Microarray Center

Luxembourg, Luxembourg

Microarray Center

Luxembourg, Luxembourg
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"Cost was a limiting factor for panels with a large number of amplicons. For researchers that need to change their gene content frequently, the lower price for oligos is really great," said Pan Zhang, Ph.D., M.D., director, Sequencing and Microarray Center at Coriell Institute for Medical Research. Adam Ameur, Ph.D., Bioinformatics Scientist, National Genomics Infrastructure, SciLifeLab at Uppsala University, added: "The majority of the projects we provide service for have only a few samples, so it is good to have a small pack size. Previously, we have been limited because of the cost, so this may open up other studies in which we look at larger genes with fewer samples." Ion AmpliSeq On-Demand Panels are custom designed by customers on the Ion AmpliSeq Designer tool (www.ampliseq.com) by selecting from a growing repository of highly optimized gene targets that are relevant in germline disorder research. The tool's disease-gene database, which allows gene selection based on disease research area, has been informed by public repositories, such as the Medical Subject Headings (MeSH) database, and includes primer sets based on 1,000's of proven designs that are also wet lab verified to guarantee performance. Panels are then ordered instantaneously in practical pack sizes that fit experiment needs and lower upfront costs. "Targeted sequencing using customer-designed custom panels has proven to be a popular method for driving translational research, but for uncommon, complex diseases such as germline disorders, most labs do not have the number of samples to justify the significant investment of time and money," said Joydeep Goswami, president of Clinical Next-Generation Sequencing and Oncology at Thermo Fisher Scientific. "By simplifying the way users can customize their content and pack delivery size, clinical researchers can focus on targets of interest that will drive greater discovery without the high upfront cost and risk of waste." Thermo Fisher will provide demonstrations of the new Ion AmpliSeq Designer Software for delegates who request them at ESHG 2017.  The company is also hosting a workshop featuring talks from early access users of Ion AmpliSeq On-Demand Panels and other new technology from Thermo Fisher. The complementary workshop, titled New Products to Enable Discovery of De Novo and Germline Mutations, will take place Sunday, May 28 at 11:15 am CET in the Ballerup Room at the Bella Center Copenhagen (BCC). Workshop presenters include: Additional Ion Torrent NGS products to be highlighted at ESHG 2017 include: For more information on the Ion AmpliSeq On-Demand Panels, stop by Thermo Fisher's booth (#438) or visit www.thermofisher.com/ampliseqondemand.html. For more information on the workshop at ESHG, visit www.thermofisher.com/eshg17. Ion AmpliSeq On-Demand Panels, Ion ReproSeq PGS Kits and Ion 510 Chip are For Research Use Only; not for use in diagnostic procedures. About Thermo Fisher Scientific Thermo Fisher Scientific Inc. is the world leader in serving science, with revenues of $18 billion and more than 55,000 employees globally. Our mission is to enable our customers to make the world healthier, cleaner and safer. We help our customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics and increase laboratory productivity. Through our premier brands – Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific and Unity Lab Services – we offer an unmatched combination of innovative technologies, purchasing convenience and comprehensive support. For more information, please visit www.thermofisher.com. To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/new-on-demand-targeted-next-generation-sequencing-panels-for-inherited-disease-research-deliver-user-customization-without-high-upfront-cost-300461447.html


"Il costo era un fattore limitante per i pannelli composti da un gran numero di ampliconi. Per i ricercatori che necessitano di modificare il contenuto genetico di frequente, un prezzo inferiore per gli oligo rappresenta un elemento davvero importante", ha detto Pan Zhang, medico e dottore, direttore presso il Sequencing and Microarray Center (Centro di sequenziamento e micromatrice) del Coriell Institute for Medical Research (Istituto Corriell per la ricerca medica). Adam Ameur, dottore e scienziato bioinformatico per la National Genomics Infrastructure (Infrastruttura genomica nazionale) dello SciLifeLab dell'Università di Uppsala, ha aggiunto: "La maggioranza dei progetti per cui offriamo assistenza posseggono pochi campioni, quindi è bene disporre di un piccolo pacchetto. In precedenza, siamo stati limitati dai costi, quindi ciò potrebbe aprire la strada ad altri studi in cui osservare i geni più grandi con meno campioni." I pannelli su richiesta Ion AmpliSeq On-Demand Panels sono personalizzati dai clienti sulla base dello strumento di progettazione Ion AmpliSeq Designer (www.ampliseq.com) selezionando da un crescente archivio composto da geni bersaglio altamente ottimizzati importanti per la ricerca sulle malattie genetiche. Il database per le malattie genetiche dello strumento, che consente la selezione dei geni in funzione dell'area di ricerca delle malattie, è composto da dati ricevuti da archivi pubblici, quale il database del Medical Subject Headings (MeSH/Termini medici), e include set di primer basati sulle migliaia di progetti sperimentati che sono anche stati verificati in wet lab (laboratorio umido) per garantirne la resa. I pannelli sono quindi ordinati istantaneamente in pratici pacchetti appositi per le esigenze sperimentali e ridurre i costi iniziali. "Il sequenziamento mirato ricorrendo a pannelli personalizzati in base al tipo di cliente ha dimostrato di essere una metodologia popolare a guida della ricerca traslazionale, ma per malattie non comuni e complesse quali quelle genetiche la maggioranza dei laboratori non hanno un numero di campioni tali da giustificare un investimento importante a livello temporale ed economico", ha detto Joydeep Goswami, presidente del Clinical Next-Generation Sequencing and Oncology (Oncologia e NGS clinici) presso Thermo Fisher Scientific. "Semplificando la modalità di personalizzazione per gli utenti quanto a contenuto e pacchetto, i ricercatori clinici possono concentrarsi sui geni bersaglio interessati che orienteranno scoperte maggiori senza elevati costi iniziali e il rischio di sprechi." Thermo Fisher illustrerà il nuovo software progettuale Ion AmpliSeq Designer Software ai delegati che lo richiederanno presso l'ESHG 2017. La società ospiterà anche un workshop con colloqui di utenti nell'accesso iniziale dei pannelli su richiesta Ion AmpliSeq On-Demand Panels e altre nuove tecnologie di Thermo Fisher. Il workshop complementare, intitolato New Products to Enable Discovery of De Novo and Germline Mutations (Nuovi prodotti per la scoperta di mutazioni genetiche e de novo), avrà luogo domenica 28 maggio alle ore 11:15 CET nella sala Ballerup Room presso il Bella Center Copenhagen (BCC). Tra i presentatori del workshop ci saranno: Informazioni su Thermo Fisher Scientific Thermo Fisher Scientific Inc. è leader mondiale al servizio della scienza, con un fatturato pari a 18 miliardi di dollari e oltre 55.000 dipendenti nel mondo. La nostra missione risiede nel consentire ai nostri clienti di rendere il mondo più salubre, pulito e sicuro. Aiutiamo i nostri clienti ad accelerare la ricerca nelle scienze naturali, risolvere problematiche analitiche complesse, migliorare le diagnosi per i pazienti e aumentare la produttività dei laboratori. Tramite i nostri marchi principali – Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific e Unity Lab Services – offriamo una combinazione ineguagliabile di tecnologie innovative, convenienza nell'acquisto e assistenza completa. Per ulteriori informazioni visitare il sito web www.thermofisher.com.


„Die Kosten haben Panels mit einer großen Zahl an Amplifikationsprodukten bislang immer eingeschränkt. Für Forscher, die häufiger den Gehalt der Gene verändern müssen, ist der niedrigere Preis für Oligonukleotide wirklich großartig", sagte Pan Zhang, Ph.D., M.D., Direktor des Sequencing and Microarray Center am Coriell Institute for Medical Research. Thermo Fisher wird Vorführungen der neuen Ion AmpliSeq Designer-Software für Konferenzteilnehmer, die dies auf der ESHG 2017 wünschen, anbieten. Das Unternehmen wird zudem einen Workshop veranstalten, bei dem Vorträge von Anwendern der Ion AmpliSeq On-Demand-Panels und weiteren neuen Technologien von Thermo Fisher angeboten werden, die von Anfang an dabei waren. Der ergänzende Workshop, der unter der Überschrift New Products to Enable Discovery of De Novo and Germline Mutations läuft, wird am Sonntag, den 28. Mai um 11.15 Uhr (CET) im Ballerup Room im Bella Center Copenhagen (BCC) stattfinden. Zu den Vortragenden auf dem Workshop gehören:


A targeted NGS approach is the preferred method for researchers who study germline disorders in an effort to understand complex diseases that require analysis of multiple genes. Compared to the time-consuming and costly whole exome or whole genome sequencing, targeted NGS has become an especially beneficial approach in clinical research settings where a more practical, efficient and economical way to resequence tens-to-hundreds of specific gene targets is often required. "Cost was a limiting factor for panels with a large number of amplicons. For researchers that need to change their gene content frequently, the lower price for oligos is really great," said Pan Zhang, Ph.D., M.D., director, Sequencing and Microarray Center at Coriell Institute for Medical Research. Adam Ameur, Ph.D., Bioinformatics Scientist, National Genomics Infrastructure, SciLifeLab at Uppsala University, added: "The majority of the projects we provide service for have only a few samples, so it is good to have a small pack size. Previously, we have been limited because of the cost, so this may open up other studies in which we look at larger genes with fewer samples." Ion AmpliSeq On-Demand Panels are custom designed by customers on the Ion AmpliSeq Designer tool (www.ampliseq.com) by selecting from a growing repository of highly optimized gene targets that are relevant in germline disorder research. The tool's disease-gene database, which allows gene selection based on disease research area, has been informed by public repositories, such as the Medical Subject Headings (MeSH) database, and includes primer sets based on 1,000's of proven designs that are also wet lab verified to guarantee performance. Panels are then ordered instantaneously in practical pack sizes that fit experiment needs and lower upfront costs. "Targeted sequencing using customer-designed custom panels has proven to be a popular method for driving translational research, but for uncommon, complex diseases such as germline disorders, most labs do not have the number of samples to justify the significant investment of time and money," said Joydeep Goswami, president of Clinical Next-Generation Sequencing and Oncology at Thermo Fisher Scientific. "By simplifying the way users can customize their content and pack delivery size, clinical researchers can focus on targets of interest that will drive greater discovery without the high upfront cost and risk of waste." Thermo Fisher will provide demonstrations of the new Ion AmpliSeq Designer Software for delegates who request them at ESHG 2017.  The company is also hosting a workshop featuring talks from early access users of Ion AmpliSeq On-Demand Panels and other new technology from Thermo Fisher. The complementary workshop, titled New Products to Enable Discovery of De Novo and Germline Mutations, will take place Sunday, May 28 at 11:15 am CET in the Ballerup Room at the Bella Center Copenhagen (BCC). Workshop presenters include: Additional Ion Torrent NGS products to be highlighted at ESHG 2017 include: For more information on the Ion AmpliSeq On-Demand Panels, stop by Thermo Fisher's booth (#438) or visit www.thermofisher.com/ampliseqondemand.html. For more information on the workshop at ESHG, visit www.thermofisher.com/eshg17. Ion AmpliSeq On-Demand Panels, Ion ReproSeq PGS Kits and Ion 510 Chip are For Research Use Only; not for use in diagnostic procedures. About Thermo Fisher Scientific Thermo Fisher Scientific Inc. is the world leader in serving science, with revenues of $18 billion and more than 55,000 employees globally. Our mission is to enable our customers to make the world healthier, cleaner and safer. We help our customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics and increase laboratory productivity. Through our premier brands – Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific and Unity Lab Services – we offer an unmatched combination of innovative technologies, purchasing convenience and comprehensive support. For more information, please visit www.thermofisher.com.


Devaux Y.,Laboratory of Cardiovascular Research | Vausort M.,Laboratory of Cardiovascular Research | Goretti E.,Laboratory of Cardiovascular Research | Nazarov P.V.,Microarray Center | And 7 more authors.
Clinical Chemistry | Year: 2012

BACKGROUND: Rapid and correct diagnosis of acute myocardial infarction (MI) has an important impact on patient treatment and prognosis. We compared the diagnostic performance of high-sensitivity cardiac troponin T (hs-cTnT) and cardiac enriched microRNAs (miRNAs) in patients with MI. METHODS: Circulating concentrations of cardiac-enriched miR-208b and miR-499 were measured by quantitative PCR in a case-control study of 510 MI patients referred for primary mechanical reperfusion and 87 healthy controls. RESULTS: miRNA-208b and miR-499 were highly increased in MI patients (>10 5-fold, P < 0.001) and nearly undetectable in healthy controls. Patients with ST-elevation MI (n=397) had higher miRNA concentrations than patients with non-ST-elevation MI (n =113) (P < 0.001). Both miRNAs correlated with peak concentrations of creatine kinase and cTnT (P <10 -9). miRNAs and hs-cTnT were already detectable in the plasma 1 h after onset of chest pain. In patients who presented <3 h after onset of pain, miR-499 was positive in 93% of patients and hs-cTnT in 88% of patients (P = 0.78). Overall, miR-499 and hs-cTnT provided comparable diagnostic value with areas under the ROC curves of 0.97. The reclassification index of miR-499 to a clinical model including several risk factors and hs-cTnT was not significant (P = 0.15). CONCLUSIONS: Circulating miRNAs are powerful markers of acute MI. Their usefulness in the establishment of a rapid and accurate diagnosis of acute MI remains to be determined in unselected populations of patients with acute chest pain. © 2011 American Association for Clinical Chemistry.


Janji B.,Laboratory of Experimental Hemato Oncology LHCE | Janji B.,Microarray Center | Vallar L.,Microarray Center | Tanoury Z.A.,Microarray Center | And 9 more authors.
Journal of Cellular and Molecular Medicine | Year: 2010

We used a tumour necrosis factor (TNF)-α resistant breast adenocarcinoma MCF-7 cell line to investigate the involvement of the actin cytoskeleton in the mechanism of cell resistance to this cytokine. We found that TNF resistance correlates with the loss of cell epithelial properties and the gain of a mesenchymal phenotype, reminiscent of an epithelial-to-mesenchymal transition (EMT). Morphological changes were associated with a profound reorganization of the actin cytoskeleton and with a change in the repertoire of expressed actin cytoskeleton genes and EMT markers, as revealed by DNA microarray-based expression profiling. L-plastin, an F-actin cross-linking and stabilizing protein, was identified as one of the most significantly up-regulated genes in TNF-resistant cells. Knockdown of L-plastin in these cells revealed its crucial role in conferring TNF resistance. Importantly, overexpression of wild-type L-plastin in TNF-sensitive MCF-7 cells was sufficient to protect them against TNF-mediated cell death. Furthermore, we found that this effect is dependent on serine-5 phosphorylation of L-plastin and that non-conventional protein kinase C isoforms and the ceramide pathway may regulate its phosphorylation state. The protective role of L-plastin was not restricted to TNF-α resistant MCF-7 cells because a correlation between the expression of L-plastin and the resistance to TNF-α was observed in other breast cancer cell lines. Together, our study discloses a novel unexpected role of the actin bundling protein L-plastin as a cell protective protein against TNF-cytotoxicity. © 2009 The Authors Journal compilation © 2010 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.


Vetter G.,University of Luxembourg | Saumet A.,French Institute of Health and Medical Research | Moes M.,University of Luxembourg | Vallar L.,Microarray Center | And 7 more authors.
Oncogene | Year: 2010

Epithelial to mesenchymal transition (EMT) is a key step toward metastasis. MCF7 breast cancer cells conditionally expressing the EMT master regulator SNAI1 were used to identify early expressed microRNAs (miRNAs) and their targets that may contribute to the EMT process. Potential targets of miRNAs were identified by matching lists of in silico predicted targets and of inversely expressed mRNAs. MiRNAs were ranked based on the number of predicted hits, highlighting miR-661, a miRNA with so far no reported role in EMT. MiR-661 was found required for efficient invasion of breast cancer cells by destabilizing two of its predicted mRNA targets, the cell-cell adhesion protein Nectin-1 and the lipid transferase StarD10, resulting, in turn, in the downregulation of epithelial markers. Reexpression of Nectin-1 or StarD10 lacking the 3′-untranslated region counteracted SNAI1-induced invasion. Importantly, analysis of public transcriptomic data from a cohort of 295 well-characterized breast tumor specimen revealed that expression of StarD10 is highly associated with markers of luminal subtypes whereas its loss negatively correlated with the EMT-related, basal-like subtype. Collectively, our non-a priori approach revealed a nonpredicted link between SNAI1-triggered EMT and the down-regulation of Nectin-1 and StarD10 through the up-regulation of miR-661, which may contribute to the invasion of breast cancer cells and poor disease outcome. © 2010 Macmillan Publishers Limited All rights reserved.


Halavatyi A.A.,University of Luxembourg | Nazarov P.V.,Microarray Center | Al Tanoury Z.,University of Luxembourg | Apanasovich V.V.,Belarusian State University | And 2 more authors.
European Biophysics Journal | Year: 2010

A novel mathematical model of the actin dynamics in living cells under steady-state conditions has been developed for fluorescence recovery after photobleaching (FRAP) experiments. As opposed to other FRAP fitting models, which use the average lifetime of actins in filaments and the actin turnover rate as fitting parameters, our model operates with unbiased actin association/dissociation rate constants and accounts for the filament length. The mathematical formalism is based on a system of stochastic differential equations. The derived equations were validated on synthetic theoretical data generated by a stochastic simulation algorithm adapted for the simulation of FRAP experiments. Consistent with experimental findings, the results of this work showed that (1) fluorescence recovery is a function of the average filament length, (2) the F-actin turnover and the FRAP are accelerated in the presence of actin nucleating proteins, (3) the FRAP curves may exhibit both a linear and non-linear behaviour depending on the parameters of actin polymerisation, and (4) our model resulted in more accurate parameter estimations of actin dynamics as compared with other FRAP fitting models. Additionally, we provide a computational tool that integrates the model and that can be used for interpretation of FRAP data on actin cytoskeleton. © 2009 European Biophysical Societies' Association.


Reinsbach S.E.,University of Luxembourg | Nazarov P.V.,Microarray Center | Philippidou D.,University of Luxembourg | Schmitt M.,University of Luxembourg | And 5 more authors.
RNA Biology | Year: 2012

MicroRNAs are major players in post-transcriptional gene regulation. Even small changes in miRNA levels may have profound consequences for the expression levels of target genes. Hence, miRNAs themselves need to be tightly, albeit dynamically, regulated. Here, we investigated the dynamic behavior of miRNAs over a wide time range following stimulation of melanoma cells with interferonγ (IFNγ), which activates the transcription factor STAT1. By applying several bioinformatic and statistical software tools for visualization and identification of differentially expressed miRNAs derived from time-series microarray experiments, 8.9% of 1105 miRNAs appeared to be directly or indirectly regulated by STAT1. Focusing on distinct dynamic expression patterns, we found that the majority of robust miRNA expression changes occurred in the intermediate time range (24-48 h). Three miRNAs (miR-27a, miR-30a and miR-34a) had a delayed regulation occurring at 72 h while none showed significant expression changes at early time points between 30 min and 6 h. Expression patterns of individual miRNAs were altered gradually over time or abruptly increased or decreased between two time points. Furthermore, we observed coordinated dynamic transcription of most miRNA clusters while few were found to be regulated independently of their genetic cluster. Most interestingly, several "star" or passenger strand sequences were specifically regulated over time while their "guide" strands were not. © 2012 Landes Bioscience.

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