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

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. 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

Interior Structure of a Charged Spinning Black Hole in (2+1)(2+1)-Dimensions

The phenomenon of mass inflation is shown to occur for a rotating black hole. We demonstrate this feature in $(2+1)$ dimensions by extending the charged spinning BTZ black hole to Vaidya form. We find that the mass function diverges in a manner quantitatively similar to its static counterparts in $(3+1)$, $(2+1)$ and $(1+1)$ dimensions.Comment: 5 pages, 2 figures (appended as postscript files), WATPHYS-TH94/0

On the determinants of local government debt: Does one size fit all?

This paper analyzes the factors that directly influence levels of debt in Spanish local governments. Specifically, the main objective is to find out the extent to which indebtedness is originated by controllable factors that public managers can influence, or whether it hinges on other variables beyond managers’ control. The importance of this issue has intensified since the start of the crisis in 2007, due to the abrupt decline of revenues and, simultaneously, to the stagnation (or even increase) in the levels of costs facing these institutions face. Results can be explored from multiple perspectives, given that the set of explanatory factors is also multiple. However, the most interesting result relates to the varying effect of each covariate depending on each municipality’s specific debt level, which suggests that economic policy recommendations should not be homogeneous across local governments

PESERA-PEAT: a fluvial erosion model for blanket peatlands

In peatlands, fluvial erosion can lead to a dramatic decline in hydrological function, major changes in the net carbon balance and loss of biodiversity. Climate and land management change are thought to be important influences on rates of peat erosion. However, sediment production in peatlands is different to that of other soils and no models of erosion specifically for peatlands currently exist. Hence, forecasting the influence of future climate or spatially-distributed management interventions on peat erosion is difficult. The PESERA-GRID model was substantially modified in this study to include dominant blanket peat erosion processes. In the resulting fluvial erosion model, PESERA-PEAT, freeze–thaw and desiccation processes were accounted for by a novel sediment supply index as key features of erosion. Land management practices were parameterized for their influence on vegetation cover, biomass and soil moisture condition. PESERA-PEAT was numerically evaluated using available field data from four blanket peat-covered catchments with different erosion conditions and management intensity. PESERA-PEAT was found to be robust in modelling fluvial erosion in blanket peat. A sensitivity analysis of PESERA-PEAT showed that modelled sediment yield was more sensitive to vegetation cover than other tested factors such as precipitation, temperature, drainage density and ditch/gully depth. Two versions of PESERA-PEAT, equilibrium and time-series, produced similar results under the same environmental conditions, facilitating the use of the model at different scales. The equilibrium model is suitable for assessing the high-resolution spatial variability of average monthly peat erosion over the study period across large areas (national or global assessments), while the time-series model is appropriate for investigating continuous monthly peat erosion throughout study periods across smaller areas or large regions using a coarser-spatial resolution. PESERA-PEAT will therefore support future investigations into the impact of climate change and management options on blanket peat erosion at various spatial and temporal scales

Vascular Endothelial Growth Factor (VEGF) as a biomarker for Cancer Associated Thrombosis: a meta-analysis

Cancer-associated thrombosis affects between 1 and 20% of all patients diagnosed with cancer and is associated with significant morbidity and poorer prognosis. VEGF is a potent angiogenic factor, produced by tumour cells, and released by platelets and is essential for tumour growth and progression as well as the promotion of thrombosis. Therefore, the potential of VEGF to be used as a biomarker to predict cancer-associated thrombosis requires further investigation. PubMed and OVID databases were systematically searched up to July 2023, and inclusion and exclusion criteria applied. Seven papers (1528 participants) were identified and included in the meta-analysis, three of which (922 participants) measured VEGF before a thrombotic event, and the remaining four (606 participants) which measured VEGF at the time of the thrombosis. Our results showed that although plasma and serum VEGF levels tended to be higher in those who subsequently developed thrombosis than those who did not (mean difference 70.2 pg/mL for serum, and 11.44 pg/mL for plasma VEGF, 95% CI -2.39 – 25.73, p= 0.10), this was not found to be statistically significant. However, analysis of VEGF following blood sampling at the time of thrombosis, showed a stronger statistically significant association between increased VEGF levels and presence of thrombosis (mean difference 117.02 pg/mL for serum, and 116.6 pg/mL for plasma VEGF, 95% CI 55.42 - 190.82, p = 0.0004). Based on current studies, whilst it is increased at the time of thrombosis, VEGF is not effective as a predictive biomarker of CAT

Analytical validation of a next generation sequencing liquid biopsy assay for high sensitivity broad molecular profiling.

Circulating tumor DNA (ctDNA) analysis is being incorporated into cancer care; notably in profiling patients to guide treatment decisions. Responses to targeted therapies have been observed in patients with actionable mutations detected in plasma DNA at variant allele fractions (VAFs) below 0.5%. Highly sensitive methods are therefore required for optimal clinical use. To enable objective assessment of assay performance, detailed analytical validation is required. We developed the InVisionFirst™ assay, an assay based on enhanced tagged amplicon sequencing (eTAm-Seq™) technology to profile 36 genes commonly mutated in non-small cell lung cancer (NSCLC) and other cancer types for actionable genomic alterations in cell-free DNA. The assay has been developed to detect point mutations, indels, amplifications and gene fusions that commonly occur in NSCLC. For analytical validation, two 10mL blood tubes were collected from NSCLC patients and healthy volunteer donors. In addition, contrived samples were used to represent a wide spectrum of genetic aberrations and VAFs. Samples were analyzed by multiple operators, at different times and using different reagent Lots. Results were compared with digital PCR (dPCR). The InVisionFirst assay demonstrated an excellent limit of detection, with 99.48% sensitivity for SNVs present at VAF range 0.25%-0.33%, 92.46% sensitivity for indels at 0.25% VAF and a high rate of detection at lower frequencies while retaining high specificity (99.9997% per base). The assay also detected ALK and ROS1 gene fusions, and DNA amplifications in ERBB2, FGFR1, MET and EGFR with high sensitivity and specificity. Comparison between the InVisionFirst assay and dPCR in a series of cancer patients showed high concordance. This analytical validation demonstrated that the InVisionFirst assay is highly sensitive, specific and robust, and meets analytical requirements for clinical applications

Validation of a Cost-Efficient Multi-Purpose SNP Panel for Disease Based Research

BACKGROUND: Here we present convergent methodologies using theoretical calculations, empirical assessment on in-house and publicly available datasets as well as in silico simulations, that validate a panel of SNPs for a variety of necessary tasks in human genetics disease research before resources are committed to larger-scale genotyping studies on those samples. While large-scale well-funded human genetic studies routinely have up to a million SNP genotypes, samples in a human genetics laboratory that are not yet part of such studies may be productively utilized in pilot projects or as part of targeted follow-up work though such smaller scale applications require at least some genome-wide genotype data for quality control purposes such as DNA "barcoding" to detect swaps or contamination issues, determining familial relationships between samples and correcting biases due to population effects such as population stratification in pilot studies. PRINCIPAL FINDINGS: Empirical performance in classification of relative types for any two given DNA samples (e.g., full siblings, parental, etc) indicated that for outbred populations the panel performs sufficiently to classify relationship in extended families and therefore also for smaller structures such as trios and for twin zygosity testing. Additionally, familial relationships do not significantly diminish the (mean match) probability of sharing SNP genotypes in pedigrees, further indicating the uniqueness of the "barcode." Simulation using these SNPs for an African American case-control disease association study demonstrated that population stratification, even in complex admixed samples, can be adequately corrected under a range of disease models using the SNP panel. CONCLUSION: The panel has been validated for use in a variety of human disease genetics research tasks including sample barcoding, relationship verification, population substructure detection and statistical correction. Given the ease of genotyping our specific assay contained herein, this panel represents a useful and economical panel for human geneticists