1,721,037 research outputs found
Advancements in Molecular Prognostics and Diagnostics of Pediatric Myelodysplastic Syndrome and Juvenile Myelomonocytic Leukemia
Full text linkMyelodysplastic syndromes (MDS) and juvenile myelomonocytic leukemia (JMML) are rare hematopoietic stem cell diseases constituting less then 5% of hematopoietic neoplasia in childhood. Pediatric MDS is an heterogeneous groups of disorders with ineffective hematopoiesis and a varying propensity to evolve into acute myeloid leukemia (AML). Juvenile myelomonocytic leukemia (JMML) is a very aggressive myeloproliferative/ myelodysplastic disease characterized by excessive proliferation of granulocytic and monocytic cells and classified by the World Health Organization (WHO) as a separate entity between myeloproliferative neoplasms (MPN) and MDS. The diagnosis of JMML and MDS is difficult and based mainly on morphological criteria, although the revised WHO classification and the proposal of minimal diagnostic criteria have largely improved the diagnosis of these uncommon but appalling childhood diseases. The International Prognostic Scoring System for MDS, which is based on BM blast percentage, cytopenia and cytogenetics, showed limited value for the diagnosis of both MDS and JMML reflecting the differences between MDS and myeloproliferatives disease in children and adults. New molecular markers are being sought to make the diagnosis and the prognosis of these disorders more efficient and rapid.
In this study we applied the most recent high throughput technologies (e.g. gene expression analysis, multiparametric phospho-flow cytometry and next generation sequencing) not only to provide new diagnostic and prognostic tools that can be used together with the well-established gold standard techniques but also to reveal new molecular pathways deregulated in these diseases.
Using gene expression based classification we identified two different signatures in both MDS and JMML with clinical relevance. In MDS patients we identified a group with high risk of evolution into AML; similarly, in JMML patients the classification identified JMML with distinct prognosis outperforming all known clinical parameters in terms of prognostic relevance. Moreover, gene expression profiling in MDS patients provided new target genes involved in the leukemic process toward AML evolution.
Aiming to provide a diagnostic tool for the rapid diagnosis of JMML, we used phospho-flow cytometry and created a simple algorithm for the diagnosis of JMML based on the percentage of p-STAT5 positive cells.
Then, we assessed the feasibility and robustness of ultra deep sequencing technology to detect the mutation load in hematological malignancies. Finally, we report the case of two twins with concordant JMML providing new insight into the pathogenesis of the disease.
In conclusion, all these data clearly showed that the application of gene expression profile analysis, next generation sequencing and phospho-flow cytometry for studying MDS and JMML provided new important tools for the prognosis and the diagnosis of these rare but aggressive diseases.Le sindromi mielodisplastiche (MDS) e la leucemia mielomonocitica giovanile (JMML) sono dei rari disordini ematologici derivanti da disfunzioni a carico delle cellule staminali ematopoietiche e costituiscono meno del 5% di tutte le malattie neoplastiche ematologiche in età pediatrica.
Le MDS sono un gruppo eterogeneo di malattie caratterizzate principalmente da un’ alterata maturazione delle cellule ematopoietiche della filiera mieloide e il maggiore fattore di rischio che le contraddistingue è l’evoluzione in leucemia mieloide acuta (LAM). La leucemia mielomonocitica giovanile è una malattia molto aggressiva, caratterizzata da un’ eccessiva proliferazione di cellule granulocitiche e monocitiche e viene classificata dall’ Organizzazione Mondiale della Sanità (OMS) come una entità separata con caratteristiche intermedie tra le neoplasie mieloproliferative e le sindromi mielodisplastiche.
La diagnosi di MDS e JMML, basata principalmente su caratteristiche morfologiche, è molto difficile; tuttavia i nuovi criteri diagnostici recentemente introdotti nella classificazione OMS ne hanno facilitato la diagnosi. Attualmente la prognosi sull’ IPSS (International Prognostic Scoring System) dell’ adulto, un sistema di assegnazione dei pazienti a diverse fasce di rischio basato sulla percentuale di blasti nel midollo osseo, presenza o meno di citopenia e dati di citogenetica, mostra delle limitazioni quando applicato alle MDS e JMML pediatriche, riconducibile alle differenze esistenti tra le malattie mieloproliferative dell’adulto e del bambino.
Nuovi markers biologici sono, perciò, necessari per migliorare non solo la diagnosi ma anche la prognosi di queste malattie.
In questo studio abbiamo impiegato le più recenti tecnologie (i.e. l’analisi dell’ espressione genica, il sequenziamento di ultima generazione e la citofluorimetria per l’ identificazione dello stato di fosforilazione) non solo per fornire dei nuovi strumenti per la diagnosi e la prognosi da affiancare alle tecniche gold-standard ma anche per individuare nuovi processi biologici alterati in queste malattie.
Mediante lo studio dell’espressione genica, abbiamo identificato la presenza di due sottogruppi con un diverso andamento clinico sia nelle MDS che nelle JMML.
Abbiamo individuato i pazienti MDS con un più alto rischio di evoluzione in LAM e classificato i pazienti JMML in due gruppi con diversa prognosi; l’analisi dell’espressione genica nelle JMML è risultata essere uno strumento in grado di superare per valore prognostico tutti i criteri clinici attualmente impiegati. Inoltre, l’analisi del profilo d’ espressione genica nelle MDS ha permesso di individuare nuovi geni target coinvolti nella progressione verso la LAM.
Al fine di fornire, poi, un nuovo strumento per la diagnosi di JMML abbiamo sviluppato un semplice algoritmo per la diagnosi di JMML basato sulla percentuale di cellule positive per STAT5 fosforilato in citofluorimetria.
Abbiamo valutato, poi, la possibilità di applicare la tecnologia del sequenziamento di ultima generazione (ultra deep sequencing) per l’ identificazione della quantità di mutazioni presente nel midollo delle JMML.
Infine, abbiamo riportato i dati relativi all’analisi di due gemelli concordanti con diagnosi di JMML al fine di fornire nuovi dati per la comprensione della patogenesi di questa malattia.
In conclusione, abbiamo potuto dimostrare come l’impiego dello studio dell’espressione genica, del sequenziamento di ultima generazione e della citofluorimetria per l’identificazione di STAT5 fosforilato siano nuovi e validi strumenti per la prognosi e la diagnosi di queste rare malattie pediatriche
iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data
Full text linkWhole exome sequencing (WES) is a powerful approach for discovering sequence variants in cancer cells but its time effectiveness is limited by the complexity and issues of WES data analysis. Here we present iWhale, a customizable pipeline based on Docker and SCons, reliably detecting somatic variants by three complementary callers (MuTect2, Strelka2 and VarScan2). The results are combined to obtain a single variant call format file for each sample and variants are annotated by integrating a wide range of information extracted from several reference databases, ultimately allowing variant and gene prioritization according to different criteria. iWhale allows users to conduct a complex series of WES analyses with a powerful yet customizable and easy-to-use tool, running on most operating systems (macOs, GNU/Linux and Windows). iWhale code is freely available at https://github.com/alexcoppe/iWhale and the docker image is downloadable from https://hub.docker.com/r/alexcoppe/iwhale
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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