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Forensic Science International. Genetics

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https://www.readbyqxmd.com/read/29128546/a-1204-single-nucleotide-polymorphism-and-insertion-deletion-polymorphism-panel-for-massively-parallel-sequencing-analysis-of-dna-mixtures
#1
Hsiao-Lin Hwa, Wan-Chia Chung, Pei-Lung Chen, Chih-Peng Lin, Huei-Ying Li, Hsiang-I Yin, James Chun-I Lee
Massively parallel sequencing (MPS) technology enables the simultaneous analysis of a huge number of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (indels). MPS also enables the detection of the alleles of minor contributors in a highly unbalanced DNA mixture. In this study, we established a 1204-marker panel optimized for MPS consisting of 987 autosomal markers (964 SNPs and 23 indels), 27 X-chromosome SNPs, 61 Y-chromosome markers (56 SNPs and 5 indels), and 129 mitochondrial SNPs...
November 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29128545/massive-parallel-sequencing-of-mitochondrial-dna-genomes-from-mother-child-pairs-using-the-ion-torrent-personal-genome-machine-pgm
#2
Ke Ma, Xueying Zhao, Hui Li, Yu Cao, Wei Li, Jian Ouyang, Lu Xie, Wenbin Liu
Mitochondrial genome analysis is a potent tool in forensic practice and in the understanding of human phylogeny in the maternal lineage. With the development of molecular biology and bioinformatics techniques, high-throughput sequencing has enabled mtDNA analysis during whole genome sequencing, which provides more comprehensive information and raises the power of discrimination. In this study, peripheral blood samples were taken from 194 mother-offspring pairs and sequenced by Ion Torrent Personal Genome Machine and obtained high-coverage mitochondrial sequencing data, demonstrating the mutation levels at each position in the mitochondrial DNA (mtDNA) between maternally related pairs...
November 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29108878/population-genetic-data-of-22-autosomal-strs-in-the-guizhou-miao-population-southwestern-china
#3
LETTER
Zheng Ren, Meiqing Yang, Hongling Zhang, Jialin Dai, Yubo Liu, Qiyan Wang, Jie Wang, Jiang Huang
No abstract text is available yet for this article.
November 3, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29107870/consent-process-for-us-based-family-reference-dna-samples
#4
Sara H Katsanis, Lindsey Snyder, Kelly Arnholt, Amy Z Mundorff
DNA collection from family members of the missing is a tenet for missing persons' and mass fatality investigations. Procedures for consenting family members are disparate, depending on the context supporting the reason for sample collection. While guidelines and best practices have been developed for handling mass fatalities and for identification of the missing, these guidelines do not address standard consent practices for living family members of potential victims. We examined the relevant U.S. laws, international guidelines and best practices, sampled consent forms currently used for DNA collection of family members, and drafted model language for a consent form to communicate the required and recommended information...
October 29, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29089250/defining-y-snp-variation-among-the-flemish-population-western-europe-by-full-genome-sequencing
#5
Maarten H D Larmuseau, Gilles P P L Otten, Ronny Decorte, Philip Van Damme, Matthieu Moisse
Y-chromosomal single nucleotide polymorphisms (Y-SNPs) represent a powerful tool in forensic research and casework, especially for inferring paternal ancestry of unknown perpetrators and unidentified bodies. However, the wealth of recently discovered Y-SNPs, the 'jungle' of different evolutionary lineage trees and nomenclatures, and the lack of population-wide data of many phylogenetically mapped Y-SNPs, limits the use of Y-SNPs in routine forensic approaches. Recently, a concise reference phylogeny of the human Y chromosome, the 'Minimal Reference Y-tree', was introduced aiming to provide a stable phylogeny with optimal global discrimination capacity by including the most resolving Y-SNPs...
October 28, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29111271/forensic-characteristics-and-phylogenetic-analysis-of-two-han-populations-from-the-southern-coastal-regions-of-china-using-27-y-str-loci
#6
Mengge Wang, Zheng Wang, Yaqing Zhang, Guanglin He, Jing Liu, Yiping Hou
Currently, the largest national database within the Y-STR Haplotype Reference Database (YHRD, https://yhrd.org, release 55) is China, which has a very large Y-STR haplotype profiles. However, no haplotype data was available for Hainan province, the smallest and southernmost province of China. Herein, 280 unrelated male Chinese Han individuals residing in Hainan province were recruited and genotyped with 27 Y-STR loci. Moreover, 136 Han individuals from Shenzhen, the largest migrant city in China, also investigated...
October 27, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29126000/direct-pcr-amplification-of-dna-from-human-bloodstains-saliva-and-touch-samples-collected-with-microfloq-%C3%A2-swabs
#7
Angie Ambers, Rachel Wiley, Nicole Novroski, Bruce Budowle
Previous studies have shown that nylon flocked swabs outperform traditional fiber swabs in DNA recovery due to their innovative design and lack of internal absorbent core to entrap cellular materials. The microFLOQ(®) Direct swab, a miniaturized version of the 4N6 FLOQSwab(®), has a small swab head that is treated with a lysing agent which allows for direct amplification and DNA profiling from sample collection to final result in less than two hours. Additionally, the microFLOQ(®) system subsamples only a minute portion of a stain and preserves the vast majority of the sample for subsequent testing or re-analysis, if desired...
October 26, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29091906/a-large-scale-dataset-of-single-and-mixed-source-short-tandem-repeat-profiles-to-inform-human-identification-strategies-provedit
#8
Lauren E Alfonse, Amanda D Garrett, Desmond S Lun, Ken R Duffy, Catherine M Grgicak
DNA-based human identity testing is conducted by comparison of PCR-amplified polymorphic Short Tandem Repeat (STR) motifs from a known source with the STR profiles obtained from uncertain sources. Samples such as those found at crime scenes often result in signal that is a composite of incomplete STR profiles from an unknown number of unknown contributors, making interpretation an arduous task. To facilitate advancement in STR interpretation challenges we provide over 25,000 multiplex STR profiles produced from one to five known individuals at target levels ranging from one to 160 copies of DNA...
October 24, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29065388/targeted-sequencing-of-clade-specific-markers-from-skin-microbiomes-for-forensic-human-identification
#9
Sarah E Schmedes, August E Woerner, Nicole M M Novroski, Frank R Wendt, Jonathan L King, Kathryn M Stephens, Bruce Budowle
The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals...
October 18, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29059581/direct-pcr-amplification-of-forensic-touch-and-other-challenging-dna-samples-a-review
#10
REVIEW
Sarah E Cavanaugh, Abigail S Bathrick
DNA evidence sample processing typically involves DNA extraction, quantification, and STR amplification; however, DNA loss can occur at both the DNA extraction and quantification steps, which is not ideal for forensic evidence containing low levels of DNA. Direct PCR amplification of forensic unknown samples has been suggested as a means to circumvent extraction and quantification, thereby retaining the DNA typically lost during those procedures. Direct PCR amplification is a method in which a sample is added directly to an amplification reaction without being subjected to prior DNA extraction, purification, or quantification...
October 18, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29035720/an-internationally-standardized-species-identification-test-for-use-on-suspected-seized-rhinoceros-horn-in-the-illegal-wildlife-trade
#11
Kyle M Ewart, Greta J Frankham, Ross McEwing, Lucy M I Webster, Sherryn A Ciavaglia, Adrian M T Linacre, Dang Tat The, Kanitia Ovouthan, Rebecca N Johnson
Rhinoceros (rhino) numbers have dwindled substantially over the past century. As a result, three of the five species are now considered to be critically endangered, one species is vulnerable and one species is near-threatened. Poaching has increased dramatically over the past decade due to a growing demand for rhino horn products, primarily in Asia. Improved wildlife forensic techniques, such as validated tests for species identification of seized horns, are critical to aid current enforcement and prosecution efforts and provide a deterrent to future rhino horn trafficking...
October 7, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29031081/optimization-of-the-promega-powerseq%C3%A2-auto-y-system-for-efficient-integration-within-a-forensic-dna-laboratory
#12
E A Montano, J M Bush, A M Garver, M M Larijani, S M Wiechman, C H Baker, M R Wilson, R A Guerrieri, E A Benzinger, D N Gehres, M L Dickens
The application of massively parallel sequencing (MPS) is growing in the forensic DNA field, as forensic DNA laboratories are continuously seeking methods to gain information from a limited or degraded forensic sample. However, the laborious nature of current MPS methodologies required for successful library preparation and sequencing leave opportunities for improvement to make MPS a practical option for processing forensic casework. In this study, the Promega PowerSeq™ Auto/Y System Prototype, a MPS laboratory workflow that incorporates multiplex amplification, was selected for optimization with the objectives to introduce automation for relieving manual processing, and to reduce the number of steps recommended by the standard protocol...
October 5, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29024922/isolation-and-whole-genome-analysis-of-endospore-forming-bacteria-from-heroin
#13
Jörn Kalinowski, Björn Ahrens, Arwa Al-Dilaimi, Anika Winkler, Daniel Wibberg, Uwe Schleenbecker, Christian Rückert, Roman Wölfel, Gregor Grass
Infections caused by endospore-forming bacteria have been associated with severe illness and death among persons who inject drugs. Analysis of the bacteria residing in heroin has thus been biased towards species that affect human health. Similarly, exploration of the bacterial diversity of seized street market heroin correlated with the skin microflora of recreational heroin users insofar as different Staphylococus spp. or typical environmental endospore formers including Bacillus cereus and other Bacilli outside the B...
October 4, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29024924/assessing-heteroplasmic-variant-drift-in-the-mtdna-control-region-of-human-hairs-using-an-mps-approach
#14
Jamie M Gallimore, Jennifer A McElhoe, Mitchell M Holland
Resolution of mitochondrial (mt) DNA heteroplasmy is possible when applying a massively parallel sequencing (MPS) approach. However, interpretation criteria for matching heteroplasmic sequences will need to be established that address a number of important topics, including the drift of variants in sample types such as human hair shafts. Prior to MPS analysis, we compared three different DNA extraction methods for hair using a custom mtDNA quantitative PCR (mtqPCR) assay, and found that a method involving bead capture significantly outperformed methods currently in place in forensic laboratories...
October 2, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29030116/population-genetic-data-for-21-autosomal-str-loci-for-the-saudi-arabian-population-using-the-globalfiler-%C3%A2-pcr-amplification-kit
#15
LETTER
Hussain M Alsafiah, William H Goodwin, Sibte Hadi, Mohammed A Alshaikhi, Pet-Paul Wepeba
No abstract text is available yet for this article.
September 29, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29055861/internal-validation-of-the-rapidhit-%C3%A2-id-system
#16
Rachel Wiley, Kelly Sage, Bobby LaRue, Bruce Budowle
Traditionally, forensic DNA analysis has required highly skilled forensic geneticists in a dedicated laboratory to generate short tandem repeat (STR) profiles. STR profiles are routinely used either to associate or exclude potential donors of forensic biological evidence. The typing of forensic reference samples has become more demanding, especially with the requirement in some jurisdictions to DNA profile arrestees. The Rapid DNA (RDNA) platform, the RapidHIT(®) ID (IntegenX(®), Pleasanton, CA), is a fully automated system capable of processing reference samples in approximately 90min with minimal human intervention...
September 23, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29024923/a-ghep-isfg-collaborative-study-on-the-genetic-variation-of-38-autosomal-indels-for-human-identification-in-different-continental-populations
#17
R Pereira, C Alves, M Aler, A Amorim, C Arévalo, E Betancor, D Braganholi, M L Bravo, P Brito, J J Builes, G Burgos, E F Carvalho, A Castillo, C I Catanesi, R M B Cicarelli, P Coufalova, P Dario, M E D'Amato, S Davison, J Ferragut, M Fondevila, S Furfuro, O García, A Gaviria, I Gomes, E González, A Gonzalez-Liñan, T E Gross, A Hernández, Q Huang, S Jiménez, L F Jobim, A M López-Parra, M Marino, S Marques, G Martínez-Cortés, V Masciovecchio, D Parra, G Penacino, M F Pinheiro, M J Porto, Y Posada, C Restrepo, T Ribeiro, L Rubio, A Sala, A Santurtún, L S Solís, L Souto, E Streitemberger, A Torres, C Vilela-Lamego, J J Yunis, I Yurrebaso, L Gusmão
A collaborative effort was carried out by the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) to promote knowledge exchange between associate laboratories interested in the implementation of indel-based methodologies and build allele frequency databases of 38 indels for forensic applications. These databases include populations from different countries that are relevant for identification and kinship investigations undertaken by the participating laboratories...
September 22, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29080494/aqme-a-forensic-mitochondrial-dna-analysis-tool-for-next-generation-sequencing-data
#18
Kimberly Sturk-Andreaggi, Michelle A Peck, Cecilie Boysen, Patrick Dekker, Timothy P McMahon, Charla K Marshall
The feasibility of generating mitochondrial DNA (mtDNA) data has expanded considerably with the advent of next-generation sequencing (NGS), specifically in the generation of entire mtDNA genome (mitogenome) sequences. However, the analysis of these data has emerged as the greatest challenge to implementation in forensics. To address this need, a custom toolkit for use in the CLC Genomics Workbench (QIAGEN, Hilden, Germany) was developed through a collaborative effort between the Armed Forces Medical Examiner System - Armed Forces DNA Identification Laboratory (AFMES-AFDIL) and QIAGEN Bioinformatics...
September 19, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28951006/genetic-portrait-of-jewish-populations-based-on-three-sets-of-x-chromosome-markers-indels-alu-insertions-and-strs
#19
J F Ferragut, K Bentayebi, R Pereira, J A Castro, A Amorim, C Ramon, A Picornell
Population genetic data for 53 X-chromosome markers (32 X-indels, 9 X-Alu insertions and 12 X-STRs) are reported for five populations with Jewish ancestry (Sephardim, North African Jews, Middle Eastern Jews, Ashkenazim, and Chuetas) and Majorca, as the host population of Chuetas. Genetic distances between these populations demonstrated significant differences, except between Sephardic and North African Jews, with the Chuetas as the most differentiated group, in accordance with the particular demographic history of this population...
September 18, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28938152/comparison-of-manual-and-automated-ampliseq%C3%A2-workflows-in-the-typing-of-a-somali-population-with-the-precision-id-identity-panel
#20
Suzanne van der Heijden, Susanne Juel de Oliveira, Marie-Louise Kampmann, Claus Børsting, Niels Morling
The Precision ID Identity Panel was used to type 109 Somali individuals in order to obtain allele frequencies for the Somali population. These frequencies were used to establish a Somali HID-SNP database, which will be used for the biostatistic calculations in family and immigration cases. Genotypes obtained with the Precision ID Identity Panel were found to be almost in complete concordance with genotypes obtained with the SNPforID PCR-SBE-CE assay. In seven SNP loci, silent alleles were identified, of which most were previously described in the literature...
September 14, 2017: Forensic Science International. Genetics
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