The Interlaboratory Robustness Of Next-Generation Sequencing (IRON) Study Phase II: Deep-Sequencing Analyses Of Hematological Malignancies Performed In 8,867 Cases By An International Network Involving 27 Laboratories

Introduction: Amplicon deep-sequencing using second-generation sequencing technology is an innovative molecular diagnostic technique and enables a highly-sensitive detection of mutations. As an international consortium we had investigated previously the robustness, precision, and reproducibility of 454 amplicon next-generation sequencing (NGS) across 10 laboratories from 8 countries (Leukemia, 2011;25:1840-8).

Aims: In Phase II of the study, we established distinct working groups for various hematological malignancies, i.e. acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), and multiple myeloma. Currently, 27 laboratories from 13 countries are part of this research consortium. In total, 74 gene targets were selected by the working groups and amplicons were developed for a NGS deep-sequencing assay (454 Life Sciences, Branford, CT). A data analysis pipeline was developed to standardize mutation interpretation both for accessing raw data (Roche Amplicon Variant Analyzer, 454 Life Sciences) and variant interpretation (Sequence Pilot, JSI Medical Systems, Kippenheim, Germany).

Results: We will report on the design, standardization, quality control aspects, landscape of mutations, as well as the prognostic and predictive utility of this assay in a cohort of 8,867 cases. Overall, 1,146 primer sequences were designed and tested. In detail, for example in AML, 924 cases had been screened for CEBPA mutations. RUNX1 mutations were analyzed in 1,888 cases applying the deep-sequencing read counts to study the stability of such mutations at relapse and their utility as a biomarker to detect residual disease. Analyses of DNMT3A (n=1,041) were focused to perform landscape investigations and to address the prognostic relevance. Additionally, this working group is focusing on TET2, ASXL1, and TP53 analyses. A novel prognostic model is being developed allowing stratification of AML into prognostic subgroups based on molecular markers only. In ALL, 1,124 pediatric and adult cases have been screened, including 763 assays for TP53 mutations both at diagnosis and relapse of ALL. Pediatric and adult leukemia expert labs developed additional content to study the mutation incidence of other B and T lineage markers such as IKZF1, JAK2, IL7R, PAX5, EP300, LEF1, CRLF2, PHF6, WT1, JAK1, PTEN, AKT1, IL7R, NOTCH1, CREBBP, or FBXW7. Further, the molecular landscape of CLL is changing rapidly. As such, a separate working group focused on analyses including NOTCH1, SF3B1, MYD88, XPO1, FBXW7 and BIRC3. Currently, 922 cases were screened to investigate the range of mutational burden of NOTCH1 mutations for their prognostic relevance. In MDS, RUNX1 mutation analyses were performed in 977 cases. The prognostic relevance of TP53 mutations in MDS was assessed in additional 327 cases, including isolated deletions of chromosome 5q. Next, content was developed targeting genes of the cellular splicing component, e.g. SF3B1, SRSF2, U2AF1, and ZRSR2. In BCR-ABL1-negative MPN, nine genes of interest (JAK2, MPL, TET2, CBL, KRAS, EZH2, IDH1, IDH2, ASXL1) have been analyzed in a cohort of 155 primary myelofibrosis cases searching for novel somatic mutations and addressing their relevance for disease progression and leukemia transformation. Moreover, an assay was developed and applied to CMML cases allowing the simultaneous analysis of 25 leukemia-associated target genes in a single sequencing run using just 20 ng of starting DNA. Finally, nine laboratories are studying CML, applying ultra-deep sequencing of the BCR-ABL1 tyrosine kinase domain. Analyses were performed on 615 cases investigating the dynamics of expansion of mutated clones under various tyrosine kinase inhibitor therapies.

Conclusion: Molecular characterization of hematological malignancies today requires high diagnostic sensitivity and specificity. As part of the IRON-II study, a network of laboratories analyzed a variety of disease entities applying amplicon-based NGS assays. Importantly, the consortium not only standardized assay design for disease-specific panels, but also achieved consensus on a common data analysis pipeline for mutation interpretation. Distinct working groups have been forged to address scientific tasks and in total 8,867 cases had been analyzed thus far.

M Dwarf Flare Continuum Variations on One-second Timescales: Calibrating and Modeling of ULTRACAM Flare Color Indices

We present a large data set of high-cadence dMe flare light curves obtained with custom continuum filters on the triple-beam, high-speed camera system ULTRACAM. The measurements provide constraints for models of the near-ultraviolet (NUV) and optical continuum spectral evolution on timescales of ≈1 s. We provide a robust interpretation of the flare emission in the ULTRACAM filters using simultaneously obtained low-resolution spectra during two moderate-sized flares in the dM4.5e star YZ CMi. By avoiding the spectral complexity within the broadband Johnson filters, the ULTRACAM filters are shown to characterize bona fide continuum emission in the NUV, blue, and red wavelength regimes. The NUV/blue flux ratio in flares is equivalent to a Balmer jump ratio, and the blue/red flux ratio provides an estimate for the color temperature of the optical continuum emission. We present a new “color-color” relationship for these continuum flux ratios at the peaks of the flares. Using the RADYN and RH codes, we interpret the ULTRACAM filter emission using the dominant emission processes from a radiative-hydrodynamic flare model with a high nonthermal electron beam flux, which explains a hot, T ≈ 104 K, color temperature at blue-to-red optical wavelengths and a small Balmer jump ratio as observed in moderate-sized and large flares alike. We also discuss the high time resolution, high signal-to-noise continuum color variations observed in YZ CMi during a giant flare, which increased the NUV flux from this star by over a factor of 100. Based on observations obtained with the Apache Point Observatory 3.5 m telescope, which is owned and operated by the Astrophysical Research Consortium, based on observations made with the William Herschel Telescope operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofsica de Canarias, and observations, and based on observations made with the ESO Telescopes at the La Silla Paranal Observatory under programme ID 085.D-0501(A).

Occurrence of the pinewood nematode, Bursaphelenchus xylophilus in Portugal and perspectives of the disease spread in Europe.

In 1999, the pinewood nematode (PWN) , Bursaphelenchus xylophilus was found and identified for the first time in Portugal and in Europe. Following detection, Portuguese authorities initiated the implementation of eradication measures during 1999 and 2000, following an alert provided to European Community officials; as a result, the nematode was confirmed to be confined in the Setúbal region, near Lisbon. A task force from the follow-up group (GANP) created by the Secretary of State for the Rural Development established a national eradication programme (PROLUNP) to (1) Contain PWN within the initial geographic limits; (2) Implement eradication measures; and (3) Monitor PWN at a national level. Research is presently being conducted both at universities as well as research institutes, focusing on the characterization ofBursaphelenchus species associated with maritime pine, as well as on the insect vector, Monochamus galloprovincialis. Recent reports indicate that the nematode may be present in Siberia (Russia), which would present a threat to Eastern European forestry. Efforts are presently being developed by several European countries to establish a research consortium to detect and study the possible presence of PWN, for a new PRAs. A recent workshop held in Portugal, in 2001, has been an oportunity for sharing experiences and techniques on detection and control. There is clearly a greater awareness of this issue in Europe.

Best Practice for Providing Social Care and Support to People Living with Concurrent Sight Loss and Dementia: Professional Perspectives

Purpose-Approximately 100,000 people in the UK aged 75 and over have concurrent dementia and sight loss, but current understanding of their experiences, needs and preferences is limited. The purpose of this paper is to report on a research project that explored the provision of social care and support for older people with both conditions. Design/methodology/approach-The project was a collaboration between the universities of York, Worcester, Bournemouth and Cambridge, supported by the Thomas Pocklington Trust and the Housing and Dementia Research Consortium. Data for this paper were drawn from focus groups held in 2013 involving 47 professionals across the dementia, sight loss and housing sectors. Findings-Thematic analysis identified five main barriers to providing high-quality, cost-effective social care and support: time constraints; financial limitations; insufficient professional knowledge; a lack of joint working; and inconsistency of services. The requirements of dementia and sight loss often conflict, which can limit the usefulness of equipment, aids and adaptations. Support and information needs to address individual needs and preferences. Research limitations/implications-Unless professionals consider dementia and sight loss together, they are unlikely to think about the impact of both conditions and the potential of their own services to provide effective support for individuals and their informal carers. Failing to consider both conditions together can also limit the availability and accessibility of social care and support services. This paper is based on input from a small sample of self-selecting professionals across three geographical regions of England. More research is needed in this area. Practical implications-There are growing numbers of people living with concurrent dementia and sight loss, many of whom wish to remain living in their own homes. There is limited awareness of the experiences and needs of this group and limited provision of appropriate services aids/adaptations. A range of measures should be implemented in order to support independence and well-being for people living with both conditions and their family carers. These include increased awareness, improved assessment, more training and greater joint working. Social implications-People living with dementia or sight loss are at high risk of social isolation, increasingly so for those with both conditions. Services that take an inclusive approach to both conditions can provide crucial opportunities for social interaction. Extra care housing has the potential to provide a supportive, community-based environment that can help residents to maintain social contact. Originality/value-This paper adds much-needed evidence to the limited existing literature, and reflects the views of diverse professionals across housing, health and social care

Las TIC en la administración de la cadena de suministro y su incidencia en el desempeño operacional

Las tecnologías de la información han empezado a ser un factor importante a tener en cuenta en cada uno de los procesos que se llevan a cabo en la cadena de suministro. Su implementación y correcto uso otorgan a las empresas ventajas que favorecen el desempeño operacional a lo largo de la cadena. El desarrollo y aplicación de software han contribuido a la integración de los diferentes miembros de la cadena, de tal forma que desde los proveedores hasta el cliente final, perciben beneficios en las variables de desempeño operacional y nivel de satisfacción respectivamente. Por otra parte es importante considerar que su implementación no siempre presenta resultados positivos, por el contrario dicho proceso de implementación puede verse afectado seriamente por barreras que impiden maximizar los beneficios que otorgan las TIC.

Liderazgo y emprendimiento. Factores culturales relacionados

El emprendimiento es una característica del liderazgo que puede contribuir al progreso económico de un país. Para que el emprendimiento como habilidad se presente en los individuos, debe existir una serie de variables relacionadas con factores internos y externos que impulsen su desarrollo. Con base en lo anterior, con este trabajo se pretende analizar el efecto que tienen los factores culturales en el emprendimiento, como característica de los líderes, a través de una revisión de la literatura, que permita, por medio de la exposición de sus hallazgos comprender estos fenómenos de manera más integral.

Los grupos paramilitares en Colombia: el incierto tránsito de la guerra a la paz

Esta investigación aborda las condiciones bajo las que se llevó a cabo en Colombia, en el primer gobierno del presidente Álvaro Uribe Vélez (2002-2006), la negociación entre el Estado y los grupos paramilitares. Se establecen las características de ese proceso de paz, su correspondencia con modelos tradicionales de negociación y sus alcances sobre el proceso de Desmovilización, Desarme y Reinserción (DDR) de las organizaciones paramilitares.

Sector agrícola y política de competencia

Los procesos de integración económica han puesto en evidencia que la separación tradicionalmente hecha entre las políticas comercial y de competencia no sólo es ficticia, sino que mantenerla es simplemente contradictorio con la realidad de la economía internacional. En la medida en que los mercados domésticos se han abierto al comercio internacional, se ha considerado que las políticas de competencia pueden hacerse redundantes, ya que la competencia extranjera tiende a garantizar que dichos mercados tienen un nivel adecuado de contestabilidad. Sin embargo, como se muestra en este documento para el caso del sector agrícola, en estas circunstancias, la política de competencia adquiere un nuevo e importante papel que cumplir. Acá se discute la relación general entre el sector agrícola y la política de competencia, en un contexto de relativa liberalización comercial. Se sostiene que es necesario aplicar la política de competencia al sector, ya que esto garantiza las mejores condiciones posibles para incentivar los procesos de cambio tecnológico, indispensables para desarrollar una agricultura dinámica. Igualmente, se afirma que es indispensable una aplicación rigurosa de la política de competencia que, teniendo en cuenta las particularidades de la estructura de mercado de los sectores vinculados a la agricultura hacia adelante y hacia atrás, garantice que el más competitivo sector agrícola no sea sujeto de prácticas anticompetitivas por otros agentes. Esto puede incluir la instauración de algunas excepciones puntuales para el sector, con relación a la política de competencia,

Evolución de la oruga o constreñimiento de la mariposa: una mirada al rol económico de China en Sudán. (1999- 2008)

La presente monografía tiene como propósito analizar el rol económico de China en Sudán de 1999 al 2008. Tras su crisis en la década de 1990, se examina el efecto que el rol chino tuvo en los sectores productivos de la economía sudanesa: el textil, el agrícola, el metalúrgico y el petrolero, aun cómo la estabilidad política en el régimen de Omar Al-Bashir en el ámbito político y el conflicto en Darfur como factor social. Como un último objetivo esta investigación, basándose en el trabajo de Mohammed Ayoob, se reevalúa el estatus de Sudán como Estado Tercermundista ilustrándolo a través del uso de la analogía de la metamorfosis de una mariposa.

Improving flood models using LiDAR: progress and problems

Airborne scanning laser altimetry (LiDAR) is an important new data source for river flood modelling. LiDAR can give dense and accurate DTMs of floodplains for use as model bathymetry. Spatial resolutions of 0.5m or less are possible, with a height accuracy of 0.15m. LiDAR gives a Digital Surface Model (DSM), so vegetation removal software (e.g. TERRASCAN) must be used to obtain a DTM. An example used to illustrate the current state of the art will be the LiDAR data provided by the EA, which has been processed by their in-house software to convert the raw data to a ground DTM and separate vegetation height map. Their method distinguishes trees from buildings on the basis of object size. EA data products include the DTM with or without buildings removed, a vegetation height map, a DTM with bridges removed, etc. Most vegetation removal software ignores short vegetation less than say 1m high. We have attempted to extend vegetation height measurement to short vegetation using local height texture. Typically most of a floodplain may be covered in such vegetation. The idea is to assign friction coefficients depending on local vegetation height, so that friction is spatially varying. This obviates the need to calibrate a global floodplain friction coefficient. It’s not clear at present if the method is useful, but it’s worth testing further. The LiDAR DTM is usually determined by looking for local minima in the raw data, then interpolating between these to form a space-filling height surface. This is a low pass filtering operation, in which objects of high spatial frequency such as buildings, river embankments and walls may be incorrectly classed as vegetation. The problem is particularly acute in urban areas. A solution may be to apply pattern recognition techniques to LiDAR height data fused with other data types such as LiDAR intensity or multispectral CASI data. We are attempting to use digital map data (Mastermap structured topography data) to help to distinguish buildings from trees, and roads from areas of short vegetation. The problems involved in doing this will be discussed. A related problem of how best to merge historic river cross-section data with a LiDAR DTM will also be considered. LiDAR data may also be used to help generate a finite element mesh. In rural area we have decomposed a floodplain mesh according to taller vegetation features such as hedges and trees, so that e.g. hedge elements can be assigned higher friction coefficients than those in adjacent fields. We are attempting to extend this approach to urban area, so that the mesh is decomposed in the vicinity of buildings, roads, etc as well as trees and hedges. A dominant points algorithm is used to identify points of high curvature on a building or road, which act as initial nodes in the meshing process. A difficulty is that the resulting mesh may contain a very large number of nodes. However, the mesh generated may be useful to allow a high resolution FE model to act as a benchmark for a more practical lower resolution model. A further problem discussed will be how best to exploit data redundancy due to the high resolution of the LiDAR compared to that of a typical flood model. Problems occur if features have dimensions smaller than the model cell size e.g. for a 5m-wide embankment within a raster grid model with 15m cell size, the maximum height of the embankment locally could be assigned to each cell covering the embankment. But how could a 5m-wide ditch be represented? Again, this redundancy has been exploited to improve wetting/drying algorithms using the sub-grid-scale LiDAR heights within finite elements at the waterline.