Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing data sets

Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-) emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants’ analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results

Characterisation of age and polarity at onset in bipolar disorder

Background Studying phenotypic and genetic characteristics of age at onset (AAO) and polarity at onset (PAO) in bipolar disorder can provide new insights into disease pathology and facilitate the development of screening tools. Aims To examine the genetic architecture of AAO and PAO and their association with bipolar disorder disease characteristics. Method Genome-wide association studies (GWASs) and polygenic score (PGS) analyses of AAO (n = 12 977) and PAO (n = 6773) were conducted in patients with bipolar disorder from 34 cohorts and a replication sample (n = 2237). The association of onset with disease characteristics was investigated in two of these cohorts. Results Earlier AAO was associated with a higher probability of psychotic symptoms, suicidality, lower educational attainment, not living together and fewer episodes. Depressive onset correlated with suicidality and manic onset correlated with delusions and manic episodes. Systematic differences in AAO between cohorts and continents of origin were observed. This was also reflected in single-nucleotide variant-based heritability estimates, with higher heritabilities for stricter onset definitions. Increased PGS for autism spectrum disorder (β = −0.34 years, s.e. = 0.08), major depression (β = −0.34 years, s.e. = 0.08), schizophrenia (β = −0.39 years, s.e. = 0.08), and educational attainment (β = −0.31 years, s.e. = 0.08) were associated with an earlier AAO. The AAO GWAS identified one significant locus, but this finding did not replicate. Neither GWAS nor PGS analyses yielded significant associations with PAO. Conclusions AAO and PAO are associated with indicators of bipolar disorder severity. Individuals with an earlier onset show an increased polygenic liability for a broad spectrum of psychiatric traits. Systematic differences in AAO across cohorts, continents and phenotype definitions introduce significant heterogeneity, affecting analyses

Marsupials from space: fluctuating asymmetry, geographical information systems and animal conservation

We report the development of a new quantitative method of assessing the effects of anthropogenic impacts on living beings; this method allows us to assess actual impacts and to travel backwards in time to assess impacts. In this method, we have crossed data on fluctuating asymmetry (FA, a measure of environmental or genetic stress), using Didelphis albiventris as a model, with geographical information systems data relating to environmental composition. Our results show that more impacted environments resulted in statistically higher levels of FA. Our method appears to be a useful and flexible conservation tool for assessing anthropogenic impacts

Relationship between morphology and trophic ecology in an assemblage of passerine birds in riparian forests of the Paraná River (Argentina)

We describe the ecomorphology of an assemblage of bird species found in riparian forests of the Middle Paraná River, Argentina. We sought to determine (1) the more important morphological characteristics that separate coexisting species, (2) whether such separation was related to the trophic ecology of each species and (3) whether a priori guilds showed morphological similarity. We tested the hypotheses that (a) a species' morphology is related to the trophic ecology of that species and (b) that species of a priori guilds are morphometrically more similar to each other than to species of different a priori guilds. For this, we considered an assemblage of 29 species of birds from riparian forest that were sampled with mist nets during the 2011 and 2014 breeding seasons. We obtained morphometric measurements of captured individuals and supplemented those data with measurements from museum specimens. Trophic characterisation (diet and trophic microhabitat) was based on a literature review. Results showed a separation of bird species as a function of variables related to trophic ecology (diets and trophic microhabitats) and morphology. After controlling for phylogenetic constraint, species' morphology partially reflected the trophic ecology of the species, supporting the central hypothesis of the ecomorphological discipline and showing that the use of trophic and morphometric data provides complementary data to improve the guild organisation of riparian bird assemblages.Fil: Quiroga, Virginia Mariela. Provincia de Entre Ríos. Centro de Investigaciones Científicas y Transferencia de Tecnología a la Producción. Universidad Autónoma de Entre Ríos. Centro de Investigaciones Científicas y Transferencia de Tecnología a la Producción. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Centro de Investigaciones Científicas y Transferencia de Tecnología a la Producción; ArgentinaFil: Lorenzón, Rodrigo Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto Nacional de Limnología. Universidad Nacional del Litoral. Instituto Nacional de Limnología; ArgentinaFil: Maglier, Gisela. Universidad Nacional del Litoral; ArgentinaFil: Ronchi Virgolini, Ana Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Autónoma de Entre Ríos; Argentin