Reanalysing genomic data by normalized coverage values uncovers CNVs in bone marrow failure gene panels

Inherited bone marrow failure syndromes (IBMFSs) are genetically heterogeneous disorders with cytopenia. Many IBMFSs also feature physical malformations and an increased risk of cancer. Point mutations can be identified in about half of patients. Copy number variation (CNVs) have been reported; however, the frequency and spectrum of CNVs are unknown. Unfortunately, current genome-wide methods have major limitations since they may miss small CNVs or may have low sensitivity due to low read depths. Herein, we aimed to determine whether reanalysis of NGS panel data by normalized coverage value could identify CNVs and characterize them. To address this aim, DNA from IBMFS patients was analyzed by a NGS panel assay of known IBMFS genes. After analysis for point mutations, heterozygous and homozygous CNVs were searched by normalized read coverage ratios and specific thresholds. Of the 258 tested patients, 91 were found to have pathogenic point variants. NGS sample data from 165 patients without pathogenic point mutations were re-analyzed for CNVs; 10 patients were found to have deletions. Diamond Blackfan anemia genes most commonly exhibited heterozygous deletions, and included RPS19, RPL11, and RPL5. A diagnosis of GATA2-related disorder was made in a patient with myelodysplastic syndrome who was found to have a heterozygous GATA2 deletion. Importantly, homozygous FANCA deletion were detected in a patient who could not be previously assigned a specific syndromic diagnosis. Lastly, we identified compound heterozygousity for deletions and pathogenic point variants in RBM8A and PARN genes. All deletions were validated by orthogonal methods. We conclude that careful analysis of normalized coverage values can detect CNVs in NGS panels and should be considered as a standard practice prior to do further investigations

Analyse électrophorétique des lipoprotéines sériques chez les animaux domestiques

Cuvelier R., Andraud G., Berger J.-A., Beaufrère , Bressou C. Analyse électrophorétique des lipoprotéines sériques chez les animaux domestiques. In: Bulletin de l'Académie Vétérinaire de France tome 111 n°5, 1958. pp. 207-221

How and why DNA barcodes underestimate the diversity of microbial eukaryotes

Background: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences. Principal Findings: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependant. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. We provide an explanation for this lineage dependency, which suggests that most species with large effective population sizes will show far less divergence in 18S than protein coding sequences. Conclusions: There is therefore a trade-off between using genes that are easy to amplify in all species, but which by their nature are highly conserved and underestimate the true number of species, and using genes that give a better description of the number of species, but which are more difficult to amplify. We have shown that this trade-off differs between unicellular and multicellular organisms as a likely consequence of differences in effective population sizes. We anticipate that biodiversity of microbial eukaryotic species is underestimated and that numerous ''cryptic species'' will become discernable with the future acquisition of genomic and metagenomic sequences

A multi-model study of the hemispheric transport and deposition of oxidised nitrogen.

Fifteen chemistry-transport models are used to quantify, for the first time, the export of oxidised nitrogen (NOy) to and from four regions (Europe, North America, South Asia, and East Asia), and to estimate the uncertainty in the results. Between 12 and 24% of the NOx emitted is exported from each region annually. The strongest impact of each source region on a foreign region is: Europe on East Asia, North America on Europe, South Asia on East Asia, and East Asia on North America. Europe exports the most NOy, and East Asia the least. East Asia receives the most NOy from the other regions. Between 8 and 15% of NOx emitted in each region is transported over distances larger than 1000 km, with 3–10% ultimately deposited over the foreign regions

The effect of cigarette smoke exposure on the development of inflammation in lungs, gut and joints of TNFΔARE mice

The inflammatory cytokine TNF-alpha is a central mediator in many immune-mediated diseases, such as Crohn's disease (CD), spondyloarthritis (SpA) and chronic obstructive pulmonary disease (COPD). Epidemiologic studies have shown that cigarette smoking (CS) is a prominent common risk factor in these TNF-dependent diseases. We exposed TNF Delta ARE mice; in which a systemic TNF-alpha overexpression leads to the development of inflammation; to 2 or 4 weeks of air or CS. We investigated the effect of deregulated TNF expression on CS-induced pulmonary inflammation and the effect of CS exposure on the initiation and progression of gut and joint inflammation. Upon 2 weeks of CS exposure, inflammation in lungs of TNF Delta ARE mice was significantly aggravated. However, upon 4 weeks of CS-exposure, this aggravation was no longer observed. TNF Delta ARE mice have no increases in CD4+ and CD8+ T cells and a diminished neutrophil response in the lungs after 4 weeks of CS exposure. In the gut and joints of TNF Delta ARE mice, 2 or 4 weeks of CS exposure did not modulate the development of inflammation. In conclusion, CS exposure does not modulate gut and joint inflammation in TNF Delta ARE mice. The lung responses towards CS in TNF Delta ARE mice however depend on the duration of CS exposure

The Influence of Foreign vs North American Emissions on Surface Ozone in the US

As part of the Hemispheric Transport of Air Pollution (HTAP; www.htap.org) project, we analyze results from 16 global and hemispheric chemical transport models and compare these to Clean Air Status and Trends Network (CASTNet) observations in the United States (US) for 2001. Using the policy-relevant maximum daily 8-h ozone (MDA8 O3) statistic, the multi-model ensemble represents the observations well (mean r2=0.57, ensemble bias=+4.1 ppbv for all regions and all seasons) despite a wide range in the individual model results. Correlations are strongest in the NorthEastern US during spring and fall (r2=0.68); and weakest in the Midwestern US in summer (r2=0.46). However, large positive mean biases exist during summer for all Eastern US regions, ranging from 10¿20 ppbv, and a smaller negative bias is present in the Western US during spring (3 ppbv). In most all other regions and seasons, the biases of the model ensemble simulations are 5 ppbv. Sensitivity simulations in which anthropogenic O3-precursor emissions (NOx+NMVOC+CO+aerosols) were decreased by 20% in each of four source regions: East Asia (EA), South Asia (SA), Europe (EU) and North America (NA) show that the greatest response of MDA8 O3 to the summed foreign emissions reductions occurs during spring in the West (0.9 ppbv reduction due to 20% reductions from EA+SA+EU). East Asia is the largest contributor to MDA8 O3 at all ranges of the O3 distribution for most regions (typically 0.45 ppbv). The exception is in the NorthEastern US where European emissions reductions had the greatest impact on MDA8 O3, particularly in the middle of the MDA8 O3 distribution (response of 0.35 ppbv between 35¿55 ppbv). In all regions and seasons, however, O3-precursor emissions reductions of 20% in the NA source region decrease MDA8 O3 the most by a factor of 2 to nearly 10 relative to foreign emissions reductions. The O3 response to anthropogenic NA emissions is greatest in the Eastern US during summer at the high end of the O3 distribution (5-6 ppbv for 20% reductions). While the impact of foreign emissions on surface O3 in the US is not negligible and is of increasing concern given the growth in emissions upwind of the US - domestic emissions reductions remain a farmore effective means of decreasing MDA8 O3 values, particularly those above 75 ppb(the current US standard).JRC.H.2-Air and Climat

Hematopoietic Cell Transplantation in Patients With Primary Immune Regulatory Disorders (PIRD): A Primary Immune Deficiency Treatment Consortium (PIDTC) Survey.

Primary Immune Regulatory Disorders (PIRD) are an expanding group of diseases caused by gene defects in several different immune pathways, such as regulatory T cell function. Patients with PIRD develop clinical manifestations associated with diminished and exaggerated immune responses. Management of these patients is complicated; oftentimes immunosuppressive therapies are insufficient, and patients may require hematopoietic cell transplant (HCT) for treatment. Analysis of HCT data in PIRD patients have previously focused on a single gene defect. This study surveyed transplanted patients with a phenotypic clinical picture consistent with PIRD treated in 33 Primary Immune Deficiency Treatment Consortium centers and European centers. Our data showed that PIRD patients often had immunodeficient and autoimmune features affecting multiple organ systems. Transplantation resulted in resolution of disease manifestations in more than half of the patients with an overall 5-years survival of 67%. This study, the first to encompass disorders across the PIRD spectrum, highlights the need for further research in PIRD management

The influence of foreign vs. North American emissions on surface ozone in the US

As part of the Hemispheric Transport of Air Pollution (HTAP; http:// www.htap.org) project, we analyze results from 15 global and 1 hemispheric chemical transport models and compare these to Clean Air Status and Trends Network (CASTNet) observations in the United States (US) for 2001. Using the policy-relevant maximum daily 8-h average ozone (MDA8 O3) statistic, the multi-model ensemble represents the observations well (mean r2=0.57, ensemble bias = +4.1 ppbv for all US regions and all seasons) despite a wide range in the individual model results. Correlations are strongest in the northeastern US during spring and fall (r2=0.68); and weakest in the midwestern US in summer (r2=0.46). However, large positive mean biases exist during summer for all eastern US regions, ranging from 10–20 ppbv, and a smaller negative bias is present in the western US during spring (~3 ppbv). In nearly all other regions and seasons, the biases of the model ensemble simulations are ≤5 ppbv. Sensitivity simulations in which anthropogenic O3-precursor emissions (NOx + NMVOC + CO + aerosols) were decreased by 20% in four source regions: East Asia (EA), South Asia (SA), Europe (EU) and North America (NA) show that the greatest response of MDA8 O3 to the summed foreign emissions reductions occurs during spring in the West (0.9 ppbv reduction due to 20% emissions reductions from EA + SA + EU). East Asia is the largest contributor to MDA8 O3 at all ranges of the O3 distribution for most regions (typically ~0.45 ppbv) followed closely by Europe. The exception is in the northeastern US where emissions reductions in EU had a slightly greater influence than EA emissions, particularly in the middle of the MDA8 O3 distribution (response of ~0.35 ppbv between 35–55 ppbv). EA and EU influences are both far greater (about 4x) than that from SA in all regions and seasons. In all regions and seasons O3-precursor emissions reductions of 20% in the NA source region decrease MDA8 O3 the most – by a factor of 2 to nearly 10 relative to foreign emissions reductions. The O3 response to anthropogenic NA emissions is greatest in the eastern US during summer at the high end of the O3 distribution (5–6 ppbv for 20% reductions). While the impact of foreign emissions on surface O3 in the US is not negligible – and is of increasing concern given the recent growth in Asian emissions – domestic emissions reductions remain a far more effective means of decreasing MDA8 O3 values, particularly those above 75 ppb (the current US standard)

Eurodelta multi-model simulated and observed particulate matter trends in Europe in the period of 1990-2010

The Eurodelta-Trends (EDT) multi-model experiment, aimed at assessing the efficiency of emission mitigation measures in improving air quality in Europe during 1990-2010, was designed to answer a series of questions regarding European pollution trends; i.e. were there significant trends detected by observations? Do the models manage to reproduce observed trends? How close is the agreement between the models and how large are the deviations from observations? In this paper, we address these issues with respect to particulate matter (PM) pollution. An in-depth trend analysis has been performed for PM10 and PM2.5 for the period of 2000-2010, based on results from six chemical transport models and observational data from the EMEP (Cooperative Programme for Monitoring and Evaluation of the Long-range Transmission of Air Pollutants in Europe) monitoring network. Given harmonization of set-up and main input data, the differences in model results should mainly result from differences in the process formulations within the models themselves, and the spread in the model-simulated trends could be regarded as an indicator for modelling uncertainty.The model ensemble simulations indicate overall decreasing trends in PM10 and PM2.5 from 2000 to 2010, with the total reductions of annual mean concentrations by between 2 and 5 (7 for PM10) mu g m(-3) (or between 10 % and 30 %) across most of Europe (by 0.5-2 mu g m(-3) in Fennoscandia, the north-west of Russia and eastern Europe) during the studied period. Compared to PM2.5, relative PM10 trends are weaker due to large interannual variability of natural coarse PM within the former. The changes in the concentrations of PM individual components are in general consistent with emission reductions. There is reasonable agreement in PM trends estimated by the individual models, with the inter-model variability below 30 %-40 % over most of Europe, increasing to 50 %-60 % in the northern and eastern parts of the EDT domain.Averaged over measurement sites (26 for PM10 and 13 for PM2.5), the mean ensemble-simulated trends are - 0.24 and -0.22 mu g m(-3) yr(-1) for PM10 and PM2.5, which are somewhat weaker than the observed trends of - 0.35 and -0.40 mu g m(-3) yr(-1) respectively, partly due to model underestimation of PM concentrations. The correspondence is better in relative PM10 and PM2.5 trends, which are -1.7 % yr(-1) and -2.0 % yr(-1) from the model ensemble and -2.1 % yr(-1) and -2.9 % yr(-1) from the observations respectively. The observations identify significant trends (at the 95 % confidence level) for PM10 at 56 % of the sites and for PM2.5 at 36 % of the sites, which is somewhat less that the fractions of significant modelled trends. Further, we find somewhat smaller spatial variability of modelled PM trends with respect to the observed ones across Europe and also within individual countries.The strongest decreasing PM trends and the largest number of sites with significant trends are found for the summer season, according to both the model ensemble and observations. The winter PM trends are very weak and mostly insignificant. Important reasons for that are the very modest reductions and even increases in the emissions of primary PM from residential heating in winter. It should be kept in mind that all findings regarding modelled versus observed PM trends are limited to the regions where the sites are located.The analysis reveals considerable variability of the role of the individual aerosols in PM10 trends across European countries. The multi-model simulations, supported by available observations, point to decreases in SO42- concentrations playing an overall dominant role. Also, we see relatively large contributions of the trends of NH4+ and NO3- to PM10 decreasing trends in Germany, Denmark, Poland and the Po Valley, while the reductions of primary PM emissions appear to be a dominant factor in bringing down PM10 in France, Norway, Portugal, Greece and parts of the UK and Russia. Further discussions are given with respect to emission uncertainties (including the implications of not accounting for forest fires and natural mineral dust by some of the models) and the effect of inter-annual meteorological variability on the trend analysis.Peer reviewe

A multi-model analysis of vertical ozone profiles

A multi-model study of the long-range transport of ozone and its precursors from major anthropogenic source regions was coordinated by the Task Force on Hemispheric Transport of Air Pollution (TF HTAP) under the Convention on Long-range Transboundary Air Pollution (LRTAP). Vertical profiles of ozone at 12-h intervals from 2001 are available from twelve of the models contributing to this study and are compared here with observed profiles from ozonesondes. The contributions from each major source region are analysed for selected sondes, and this analysis is supplemented by retroplume calculations using the FLEXPART Lagrangian particle dispersion model to provide insight into the origin of ozone transport events and the cause of differences between the models and observations. In the boundary layer ozone levels are in general strongly affected by regional sources and sinks. With a considerably longer lifetime in the free troposphere, ozone here is to a much larger extent affected by processes on a larger scale such as intercontinental transport and exchange with the stratosphere. Such individual events are difficult to trace over several days or weeks of transport. This may explain why statistical relationships between models and ozonesonde measurements are far less satisfactory than shown in previous studies for surface measurements at all seasons. The lowest bias between model-calculated ozone profiles and the ozonesonde measurements is seen in the winter and autumn months. Following the increase in photochemical activity in the spring and summer months, the spread in model results increases, and the agreement between ozonesonde measurements and the individual models deteriorates further. At selected sites calculated contributions to ozone levels in the free troposphere from intercontinental transport are shown. Intercontinental transport is identified based on differences in model calculations with unperturbed emissions and emissions reduced by 20% by region. Intercontinental transport of ozone is finally determined based on differences in model ensemble calculations. With emissions perturbed by 20% per region, calculated intercontinental contributions to ozone in the free troposphere range from less than 1 ppb to 3 ppb, with small contributions in winter. The results are corroborated by the retroplume calculations. At several locations the seasonal contributions to ozone in the free troposphere from intercontinental transport differ from what was shown earlier at the surface using the same dataset. The large spread in model results points to a need of further evaluation of the chemical and physical processes in order to improve the credibility of global model results