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Toedling J.,University Pierre and Marie Curie | Toedling J.,French Institute of Health and Medical Research | Toedling J.,MINES ParisTech | Toedling J.,French National Center for Scientific Research | And 16 more authors.
PLoS ONE | Year: 2012

Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons. © 2012 Toedling et al.

Guex N.,Swiss Institute of Bioinformatics | Iseli C.,Swiss Institute of Bioinformatics | Syngelaki A.,Kings College London | Deluen C.,Fasteris | And 4 more authors.
Prenatal Diagnosis | Year: 2013

What's already known about this topic?Non-invasive genome-wide screening of fetal aneuploidy by shotgun sequencing cell-free DNA in maternal blood has been shown to effectively identify fetal trisomy 21, but the performance of screening for other aneuploidies is variable. What does this study add?Optimizing all individual steps in the procedure and performing rigorous quality control provides a test capable of replacing invasive testing for the major aneuploidies. © 2013 John Wiley & Sons, Ltd.

Tiacci E.,University of Perugia | Trifonov V.,Center for Computational Biology and Bioinformatics | Schiavoni G.,University of Perugia | Holmes A.,Center for Computational Biology and Bioinformatics | And 33 more authors.
New England Journal of Medicine | Year: 2011

Background: Hairy-cell leukemia (HCL) is a well-defined clinicopathological entity whose underlying genetic lesion is still obscure. Methods: We searched for HCL-associated mutations by performing massively parallel sequencing of the whole exome of leukemic and matched normal cells purified from the peripheral blood of an index patient with HCL. Findings were validated by Sanger sequencing in 47 additional patients with HCL. Results: Whole-exome sequencing identified five missense somatic clonal mutations that were confirmed on Sanger sequencing, including a heterozygous mutation in BRAF that results in the BRAF V600E variant protein. Since BRAF V600E is oncogenic in other tumors, further analyses were focused on this genetic lesion. The same BRAF mutation was noted in all the other 47 patients with HCL who were evaluated by means of Sanger sequencing. None of the 195 patients with other peripheral B-cell lymphomas or leukemias who were evaluated carried the BRAF V600E variant, including 38 patients with splenic marginal-zone lymphomas or unclassifiable splenic lymphomas or leukemias. In immunohistologic and Western blot studies, HCL cells expressed phosphorylated MEK and ERK (the downstream targets of the BRAF kinase), indicating a constitutive activation of the RAF-MEK-ERK mitogen-activated protein kinase pathway in HCL. In vitro incubation of BRAF-mutated primary leukemic hairy cells from 5 patients with PLX-4720, a specific inhibitor of active BRAF, led to a marked decrease in phosphorylated ERK and MEK. Conclusions: The BRAF V600E mutation was present in all patients with HCL who were evaluated. This finding may have implications for the pathogenesis, diagnosis, and targeted therapy of HCL. (Funded by Associazione Italiana per la Ricerca sul Cancro and others.) Copyright © 2011 Massachusetts Medical Society.

Vincent N.,Fasteris | Osteras M.,Fasteris | Otten P.,Fasteris | Leclerc M.,556 rue Isabelle Romee
Meta Gene | Year: 2014

The sea star Asterias rubens reacts specifically to the antigen:HRP (horseradish peroxydase) and produces an antibody anti-HRP. We previously identified a candidate Ig kappa gene corresponding to this manuscript. We show now the gene referred to as: "sea star Ig kappa gene in its specificity". © 2014 The Authors.

Leclerc M.,University of Orleans | Otten P.,Fasteris | Osteras M.,Fasteris
American Journal of Immunology | Year: 2013

The axial organ of the sea-star Asterias rubens is a primitive immune organ. The B-like cells, when stimulated by various antigens, produce antibody substances correlated with Ig Kappa gene. A candidate Ig kappa gene (IgK chain V-IV region S107B precursor) more convincing in term of genome was shown. © 2013 Science Publication.

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