10 research outputs found
CENTRE-PD Top 10 Publication Supplementary Material and Raw Data
Supplementary material and Raw Data for CENTRE-PD Top 10
Blueprint for building a biorepository in a resource-limited setting that follows international best practices
Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe
Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense using various mitochondrial DNA markers on modern and/or ancient specimens. This tends to confound the identification of refugial areas and post-glacial colonization patterns in this group. In this study we used Genotyping-by-Sequencing (GBS) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), in Europe by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g. Iberia) and sources of post-glacial re-expansion (e.g. Carpathians and Balkans) across northern regions of the continent. In addition, we tested multiple post-glacial re-colonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach. We identified the role of ancient and temporary land-bridges in the colonization of Scandinavia and the British Isles, with a natural colonization of Ireland deemed more likely than an ancient human-mediated introduction as has previously been proposed. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not always evident from using more limited marker sets
Immune-escape mutations and stop-codons in HBsAg develop in a large proportion of patients with chronic HBV infection exposed to anti-HBV drugs in Europe
Abstract Background HBsAg immune-escape mutations can favor HBV-transmission also in vaccinated individuals, promote immunosuppression-driven HBV-reactivation, and increase fitness of drug-resistant strains. Stop-codons can enhance HBV oncogenic-properties. Furthermore, as a consequence of the overlapping structure of HBV genome, some immune-escape mutations or stop-codons in HBsAg can derive from drug-resistance mutations in RT. This study is aimed at gaining insight in prevalence and characteristics of immune-associated escape mutations, and stop-codons in HBsAg in chronically HBV-infected patients experiencing nucleos(t)ide analogues (NA) in Europe. Methods This study analyzed 828 chronically HBV-infected European patients exposed to ≥ 1 NA, with detectable HBV-DNA and with an available HBsAg-sequence. The immune-associated escape mutations and the NA-induced immune-escape mutations sI195M, sI196S, and sE164D (resulting from drug-resistance mutation rtM204 V, rtM204I, and rtV173L) were retrieved from literature and examined. Mutations were defined as an aminoacid substitution with respect to a genotype A or D reference sequence. Results At least one immune-associated escape mutation was detected in 22.1% of patients with rising temporal-trend. By multivariable-analysis, genotype-D correlated with higher selection of ≥ 1 immune-associated escape mutation (OR[95%CI]:2.20[1.32–3.67], P = 0.002). In genotype-D, the presence of ≥ 1 immune-associated escape mutations was significantly higher in drug-exposed patients with drug-resistant strains than with wild-type virus (29.5% vs 20.3% P = 0.012). Result confirmed by analysing drug-naïve patients (29.5% vs 21.2%, P = 0.032). Strong correlation was observed between sP120T and rtM204I/V (P
Immune-escape mutations and stop-codons in HBsAg develop in a large proportion of patients with chronic HBV infection exposed to anti-HBV drugs in Europe
Abstract Background HBsAg immune-escape mutations can favor HBV-transmission also in vaccinated individuals, promote immunosuppression-driven HBV-reactivation, and increase fitness of drug-resistant strains. Stop-codons can enhance HBV oncogenic-properties. Furthermore, as a consequence of the overlapping structure of HBV genome, some immune-escape mutations or stop-codons in HBsAg can derive from drug-resistance mutations in RT. This study is aimed at gaining insight in prevalence and characteristics of immune-associated escape mutations, and stop-codons in HBsAg in chronically HBV-infected patients experiencing nucleos(t)ide analogues (NA) in Europe. Methods This study analyzed 828 chronically HBV-infected European patients exposed to ≥ 1 NA, with detectable HBV-DNA and with an available HBsAg-sequence. The immune-associated escape mutations and the NA-induced immune-escape mutations sI195M, sI196S, and sE164D (resulting from drug-resistance mutation rtM204 V, rtM204I, and rtV173L) were retrieved from literature and examined. Mutations were defined as an aminoacid substitution with respect to a genotype A or D reference sequence. Results At least one immune-associated escape mutation was detected in 22.1% of patients with rising temporal-trend. By multivariable-analysis, genotype-D correlated with higher selection of ≥ 1 immune-associated escape mutation (OR[95%CI]:2.20[1.32–3.67], P = 0.002). In genotype-D, the presence of ≥ 1 immune-associated escape mutations was significantly higher in drug-exposed patients with drug-resistant strains than with wild-type virus (29.5% vs 20.3% P = 0.012). Result confirmed by analysing drug-naïve patients (29.5% vs 21.2%, P = 0.032). Strong correlation was observed between sP120T and rtM204I/V (P
Metadata record for: Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study
This dataset contains key characteristics about the data described in the Data Descriptor Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study. Contents: 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON forma
Metadata record for: Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study
This dataset contains key characteristics about the data described in the Data Descriptor Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study. Contents: 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON forma
Animal disease data complementing the European Union One Health 2021 Zoonoses Report
This dataset contains the mandatory annual data reported for bovine tuberculosis and for bovine and ovine and caprine brucellosis based on Directive 2003/99.EU; Excel; [email protected]
EVS Trend File 1981-2017 – Sensitive Dataset
The European Values Study is a large-scale, cross-national and longitudinal survey research program on how Europeans think about family, work, religion, politics, and society. Repeated every nine years in an increasing number of countries, the survey provides insights into the ideas, beliefs, preferences, attitudes, values, and opinions of citizens all over Europe. The EVS Trend File 1981-2017 is constructed from the five EVS waves and covers almost 40 years. In altogether 160 surveys, more than 224.000 respondents from 48 countries/regions were interviewed. It is based on the updated data of the EVS Longitudinal Data File 1981-2008 (v.3.1.0) and the current EVS 2017 Integrated Dataset (v.5.0.0). For the EVS Trend File, a Restricted-Use File (ZA7504) is available in addition to the (factually anonymised) Scientific-Use File (ZA7503). The EVS Trend File – Sensitive Dataset (ZA7504) is provided as an add-on file. In addition to a small set of admin and protocol variables needed to merge with the SUF data, the Sensitive Dataset contains the following variables that could not be included in the scientific-use file due to their sensitive nature: W005_3 Job profession/industry (3-digit ISCO88) - spouse/partner EVS 2008W005_3_01 Job profession/industry (3-digit ISCO08) - spouse/partner EVS 2017W005_4 Job profession/industry (4-digit ISCO88) - spouse/partner EVS 2008X035_3 Job profession/industry (3-digit ISCO88) – respondent EVS 1999, EVS 2008 X035_3_01 Job profession/industry (3-digit ISCO08) - respondent EVS 2017X035_4 Job profession/industry (4-digit ISCO88) – respondent EVS 1999, EVS 2008 x048c_n3 Region where the interview was conducted (NUTS-3): NUTS version 2006 EVS 2008X048J_N3 Region where the interview was conducted (NUTS-3): NUTS version 2016 EVS 2017X049 Size of town (8 categories) EVS 2008, EVS 2017 Detailed information on the anonymization process in the EVS Trend File is provided in the EVS Trend File Variable Report