothnagel
Typing of X chromosomal short tandem repeat (X STR) markers has become a standard element of human forensic genetic analysis. Joint consideration of many X STR markers at a time increases their discriminatory power but, owing to physical linkage, requires inter-marker recombination rates to be accurately known. We estimated the recombination rates between 15 well established X STR markers using genotype data from 158 families (1041 individuals) and following a previously proposed likelihood-based approach that allows for single-step mutations...
July 25, 2016: Forensic Science International. Genetics
Francesc Calafell, Roger Anglada, Núria Bonet, Mercedes González-Ruiz, Gemma Prats-Muñoz, Raquel Rasal, Carles Lalueza-Fox, Jaume Bertranpetit, Assumpció Malgosa, Ferran Casals
Next generation sequencing technologies have opened new opportunities in forensic genetics. Here we assess the applicability and performance of the MiSeq FGx™ & ForenSeq™ DNA Signature Prep Kit (Illumina) to the identification of individuals from the mass graves of the Spanish Civil War (1936-1939). The main limitations for individual identification are the low number of possible first-degree living relatives and the high levels of DNA degradation reported in previous studies. Massively parallel sequencing technologies enabling the analysis of hundreds of regions and prioritizing short length amplicons constitute a promising tool for this kind of approaches...
August 4, 2016: Electrophoresis
Chie Morimoto, Sho Manabe, Takahisa Kawaguchi, Chihiro Kawai, Shuntaro Fujimoto, Yuya Hamano, Ryo Yamada, Fumihiko Matsuda, Keiji Tamaki
We developed a new approach for pairwise kinship analysis in forensic genetics based on chromosomal sharing between two individuals. Here, we defined "index of chromosome sharing" (ICS) calculated using 174,254 single nucleotide polymorphism (SNP) loci typed by SNP microarray and genetic length of the shared segments from the genotypes of two individuals. To investigate the expected ICS distributions from first- to fifth-degree relatives and unrelated pairs, we used computationally generated genotypes to consider the effect of linkage disequilibrium and recombination...
2016: PloS One
Chengchen Shao, Mingxi Lin, Zhihan Zhou, Yueqin Zhou, Yiwen Shen, Aimin Xue, Huaigu Zhou, Qiqun Tang, Jianhui Xie
The mutation of short tandem repeat (STR) loci is affected by several factors, such as sex, age, and DNA architectures. Previous studies have shown a different profile of mutation rates at autosomal STR loci among populations. It is important to provide population data and reveal underlying factors influencing the evaluation of STR mutation rates. In this study, we performed a comprehensive analysis on the mutation of 19 autosomal STR loci through 124,773 parent-child allelic transfers from 5846 paternity testing cases...
November 2016: International Journal of Legal Medicine
Martin Bodner, Ingo Bastisch, John M Butler, Rolf Fimmers, Peter Gill, Leonor Gusmão, Niels Morling, Christopher Phillips, Mechthild Prinz, Peter M Schneider, Walther Parson
The statistical evaluation of autosomal Short Tandem Repeat (STR) genotypes is based on allele frequencies. These are empirically determined from sets of randomly selected human samples, compiled into STR databases that have been established in the course of population genetic studies. There is currently no agreed procedure of performing quality control of STR allele frequency databases, and the reliability and accuracy of the data are largely based on the responsibility of the individual contributing research groups...
September 2016: Forensic Science International. Genetics
Christophe Frippiat, Fabrice Noel
The collection of traces is the first step in the process of forensic genetics analysis. Currently, several different techniques are used (eg. gauze). Nevertheless, swabbing appears to be the most common of these. In a second step, the sampling devices should allow the use of preliminary tests in combination with an immunological confirmatory test (e.g. Hexagon Obti or Hemdirect). Our previous study shows that sampling with Genetics 4N6FLOQswabs™ coated with surfactant reduces by a factor of at least 100 the detection threshold of blood using two immunological tests...
August 2016: Journal of Forensic and Legal Medicine
Ke Ma, Hui Li, Yu Cao, Xuejun Zhao, Wenbin Liu, Xueying Zhao
Investigations into the use of mitochondrial genome (mtGenome) typing by massively parallel sequencing technologies are well underway in many areas, including forensic genetics. Previous studies have demonstrated that mtGenome sequencing data generated from Ion torrent personal genome machine (PGM) system were highly viable and reliable in forensic research. In this study, 145 whole mtGenomes from unrelated Chinese Han population were sequenced using the Ion PGM system. Results showed that 145 distinct haplotypes were obtained at a relatively high coverage with limited strand bias...
June 16, 2016: Journal of Human Genetics
Lia Hadas, Dalia Hermon, Gila Kahila Bar-Gal
Throughout their habitats gazelles (genus Gazella) face immediate threats due to anthropogenic effects and natural environmental changes. Excessive poaching plays a major role in their populations decline. Three unique populations of gazelles currently live in Israel: mountain gazelle (Gazella gazella), Dorcas gazelle (Gazella Dorcas) and acacia gazelle (Gazella arabica acacia). Ongoing habitat degradation and constant pressure from illegal hunting has caused a continuous decrease in the last 10 years, stressing the need for drastic measures to prevent species extinction...
September 2016: Forensic Science International. Genetics
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