I will present to what extent SNPs in primer annealing regions impact qPCR assay performance and how we can take advantage of this information to improve assay design and develop a novel, robust and cost-effective qPCR method for genotyping and allele-specific expression analysis.
Taking Expression Profiling to New Dimensions
Tuesday, 4 September 2012 at 14:15
First step in new projects is usually exploratory aiming to identify interesting expression markers by screening. In classical analysis the expression of each gene is compared separately under the studied conditions and those genes that show most significant differential expression are considered important. However, variation between individuals and processing noise confounds the measured results and some of the selected genes are usually invariant of treatment but appear as false positives, while other genes that are sensitive to treatment escape notice because of the confounding variance. In my talk I will show how the precision in the selection is dramatically improved using multivariate methods that exploit correlation between genes’ expressions. The approach is particularly powerful on disintegrated samples analyzed on single cell level, since complexity is dramatically reduced. Single cell expression data are collected on high-throughput BioMark and OpenArray qPCR instrument, genes with correlated expressions are identified using GenEx, and submitted to Ingenuity database to link expression to biology. This exceedingly powerful workflow we use to study astrocytes, characterizing subtypes and changes induced under conditions such as aging and healing after induced brain damage.
Recommandations for Precise and Robust qPCR Efficiency Estimation
Wednesday, 5 September 2012 at 14:15
Imprecisions and robustness of determination of PCR efficiency was reviewed within controlled experiment employing simulation and recommandations were agregated based on literature reviewed, existing guidelines and our knowledge.
qPCR Analyses in the Diagnosis of Prostate Cancer
Wednesday, 5 September 2012 at 08:45
qPCR analysis of PCA3 mRNA in urine allows detection of prostate cancer cells. PCA3 mRNA levels indicate the likelihood for a positive prostate biopsy and the presence of cancer.
Detecting and Resolving Position-Dependent Temperature Effects in quantitative PCR
Wednesday, 5 September 2012 at 16:15
Positional effects due to temperature inhomogeneities of the qPCR instrument are not uncommon in qPCR. We demonstrate how such effects can be detected and resolved in order to achieve highest precision in qPCR.
Development and Clinical Applications of Molecular Methods for the Detection and Molecular Characterization of Circulating Tumor Cells
Wednesday, 5 September 2012 at 09:15
Molecular characterization of CTC is very important for the identification of therapeutic targets and resistance mechanisms in CTCs as well as for the stratification of patients and real-time monitoring of systemic therapies
Systems-Based, Quantitative Analysis of the Regulatory Networks Underlying Cellular Differentiation
Wednesday, 5 September 2012 at 15:45
Presentation of our latest efforts using integrative genomics and targeted proteomics approaches as well as our gene-specific or transcript-specific qPCR primer database GETPrime to derive novel regulatory mechanisms underlying cellular differentiation.
DNA Methylation and the Cancer Epigenome Biological and Translations Implications
Tuesday, 4 September 2012 at 14:15
We are in an exciting period of increased understanding of the molecular origins of epigenetic abnormalities in cancer. The resultant biological insights are increasingly important for developing strategies for “epigenetic therapies” for cancer and biomarker development.
Genome-wide Gene Expression Profiles for the Characterization and Prediction of Heterosis in Zea mays L.
Wednesday, 5 September 2012 at 14:15
A transcriptome-based approach to predict heterosis and to reveal its genetic basis - Identifying QTL underlying genes in breeding populations.
Improving sigmoidal fitting of real-time PCR curves
Wednesday, 5 September 2012 at 14:45
A major drawback of fitting sigmoidal models to real-time PCR data is the low performance in the noisy baseline region, making the extrapolation of F0 (fluorescence at cycle 0) inaccurate. We will show that modifications such as variance-weighted fitting, robust nonlinear fitting and the application of linear-quadratic-sigmoidal hybrid models can substantially increase the accuracy of deduced parameters such as F0, efficiency and threshold cycle.
The Advantages of Targeting Genomic DNA in RT-qPCR Experiments
Wednesday, 5 September 2012 at 11:45
We recently developed ValidPrime, which quantifies and subtracts confounding signals derived from genomic DNA (gDNA) in RT-qPCR experiments. ValidPrime replaces the need for reverse transcriptase negative (RT-minus) reactions, and reduces the number of required control samples.
A Genome-wide siRNA Screen for the Identification of Cisplatin Resistance Mechanisms in Cancer
Tuesday, 4 September 2012 at 11:45
Patients with non-small cell lung cancer (NSCLC) are routinely treated with cytotoxic agents such as cisplatin. To identify novel factors involved in the cellular response to cisplatin, we transfected human NSCLC A549 cells with a panel of small interfering RNAs covering the entire genome (two siRNAs targeting a total of 23,078 gene products) and then explored the effects of the transfection on cisplatin-mediated cytotoxicity and reduction in cell numbers by measuring the release of lactate dehydrogenase (LDH) into the cell supernatant and the conversion of a tetrazolium salt (WST1, respectively.
Arabidopsis Natural Variation in Response to an Oomycetal Necrotic Elicitor
Tuesday, 4 September 2012 at 11:15
I will present results obtained on the natural variation observed in Arabidopsis accessions to a microbial inducer of plant immunity. This work will give new clues for the characterization of plant genetic determinants involved in response to pathogens.
Genomics for Lower Carbon Footprint Livestock?
Wednesday, 5 September 2012 at 14:45
To achieve impact, genomic solutions to reduce methane emissions from sheep and cattle must be adopted by farmers. I will summarise empirical evidence on farmer attitudes to genomic technologies and methane emissions and identify some barriers to adoption.
Characterization of Tumor Cell Lines at Single-Cell Level
Tuesday, 4 September 2012 at 00:00
In this presentation we will discuss how single-cell analysis can be used to gain detailed information about tumor cell types, biomarkers, cell differentiation and cell functions in clonal tumor cell lines.
Non-Coding RNA and Chromatin Remodeling: Epigenetic Control of Transcription
Tuesday, 4 September 2012 at 09:00
I will summarize the molecular mechanisms underlying ncRNA-mediated epigenetic gene silencing, while focusing on the role of RNA in targeting chromatin modifying enzymes to regulatory gene sequences.
A Tale of Two (Epigenetic) Switches
Tuesday, 4 September 2012 at 10:00
I describe our understanding of the dynamics of two different epigenetic switches in budding yeast and how this relates to whether the epigenetic state is molecularly encoded in cis or trans.
Epigenetic Regulators Involved in Cancer
Wednesday, 5 September 2012 at 15:45
Misregulation of epigenetic regulators underpins the molecular pathogenesis of several haematological malignancies. Therefore, understanding the molecular mechanisms by which these chromatin regulators contribute to cancer will provide a unique opportunity to target these factors with novel epigenetic therapies.
Once Upon a Time There was Simply Hypermethylation and Hypomethylation
Wednesday, 5 September 2012 at 10:00
Over the last decade, the simple concept of focal hypermethylation and global hypomethylation as the typical alterations of DNA methylation in human cancers has matured and interactions between changes in DNA methylation and chromatin states are better understood.
Acetylated Histone H2A.Z is a Key Feature of Enhancers and the Promoters of Both Active and Bivalent Genes in Mouse ESCs
Wednesday, 5 September 2012 at 11:45
The epigenetic landscape of the histone variant H2A.Z, both acetylated and non-acetylated, is determined in mouse ESCs using ChIP-Seq. AcH2A.Z is present at the promoters of both active and poised (bivalent) genes and correlates with histone H3K4me3.
Genetic and Genomic Markers of Beef Quality
Wednesday, 5 September 2012 at 11:15
Many genomic markers of beef tenderness were identified but they are often specific to muscle type, animal type or environmental conditions. However, genes related to the heat shock protein family or muscle characteristics are potential markers of beef tenderness.
Registration
Tuesday, 4 September 2012 at 08:00
Enhancing Plant Resistance to Disease
Tuesday, 4 September 2012 at 08:55
Coffee and Networking in Exhibition Hall
Tuesday, 4 September 2012 at 10:30
Optimisation of Growth for Food and Biofuel
Tuesday, 4 September 2012 at 14:40
Lunch and Networking in Exhibition Hall
Tuesday, 4 September 2012 at 12:15
Poster Viewing Session
Tuesday, 4 September 2012 at 13:30
Coffee and Networking in Exhibition Hall
Tuesday, 4 September 2012 at 15:15
Drinks Reception
Tuesday, 4 September 2012 at 16:30
Genetic Engineering to Increase Yield from Livestock
Wednesday, 5 September 2012 at 11:10
RNA Silencing Mechanisms in Plants
Tuesday, 4 September 2012 at 11:40
Coffee and Networking in Exhibition Hall
Wednesday, 5 September 2012 at 10:30
Lunch and Networking in Exhibition Hall
Wednesday, 5 September 2012 at 12:15
Poster Viewing Session
Wednesday, 5 September 2012 at 13:30
Coffee and Networking in Exhibition Hall
Wednesday, 5 September 2012 at 15:15
Close of Conference
Wednesday, 5 September 2012 at 15:45
From Tissue Slide to Clinical Molecular Pathological Test Results. The Implementation of a Workflow.
Tuesday, 4 September 2012 at 11:45
The reliable, efficient and fast delivery of molecular pathological qPCR-test results to the clinic is challenging. We present which steps in the process can be partly or completely automated even if only very small amounts of tissue are available.
Characterization of Tumor Cell Lines at Single-Cell Level
Tuesday, 4 September 2012 at 14:45
In this presentation we will discuss how single-cell analysis can be used to gain detailed information about tumor cell types, biomarkers, cell differentiation and cell functions in clonal tumor cell lines.
Coffee Break & Networking in Exhibition Hall
Tuesday, 4 September 2012 at 10:30
Coffee Break & Networking in Exhibition Hall
Tuesday, 4 September 2012 at 15:15
Lunch & Networking in Exhibition Hall
Tuesday, 4 September 2012 at 12:30
Poster Viewing Session
Tuesday, 4 September 2012 at 13:30
Drinks Reception
Tuesday, 4 September 2012 at 16:30
Isolate. Convert. Quantify. Sigma's Complete Workflow Solution for
RT-qPCR microRNA Expression Analysis
Wednesday, 5 September 2012 at 10:15
Sigma® Life Science has provided solutions for the
functional analysis of microRNAs since 2008 with MISSION® microRNA mimics.
Since then, Sigma has developed more tools for understanding what genes
microRNAs regulate (MISSION Target ID Library) and validating these targets
(MISSION 3' UTR Lenti GoClone™). Now, we complement the workflow at the
discovery level with the MystiCq™ microRNA products for microRNA RT-qPCR
analysis.
Coffee Break & Networking in Exhibition Hall
Wednesday, 5 September 2012 at 15:30
Lunch & Networking in Exhibition Hall
Wednesday, 5 September 2012 at 12:15
Poster Viewing Session
Wednesday, 5 September 2012 at 13:30
Close of Conference
Wednesday, 5 September 2012 at 16:45
LATE-PCR
Tuesday, 4 September 2012 at 09:14
Clinical Applications
Tuesday, 4 September 2012 at 11:14
Expression Profiling
Tuesday, 4 September 2012 at 14:14
qPCR in Diagnostics
Wednesday, 5 September 2012 at 08:40
Analysis
Wednesday, 5 September 2012 at 14:10
Registration
Tuesday, 4 September 2012 at 08:00
Coffee Break and Networking in the Exhibition Hall
Tuesday, 4 September 2012 at 10:30
Lunch and Networking in the Exhibition Hall
Tuesday, 4 September 2012 at 12:15
Poster Viewing Session
Tuesday, 4 September 2012 at 13:15
Coffee Break and Networking in the Exhibition Hall
Tuesday, 4 September 2012 at 15:15
Drinks Reception
Tuesday, 4 September 2012 at 17:30
Coffee Break and Networking in the Exhibition Hall
Wednesday, 5 September 2012 at 10:30
Lunch and Networking in the Exhibition Hall
Wednesday, 5 September 2012 at 12:15
Poster Viewing Session
Wednesday, 5 September 2012 at 13:15
Coffee Break and Networking in the Exhibition Hall
Wednesday, 5 September 2012 at 15:15
Close of Conference
Wednesday, 5 September 2012 at 16:45
miRNAs and siRNAs in Cancer
Tuesday, 4 September 2012 at 08:40
Myc-regulated microRNAs in B-Lymphomagenesis
Tuesday, 4 September 2012 at 09:00
Maturation and Function of Long Noncoding RNA SPRY4-IT1 in Human Melanomas
Tuesday, 4 September 2012 at 09:30
Recently, we reported that the long noncoding RNA SPRY4-IT1, which is transcribed from the intronic region of the Sprouty4 gene, is upregulated in human melanomas compared to melanocytes and keratinocytes (Khaitan et al., 2011 Cancer Research). We report here that SPRY4-IT1 is part of a larger (1.8Kb) noncoding RNA variant (SPRY4-IT) and 5’ region of this transcript is removed during the nuclear RNA processing.
miRNA Regulation of Signaling Pathways in Breast Cancer
Tuesday, 4 September 2012 at 10:00
In the present study we performed a whole-Genome miRNA screen to identify novel miRNA-regulators of the NF-kB signaling in cancer. We focused on miRNA-families (miRNAs with homologous seed regions) and we further characterized their function and clinical relevance in breast cancer.
Coffee Break and Networking in Exhibition Hall
Tuesday, 4 September 2012 at 10:30
2-D DIGE and siRNA to find New Cancer Targets
Tuesday, 4 September 2012 at 11:15
Here two powerful methods, siRNA and 2-D DIGE, were combined to investigate a signaling pathway, pivotal in cancer biology. Silencing of the target protein allowed identification of differentially regulated proteins, but also to resolve time dependency of protein regulation.
Lunch Break and Networking in Exhibition Hall
Tuesday, 4 September 2012 at 12:45
Poster Viewing Session
Tuesday, 4 September 2012 at 13:30
The MicroRNA and Exosomes Spaces: Analysis of Market Segments, Research Trends, and Potential Utility as Biomarkers.
Tuesday, 4 September 2012 at 17:00
Select Biosciences industry tracking of the microRNA and Exosome fields has focused on qualitative and quantitative market trends based on primary market analyses. We have also conducted extensive analysis of all the publications in these fields which allow us to track the evolution of research trends in this interrelated spaces. These market analyses have been recently published in the Select Biosciences MicroRNAs and Exosomes 2012 Market Report, and in this presentation I will present a snapshot of the research trends in microRNAs and exosomes and frame them into their potential utility as biomarker classes for the future.
Coffee Break and Networking in Exhibition Hall
Tuesday, 4 September 2012 at 15:15
miRNAs in Body Fluids such as CSF - Potentials and Limitations
Wednesday, 5 September 2012 at 09:30
We were able to demonstrate for the first time damage specific packing of mature miRNA species into CSF-microparticles and the uptake of miRNA by host cells underlines their predicted role for microparticles in cell-cell communication. To our knowledge there are no reports to date on the role of microparticles in the cerebral environment.
Identifying miRNA in Biofluids to be Applied as Robust Biomarkers for Disease, Toxicology or Injury Studies – The case of Minimally Invasive Colorectal Cancer Detection
Wednesday, 5 September 2012 at 10:00
Using LNA™ based Universal RT-PCR system, we have profiled microRNA in thousands of biofluid samples including blood plasma/serum and urine. Implementation of extensive sample and data QC procedures will support development of robust biomarkers in disease, toxicology and injury studies.
Drinks Reception and Networking in Exhibition Hall
Tuesday, 4 September 2012 at 17:30
Argonautes, microRNA Biogenesis & RNA Interference
Tuesday, 4 September 2012 at 16:00
Argonaute proteins had been discovered as the effector proteins of the microRNA pathway. However, I would like to shed some new light on the many roles that Argonaute proteins can play in microRNA processing, stabilization, strand selection and RNA interference.
miRNA Biology
Tuesday, 4 September 2012 at 14:10
Analysis of the Accessibility of PAR-CLIP Bound Sites Reveals that Nucleation of the miRNA:mRNA Pairing Occurs Preferentially at the 3'-end of the Seed Match
Tuesday, 4 September 2012 at 16:30
Detailed analysis of PAR-CLIP miRNA binding sites demonstrates that miRNA target binding starts preferentially at the 3' end of the seed match. Complementary analysis of mRNA and protein levels shows that genes with accessible nucleation regions at the 3'-end are more strongly downregulated than other genes.
Coffee Break and Networking in Exhibition Hall
Wednesday, 5 September 2012 at 10:30
siRNA, miRNA and RNAi Therapeutics in Cancer and Disease
Wednesday, 5 September 2012 at 11:10
Therapeutic Targeting of Neuroendocrine Tumours Utilising microRNAs
Wednesday, 5 September 2012 at 11:45
This talk will focus on published and novel work regarding miRNAs as diagnostic and prognostic markers in neuroendocrine cancers, their role in the induction of autophagy as a therapeutic modality and describe preliminary work utilising nanoparticle mediated therapeutic delivery of miRNAs .
Lunch Break and Networking in Exhibition Hall
Wednesday, 5 September 2012 at 12:15
Poster Viewing Session
Wednesday, 5 September 2012 at 13:30
Discovery of Cancer Drug Targets using RNAi Screening with Pooled Lentiviral shRNA Libraries
Wednesday, 5 September 2012 at 14:45
Cellecta offers a novel, free public resource for genome-wide RNAi screens – DECIPHER pooled lentiviral shRNA libraries (www.decipherproject.net). Using a combination of in vitro and ex vivo RNAi screening strategies, we have identified and validated hundreds of key viability genes in oncogenic cells.
Coffee Break and Networking in Exhibition Hall
Wednesday, 5 September 2012 at 15:15
Functional microRNA Profiling for Improved iPSC Reprogramming
Wednesday, 5 September 2012 at 16:15
The role of miR overexpression during cell reprogramming was validated by miR screening. Specific miRs were identified that enhanced iPSC generation and are further candidates for extensive characterization.
Close of Conference
Wednesday, 5 September 2012 at 16:45
Registration
Tuesday, 4 September 2012 at 08:00
The Epigenome - The Genome’s Memory of Past Experiences
Wednesday, 5 September 2012 at 14:15
We aim to discover epigenomic marks susceptible to the (prenatal) environment and their contribution to human disease and ageing. We apply a mix of study designs, epigenomics technologies, and data analysis approaches for example within the setting of the Dutch Hunger Winter.
Digital PCR - Clinical and Translational Application
Tuesday, 4 September 2012 at 11:15
I will review the basic concepts underpinning digital PCR and focus on the potential application of this powerful and versatile technique in the delivery of personalised medicine and translational medical research.
Droplet Digital™ PCR: a Revolutionary Approach to quantitative PCR
Tuesday, 4 September 2012 at 12:15
Droplet Digital PCR (ddPCR) provides an absolute measure of target DNA molecules with unrivalled precision and sensitivity. In ddPCR, a DNA or RNA sample is partitioned into 20,000 individual nanolitre-sized droplets. After endpoint PCR is performed, the samples are read. Each droplet provides a fluorescent positive or negative signal indicating the target sequence was present or not after partitioning. The initial amount of target molecules is then quantified by counting the number of droplets with a positive amplification. ddPCR provides a revolutionary approach to target DNA or RNA quantification.
Registration
Tuesday, 4 September 2012 at 08:00
Transcriptional Biomarkers- the Gap Between Most Differentially and Most Specifically Expressed
Tuesday, 4 September 2012 at 16:00
Most biomarker identification strategies rely on comparing diseased versus healthy. We present a new, compendium-wide search strategy identifying genes that are specifically expressed in an individual target condition as compared to thousands of other conditions (not only to healthy controls), resulting in a much higher specificity.
Dissecting Non-coding RNA Function through Integrative Genomics
Tuesday, 4 September 2012 at 14:15
Protein and RNA Interactors of Human Argonaute Proteins
Tuesday, 4 September 2012 at 14:45
microRNAs (miRNAs) are small non-coding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3’ untranslated region (UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer-independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins.
UNA (Unlocked Nucleic Acid) as a Key Modification for RNAi Applications
Wednesday, 5 September 2012 at 15:45
UNA (unlocked nucleic acid) and LNA (locked nucleic acid) are two RNA analogs which display very different RNA-binding properties. It will be reviewed how UNA and LNA modifications can be used to target RNA segments with one focus being on how strategic incorporations of UNA monomers in siRNA constructs enable a combination of potent gene silencing and reduced off-target effects.
A High Content Imaging Approach to Investigate the Role of microRNA in Regenerative Medicine
Wednesday, 5 September 2012 at 11:15
A phenotypic imaging approach using automated microscopy was employed to investigate miRNA control in 3 cell lineages; osteogenesis, adipogenesis and skeletal myogenesis. Novel miRNAs identified and their endogenous mRNA targets may represent potential therapeutic opportunities in regenerative medicine.
Coffee Break & Networking in Exhibition Hall
Wednesday, 5 September 2012 at 10:30
An ENU mutagenesis screen identifies the first mouse mutants of a novel epigenetic modifier, Rearranged L-Myc Fusion (Rlf).
Tuesday, 4 September 2012 at 17:00
A mutagenesis screen, using mice carrying an epigenetically sensitive GFP reporter was established to identify genes involved in epigenetic reprogramming. So far, over 50 mutant lines have been produced, including both well-known epigenetic genes e.g. Dnmt1 and novel genes e.g.Rlf.
Epigenetic Reprogramming
Tuesday, 4 September 2012 at 16:55
Targeted Integration and Expression of shRNA using Zinc Finger Nucleases
Tuesday, 4 September 2012 at 12:15
Viral delivery of shRNA has been a powerful tool to investigate gene function in various cellular systems. The integration of virally delivered constructs occurs randomly within the genome, which can disrupt non-targeted genes, potentially causing undesirable phenotypes and causing epigenetic cell-to-cell variations. Now, using targeted genome editing technology, we can deliver an shRNA expressing construct directly to a single endogenous “safe harbor” locus within the human genome. This approach enables shRNA expression without disrupting surrounding genes, leading to an efficient knockdown of the target gene. Here, we will discuss studies demonstrating the combination of genome-wide shRNA library coverage with targeted integration using Zinc Finger Nucleases.
miRNAs and siRNAs in Cancer
Wednesday, 5 September 2012 at 09:25
Optimisation of Growth for Food and Biofuel Cont'd
Wednesday, 5 September 2012 at 09:25
The Use of Next generation Sequencing and Bioinformatics
Wednesday, 5 September 2012 at 11:40
MicroRNA Expression and Profiling in a High-throughput Format
Wednesday, 5 September 2012 at 14:30
Profiling the differences in global miRNA expression among samples is a useful first step in identifying specific miRNAs that influence a biological process. The QuantStudio™ 12K Flex Real-Time PCR System sets a new standard for automated analysis for researchers conducting large miRNA profiling studies. Combining flexible throughput capabilities with a streamlined workflow, intuitive software, and a state-of-the-art industrial design, the QuantStudio™ 12K Flex system can generate over 43,000 expression profiles in an 8-hour day with minimal training and as little as 20 minutes of hands-on time per run.
Tuesday, 4 September 2012 at 07:00
