Benchmarking whole exome sequencing in the German Network for Personalized Medicine

Introduction Whole Exome Sequencing (WES) has emerged as an efficient tool in clinical cancer diagnostics to broaden the scope from panel-based diagnostics to screening of all genes and enabling robust determination of complex biomarkers in a single analysis. Methods To assess concordance, six formalin-fixed paraffin-embedded (FFPE) tissue specimens and four commercial reference standards were analyzed by WES as matched tumor-normal DNA at 21 NGS centers in Germany, each employing local wet-lab and bioinformatics investigating somatic and germline variants, copy-number alteration (CNA), and different complex biomarkers. Somatic variant calling was performed in 494 diagnostically relevant cancer genes. In addition, all raw data were re-analyzed with a central bioinformatic pipeline to separate wet- and dry-lab variability. Results The mean positive percentage agreement (PPA) of somatic variant calling was 76% and positive predictive value (PPV) 89% compared a consensus list of variants found by at least five centers. Variant filtering was identified as the main cause for divergent variant calls. Adjusting filter criteria and re-analysis increased the PPA to 88% for all and 97% for clinically relevant variants. CNA calls were concordant for 82% of genomic regions. Calls of homologous recombination deficiency (HRD), tumor mutational burden (TMB), and microsatellite instability (MSI) status were concordant for 94%, 93%, and 93% respectively. Variability of CNAs and complex biomarkers did not increase considerably using the central pipeline and was hence attributed to wet-lab differences. Conclusion Continuous optimization of bioinformatic workflows and participating in round robin tests are recommend

Organisms Diversity & Evolution

p. 47-57Mesopneumonia of 28 and lungs of 44 species of scincomorph lizards are described, representing mesopneumonia in six of the seven scincomorph families and lungs of all seven families of this taxon. Except for gymnophthalmids and scincids, a family typical organization of mesopneumonia occurs. In cordylids, gerrhosaurids, xantusiids and lacertids the complete right ventral mesopneumonium (VMp) inserts cranially on the posterior vena cava and caudally on the dorsal surface of the right liver lobe. The left VMp is attached to the ventrolateral body wall in cordylids and lacertids; in gerrhosaurids the left VMp is short and inserts on the pericardium and the posterior vena cava; in xantusiids the left VMp is reduced and the lungs are fused cranially with the pericardium. In scincids the VMp of both sides vary in length and insert on the ventral mesentery, or may be lacking completely. The visceral topology of the gymnophthalmids Calyptommatus and Notobachia differs from the general scincomorph pattern, with the liver and stomach elongated and situated on the right and left side of the body cavity, respectively. The left and the right VMp extend over the entire length of the lungs and insert on the ventral mesentery. All lungs examined in the study are single-chambered and show no major structural variability of the inner surfaces, except in lacertids, some gerrhosaurids, Cordylus, and two genera of gymnophthalmids (Echinosaura and Neusticurus). In these groups, rows of dorsomedial niches are present. r 2005 Elsevier GmbH. All rights reserved

Akt and mTORC1 signaling as predictive biomarkers for the EGFR antibody nimotuzumab in glioblastoma

Glioblastoma (GB) is the most frequent primary brain tumor in adults with a dismal prognosis despite aggressive treatment including surgical resection, radiotherapy and chemotherapy with the alkylating agent temozolomide. Thus far, the successful implementation of the concept of targeted therapy where a drug targets a selective alteration in cancer cells was mainly limited to model diseases with identified genetic drivers. One of the most commonly altered oncogenic drivers of GB and therefore plausible therapeutic target is the epidermal growth factor receptor (EGFR). Trials targeting this signaling cascade, however, have been negative, including the phase III OSAG 101-BSA-05 trial. This highlights the need for further patient selection to identify subgroups of GB with true EGFR-dependency. In this retrospective analysis of treatment-naïve samples of the OSAG 101-BSA-05 trial cohort, we identify the EGFR signaling activity markers phosphorylated PRAS40 and phosphorylated ribosomal protein S6 as predictive markers for treatment efficacy of the EGFR-blocking antibody nimotuzumab in MGMT promoter unmethylated GBs. Considering the total trial population irrespective of MGMT status, a clear trend towards a survival benefit from nimotuzumab was already detectable when tumors had above median levels of phosphorylated ribosomal protein S6. These results could constitute a basis for further investigations of nimotuzumab or other EGFR- and downstream signaling inhibitors in selected patient cohorts using the reported criteria as candidate predictive biomarkers

Integrating Nitrogen Fluxes at the European Scale

Environmental problems related to nitrogen concern all economic sectors and impact all media: atmosphere, pedosphere, hydrosphere and anthroposphere. Therefore, the integration of fl uxes allows an overall coverage of problems related to reactive nitrogen (N r ) in the environment, which is not accessible from sectoral approaches or by focusing on specifi c media. This chapter presents a set of high resolution maps showing key elements of the N fl ux budget across Europe, including N2 and Nr fluxes. Comparative nitrogen budgets are also presented for a range of European countries, highlighting the most effi cient strategies for mitigating Nr problems at a national scale. A new European Nitrogen Budget (EU-27) is presented on the basis of state-of-the-art Europe-wide models and databases focusing on diff erent segments of Europe’s society. From c . 18 Tg Nr yr−1 input to agriculture in the EU-27, only about 7 Tg N r yr− 1 fi nd their way to the consumer or are further processed by industry. Some 3.7 Tg N r yr −1 is released by the burning of fossil fuels in the EU-27, whereby the contribution of the industry and energy sectors is equal to that of the transport sector. More than 8 Tg N r yr −1 are disposed of to the hydrosphere, while the EU-27 is a net exporter of reactive nitrogen through atmospheric transport of c . 2.3 Tg N r yr−1. The largest single sink for Nr appears to be denitrifi cation to N 2 in European coastal shelf regions (potentially as large as the input of mineral fertilizer, about 11 Tg N yr –1 for the EU-27); however, this sink is also the most uncertain, because of the uncertainty of N r import from the open ocean. Major uncertainties: National nitrogen budgets are diffi cult to compile using a large range of data sources and are currently available only for a limited number of countries. Modelling approaches have been used to fi ll in the data gaps in some of these budgets, but it became obvious during this study that further research is needed in order to collect necessary data and make national nitrogen budgets inter-comparable across Europe. In some countries, due to inconsistent or contradictory information coming from diff erent data sources, closure of the nitrogen budget was not possible. Recommendations: • The large variety of problems associated with the excess of Nr in the European environment, including adverse impacts, requires an integrated nitrogen management approach that would allow for creation and closure of N budgets within European environments. • Development of nitrogen budgets nationwide, their assessment and management could become an eff ective tool to prioritize measures and prevent unwanted side effects.JRC.DDG.H.2-Climate change and air qualit

Integrating nitrogen fluxes at the European scale

Executive summary Nature of the problem • Environmental problems related to nitrogen concern all economic sectors and impact all media: atmosphere, pedosphere, hydrosphere and anthroposphere. • Therefore, the integration of fluxes allows an overall coverage of problems related to reactive nitrogen (Nr) in the environment, which is not accessible from sectoral approaches or by focusing on specific media. Approaches • This chapter presents a set of high resolution maps showing key elements of the N flux budget across Europe, including N2 and Nr fluxes. • Comparative nitrogen budgets are also presented for a range of European countries, highlighting the most efficient strategies for mitigating Nr problems at a national scale. A new European Nitrogen Budget (EU-27) is presented on the basis of state-of-the-art Europe-wide models and databases focusing on different segments of Europe’s society. Key findings • From c. 18 Tg Nr yr −1 input to agriculture in the EU-27, only about 7 Tg Nr yr− 1 find their way to the consumer or are further processed by industry. • Some 3.7 Tg Nr yr−1 is released by the burning of fossil fuels in the EU-27, whereby the contribution of the industry and energy sectors is equal to that of the transport sector. More than 8 Tg Nr yr−1 are disposed of to the hydrosphere, while the EU-27 is a net exporter of reactive nitrogen through atmospheric transport of c. 2.3 Tg Nr yr−1. • The largest single sink for Nr appears to be denitrifi cation to N2 in European coastal shelf regions (potentially as large as the input of mineral fertilizer, about 11 Tg N yr–1 for the EU-27); however, this sink is also the most uncertain, because of the uncertainty of Nr import from the open ocean. Major uncertainties • National nitrogen budgets are diffi cult to compile using a large range of data sources and are currently available only for a limited number of countries. • Modelling approaches have been used to fill in the data gaps in some of these budgets, but it became obvious during this study that further research is needed in order to collect necessary data and make national nitrogen budgets inter-comparable across Europe. • In some countries, due to inconsistent or contradictory information coming from different data sources, closure of the nitrogen budget was not possible. Recommendations • The large variety of problems associated with the excess of Nr in the European environment,including adverse impacts, requires an integrated nitrogen management approach that would allow for creation and closure of N budgets within European environments. • Development of nitrogen budgets nationwide, their assessment and management could become an effective tool to prioritize measures and prevent unwanted side effects