Analysis of DNA profiles of ash (Fraxinus excelsior L.) to provide evidence of illegal logging

Tereba, Anna; Woodward, Stephen; Konecka, Agata; Borys, M.W.; Nowakowska, Justyna A.

doi:10.1007/s00226-017-0942-5

Cited by 18 publications

(15 citation statements)

References 27 publications

(37 reference statements)

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“…PowerStats 1.2 Microsoft® Excel spreadsheet (Promega, Madison, WI) was used to calculate allele frequencies and bio‐statistic forensic parameters useful to assess the utility of the loci for forensic and paternity purposes, namely Observed Heterozygosity, Expected Heterozygosity (He), Power of Discrimination (PD), Power of Exclusion, Match Probability, Polymorphic Information Content, Typical Paternity Index, and exact test ( p ) were estimated.…”

Section: Methodsmentioning

confidence: 99%

Optimization of a reduced volume PCR amplification for PowerPlex® Fusion kit using FTA™ cards and generation of population genetic data for Brunei population

et al. 2018

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The commercial PowerPlex® Fusion kit is an autosomal STR multiplex kit that has high discrimination power and is more informative in forensic, paternity, and relationship-testing cases. Key features of this multiplex system are the possibility to direct amplify FTA™ card punches as well as non-FTA cards and commonly used swabs; optimised inhibitor tolerance and high sensitivity generating full profiles from amount as little as 100 pg of human DNA. This study focused on the optimization of performance variables such as FTA™ punch sizes, reduced reaction volumes, and FTA™ purification reagent aiming to increase the analytical sensitivity, decrease the sample consumption, and cost effectiveness. LOD and LOQ values demonstrated high sensitivity of the PowerPlex® Fusion system. In addition, population databases of Brunei Malay and Chinese from the Brunei Darussalam were established, and parameters of forensic importance were calculated. Overall, the forensic parameters indicated an enhanced utility of the PowerPlex® Fusion kit for forensic evidence analysis and paternity testing in Brunei Malay and Chinese populations.

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Section: Methodsmentioning

confidence: 99%

Optimization of a reduced volume PCR amplification for PowerPlex® Fusion kit using FTA™ cards and generation of population genetic data for Brunei population

et al. 2018

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“…F ST values and the exact test for Hardy Weinberg equilibrium (HWE) and linkage equilibrium (LE) were carried out using Arlequin version 3.5 . Forensic parameters were calculated using PowerStats version 1.2 . Population attribution was estimated using Arlequin version 3.5 and Snipper version 2.5 .…”

Section: Methodsmentioning

confidence: 99%

Analysis of four PCR/SNaPshot multiplex assays analyzing 52 SNPforID markers

Goodwin

Alimat

2017

Electrophoresis

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The SNPforID consortium identified a panel of 52 SNPs for 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. We have modified the original assay and split it into four multiplex reactions, each followed by an SBE assay. These multiplex assays were analyzed using polymer POP-4™ on ABI 310 PRISM® and polymers POP-4™, POP-6™ and POP-7™ on the 3500 Genetic Analyzer. The assays were sensitive and reproducible with input DNA as low as 60 pg using both the ABI 310 and 3500. In addition, we found that POP-6™ was most effective with the 3500, based on the parameters that we assessed, achieving better separation of the small SBE products; this conflicted with the recommended use of POP-7™ by the instrument manufacturer. To support the use of the SNP panel in casework in Malaysia we have created an allele frequency database from 325 individuals, representing the major population groups within Malaysia. Population and forensic parameters were estimated for all populations and its efficacy evaluated using 51 forensic samples from challenging casework.

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“…Genetic diversity parameters, allele frequencies, observed and expected heterozygosities, and HWE were estimated with Arlequin v.3.5 . Forensic genetic parameters discrimination power (DP), match probability (MP), polymorphic information content (PIC), typical paternity index (TPI), and power of exclusion (PE), Combined Power of Discrimination (CPD), Combined Match Probability (CMP), Combined Power of Exclusion (CPE) were estimated per loci, population and overall using Powerstats v.1.2 (Promega Corporation).…”

Section: Methodsmentioning

confidence: 99%

Forensic performance of Investigator DIPplex indels genotyping kit in native, immigrant, and admixed populations in South Africa

2015

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The utilization of binary markers in human individual identification is gaining ground in forensic genetics. We analyzed the polymorphisms from the first commercial indel kit Investigator DIPplex (Qiagen) in 512 individuals from Afrikaner, Indian, admixed Cape Colored, and the native Bantu Xhosa and Zulu origin in South Africa and evaluated forensic and population genetics parameters for their forensic application in South Africa. The levels of genetic diversity in population and forensic parameters in South Africa are similar to other published data, with lower diversity values for the native Bantu. Departures from Hardy-Weinberg expectations were observed in HLD97 in Indians, Admixed and Bantus, along with 6.83% null homozygotes in the Bantu populations. Sequencing of the flanking regions showed a previously reported transition G>A in rs17245568. Strong population structure was detected with Fst, AMOVA, and the Bayesian unsupervised clustering method in STRUCTURE. Therefore we evaluated the efficiency of individual assignments to population groups using the ancestral membership proportions from STRUCTURE and the Bayesian classification algorithm in Snipper App Suite. Both methods showed low cross-assignment error (0-4%) between Bantus and either Afrikaners or Indians. The differentiation between populations seems to be driven by four loci under positive selection pressure. Based on these results, we draw recommendations for the application of this kit in SA.

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Analysis of DNA profiles of ash (Fraxinus excelsior L.) to provide evidence of illegal logging

Cited by 18 publications

References 27 publications

Optimization of a reduced volume PCR amplification for PowerPlex® Fusion kit using FTA™ cards and generation of population genetic data for Brunei population

Optimization of a reduced volume PCR amplification for PowerPlex® Fusion kit using FTA™ cards and generation of population genetic data for Brunei population

Analysis of four PCR/SNaPshot multiplex assays analyzing 52 SNPforID markers

Forensic performance of Investigator DIPplex indels genotyping kit in native, immigrant, and admixed populations in South Africa

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