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https://www.readbyqxmd.com/read/28324847/species-identification-in-forensic-samples-using-the-spindel-approach-a-ghep-isfg-inter-laboratory-collaborative-exercise
#1
Cíntia Alves, Rui Pereira, Lourdes Prieto, Mercedes Aler, Cesar R L Amaral, Cristina Arévalo, Gabriela Berardi, Florencia Di Rocco, Mariela Caputo, Cristian Hernandez Carmona, Laura Catelli, Heloísa Afonso Costa, Pavla Coufalova, Sandra Furfuro, Óscar García, Anibal Gaviria, Ana Goios, Juan José Builes Gómez, Alexis Hernández, Eva Del Carmen Betancor Hernández, Luís Miranda, David Parra, Susana Pedrosa, Maria João Anjos Porto, Maria de Lurdes Rebelo, Matteo Spirito, María Del Carmen Villalobos Torres, António Amorim, Filipe Pereira
DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis...
March 7, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28314239/likelihood-ratio-and-posterior-odds-in-forensic-genetics-two-sides-of-the-same-coin
#2
Amke Caliebe, Susan Walsh, Fan Liu, Manfred Kayser, Michael Krawczak
It has become widely accepted in forensics that, owing to a lack of sensible priors, the evidential value of matching DNA profiles in trace donor identification or kinship analysis is most sensibly communicated in the form of a likelihood ratio (LR). This restraint does not abate the fact that the posterior odds (PO) would be the preferred basis for returning a verdict. A completely different situation holds for Forensic DNA Phenotyping (FDP), which is aimed at predicting externally visible characteristics (EVCs) of a trace donor from DNA left behind at the crime scene...
March 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28279935/evaluation-of-the-illumina-forenseq%C3%A2-dna-signature-prep-kit-mps-forensic-application-for-the-miseq-fgx%C3%A2-benchtop-sequencer
#3
Catarina Xavier, Walther Parson
Massively Parallel (Next Generation) Sequencing (MPS) technologies have recently been proven useful and successful in typing various markers relevant in forensic genetics, such as STRs, SNPs and mitochondrial genomes. Early studies investigated self-developed DNA libraries, commercially supplied kits are currently being made available to allow a smoother and gradual implementation of such technologies in forensic laboratories. The ForenSeq™ DNA Signature Prep Kit (Illumina, CA) is the first commercially available STR kit that can be used on the MiSeq FGx™ (Illumina, CA) benchtop high-throughput sequencer...
March 1, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28273506/evaluation-of-the-precision-id-ancestry-panel-for-crime-case-work-a-snp-typing-assay-developed-for-typing-of-165-ancestral-informative-markers
#4
Vania Pereira, Helle S Mogensen, Claus Børsting, Niels Morling
The application of massive parallel sequencing (MPS) methodologies in forensic genetics is promising and it is gradually being implemented in forensic genetic case work. One of the major advantages of these technologies is that several traditional electrophoresis assays can be combined into one single MPS assay. This reduces both the amount of sample used and the time of the investigations. This study assessed the utility of the Precision ID Ancestry Panel (Thermo Fisher Scientific, Waltham, USA) in forensic genetics...
February 24, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28242603/optimization-and-validation-of-analysis-method-based-on-27-plex-snp-panel-for-ancestry-inference
#5
Jiang Li, Sun Qifan, Ma Quan, Zhao Wenting, Liu Jing, Zhao Lei, Ji Anquan, Li Caixia
Anthropology generally divides the individuals into the East Asian Mongolia race, European Caucasian race and African Nigro race. The 27-plex single nucleotide polymorphism (SNP) panel for ancestry information has been established to differentiate samples from East Asian, European, African and admixture populations of East Asian and European origin by genotyping and ancestry inference. To infer ancestry for unknown individuals, we established an optimized analysis pipeline based on the likelihood ratio, ancestry component and individual ancestry assignment...
February 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28168762/developing-a-new-nonbinary-snp-fluorescent-multiplex-detection-system-for-forensic-application-in-china
#6
Yanfang Liu, Huidan Liao, Ying Liu, Juanjuan Guo, Yi Sun, Xiaoliang Fu, Ding Xiao, Jifeng Cai, Lingmei Lan, Pingli Xie, Lagabaiyila Zha
Nonbinary single-nucleotide polymorphisms (SNPs) are potential forensic genetic markers because that their discrimination power is greater than that of normal binary SNPs, and that they can detect highly degraded samples. We previously developed a nonbinary SNP multiplex typing assay. In the present study, we selected additional 20 nonbinary SNPs from the NCBI SNP database and verified them through pyrosequencing. These 20 nonbinary SNPs were analyzed using the fluorescent-labeled SNaPshot multiplex SNP typing method...
February 6, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28164539/post-mortem-identification-of-a-fire-carbonized-body-by-str-genotyping
#7
Raluca Dumache, Camelia Muresan, Veronica Ciocan, Alexandru F Rogobete, Alexandra Enache
BACKGROUND: Identification of bodies of unknown identity that are victims of exposure to very high temperatures, resulting from fires, plane crashes, and terrorist attacks, represents one of the most difficult sides of forensic genetics, because of the advanced state of decomposition. The aim of this study was the identification of the carbonized cadaver of a fire victim through STR genotyping. METHODS: We used blood samples obtained from the iliac artery during the autopsy examination as biological samples from the unidentified victim...
October 1, 2016: Clinical Laboratory
https://www.readbyqxmd.com/read/28101645/forensic-parameters-of-19-x-str-polymorphisms-in-two-chinese-populations
#8
Chuncao Deng, Feng Song, Jienan Li, Yi Ye, Lushun Zhang, Weibo Liang, Haibo Luo, Yingbi Li
Application of X-STRs as complements of autosomal STR application in the forensic genetics has become a tendency for kinship testing, especially in deficiency paternity cases. Recently, a novel kit of 19 X-STR loci was developed, which permitted the analysis of 19 STR in the same PCR reaction, and these markers can be clustered into seven groups for the physical linkage. The objective of this study was to evaluate the allele and haplotype diversity of 19 X-STR loci in the Uygur (n = 220) and Tibetan nationality (n = 270) and to estimate the usefulness for complex kinship analysis...
January 18, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28078776/performance-of-the-forenseq-tm-dna-signature-prep-kit-on-highly-degraded-samples
#9
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 this 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 2800 M, 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/28073088/characterization-of-the-iberian-y-chromosome-haplogroup-r-df27-in-northern-spain
#10
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/28012376/importance-sampling-allows-hd-true-tests-of-highly-discriminating-dna-profiles
#11
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/27951431/developmental-validation-of-a-custom-panel-including-273-snps-for-forensic-application-using-ion-torrent-pgm
#12
Suhua Zhang, Yingnan Bian, Anqi Chen, Hancheng Zheng, Yuzhen Gao, Yiping Hou, Chengtao Li
Utilizing massively parallel sequencing (MPS) technology for SNP testing in forensic genetics is becoming attractive because of the shortcomings of STR markers, such as their high mutation rates and disadvantages associated with the current PCR-CE method as well as its limitations regarding multiplex capabilities. MPS offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. In this study, we designed a customized SNP panel that includes 273 forensically relevant identity SNPs chosen from SNPforID, IISNP, and the HapMap database as well as previously related studies and evaluated the levels of genotyping precision, sequence coverage, sensitivity and SNP performance using the Ion Torrent PGM...
December 7, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27890097/forensic-genetic-study-of-29-y-strs-in-korean-population
#13
Ju Yeon Jung, Ji-Hye Park, Yu-Li Oh, Han-Sol Kwon, Hyun-Chul Park, Kyung-Hwa Park, Eun Hye Kim, Dong-Sub Lee, Si-Keun Lim
In this study, we compared two recently released commercial Y-chromosomal short tandem repeat (Y-STR) kits: the PowerPlex Y23 System (PPY23) and Yfiler® Plus PCR amplification kit (YPlus). We performed validation studies, including sensitivity, tolerance to PCR inhibitors, and mixture analysis, and a population genetics study using 306 unrelated South Korean males. PPY23 and YPlus showed similar sensitivity, but PPY23 showed higher tolerance to humic acid than YPlus. Furthermore, the detection rate of unique minor alleles called from male/male mixtures was higher for PPY23 than for YPlus...
November 2016: Legal Medicine
https://www.readbyqxmd.com/read/27826995/molecular-diversity-of-23-y-chromosome-short-tandem-repeat-loci-in-the-population-of-tuzla-canton-bosnia-and-herzegovina
#14
Naida Babić, Serkan Dogan, Jasmina Čakar, Amela Pilav, Damir Marjanović, Vesna Hadžiavdić
BACKGROUND: Tuzla Canton is the most populated region in the ethnically mixed territory of Bosnia and Herzegovina, whose genetic analysis could provide an insight into past demographic events. AIM: Analysis of 23 Y-chromosome STR markers in the population of Tuzla Canton and investigation of the genetic relationship of the male population of the Tuzla Canton and that of the larger Bosnian and Herzegovinian population as well as neighbouring and other European populations...
November 30, 2016: Annals of Human Biology
https://www.readbyqxmd.com/read/27819737/human-autosomal-dna-and-x-chromosome-str-profiles-obtained-from-chrysomya-albiceps-diptera-calliphoridae-larvae-used-as-a-biological-trace
#15
T C Oliveira, A B R Santos, K C N Rabelo, C A Souza, S M Santos, S Crovella
The use of insects to answer questions in criminal investigations, as well as a combination of forensic genetic techniques to obtain human DNA from the organisms, especially necrophagous dipterians, have gained ground in recent decades among researchers and professionals in this area. The objective of our study was to evaluate and compare two methods of human DNA extraction, commonly used for forensic samples, to obtain human autosomal DNA and X chromosome short tandem repeat profiles from the digestive tract of Chrysomya albiceps (Diptera: Calliphoridae) larvae...
November 3, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27816849/a-collaborative-ednap-exercise-on-snapshot%C3%A2-based-mtdna-control-region-typing
#16
N E C Weiler, K Baca, D Ballard, F Balsa, M Bogus, C Børsting, F Brisighelli, J Červenáková, L Chaitanya, M Coble, V Decroyer, S Desmyter, K J van der Gaag, K Gettings, C Haas, J Heinrich, M João Porto, A J Kal, M Kayser, A Kúdelová, N Morling, A Mosquera-Miguel, F Noel, W Parson, V Pereira, C Phillips, P M Schneider, D Syndercombe Court, M Turanska, A Vidaki, P Woliński, L Zatkalíková, T Sijen
A collaborative European DNA Profiling (EDNAP) Group exercise was undertaken to assess the performance of an earlier described SNaPshot™-based screening assay (denoted mini-mtSNaPshot) (Weiler et al., 2016) [1] that targets 18 single nucleotide polymorphism (SNP) positions in the mitochondrial (mt) DNA control region and allows for discrimination of major European mtDNA haplogroups. Besides the organising laboratory, 14 forensic genetics laboratories were involved in the analysis of 13 samples, which were centrally prepared and thoroughly tested prior to shipment...
January 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27796588/study-of-indel-genetic-markers-with-forensic-and-ancestry-informative-interest-in-palop-s-immigrant-populations-in-lisboa
#17
REVIEW
Ana Inácio, Heloísa Afonso Costa, Cláudia Vieira da Silva, Teresa Ribeiro, Maria João Porto, Jorge Costa Santos, Gilberto Igrejas, António Amorim
The migratory phenomenon in Portugal has become one of the main factors for the genetic variability. In the last few years, a new class of autosomal insertion/deletion markers-InDel-has attracted interest in forensic genetics. Since there is no data for InDel markers of Portuguese-speaking African countries (PALOP) immigrants living in Lisboa, our aim is the characterization of those groups of individuals by typing them with at least 30 InDel markers and to compare different groups of individuals/populations...
October 29, 2016: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/27792894/seq-mapper-a-dna-sequence-searching-tool-for-massively-parallel-sequencing-data
#18
James Chun-I Lee, Bill Tseng, Liang-Kai Chang, Adrian Linacre
The development of massively parallel sequencing (MPS) has increased greatly the scale of DNA sequencing. The analysis of massive data-files from single MPS analysis can be a major challenge if examining the data for potential polymorphic loci. To aid in the analysis of both short tandem repeat (STR) and single nucleotide polymorphisms (SNP), we have designed a new program called SEQ Mapper to search for genetic polymorphisms within a large number of reads generated by MPS. This new program has been designed to perform sequence mapping between reference data and generated reads...
January 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27766958/more-comprehensive-forensic-genetic-marker-analyses-for-accurate-human-remains-identification-using-massively-parallel-dna-sequencing
#19
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
https://www.readbyqxmd.com/read/27736937/outlining-the-ancestry-landscape-of-colombian-admixed-populations
#20
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
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