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SELECTBIO Conferences New Applications of NGS and PCR

New Applications of NGS and PCR Agenda

Other Track Agendas

Epigenetics, microRNAs and non Coding RNAs in Disease | New Applications of NGS and PCR | 

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Wednesday, 16 October 2013



NGS: Informing Cancer Diagnosis & Treatment


Nazneen RahmanKeynote Presentation

Using Next-generation Sequencing to Bring Routine Genetic Testing into Cancer Medicine
Nazneen Rahman, Head of the Division of Genetics and Epidemiology, Institute of Cancer Research, United Kingdom

Next-generation sequencing offers the potential to revolutionise clinical diagnostics. This is particularly true in cancer; nearly 100 cancer predisposition genes with clinical utility are recognised, but clinical testing for the majority is not available or is very restricted. The Mainstreaming Cancer Genetics Programme ( is seeking to address this, and a primary projective is the development of an NGS panel that can consistently and robustly identify genetic variants of relevance to cancer.


Coffee & Networking in Exhibition Hall


Personalised Cancer Medicine in the Era of Genome Sequencing
Ultan McDermott, CDF Group Leader, The Wellcome Trust Sanger Institute, United Kingdom

Over the last decade we have witnessed the convergence of two powerful experimental datasets towards a common goal of defining the molecular subtypes that underpin the likelihood of a cancer patient responding to treatment in the clinic. The first of these ‘experiments’ has been the systematic sequencing of large numbers of cancer genomes through the International Cancer Genome Consortium and The Cancer Genome Atlas. This endeavour is beginning to yield a complete catalogue of the cancer genes that are critical for tumourigenesis and amongst which we will find tomorrow’s biomarkers and drug targets. The second ‘experiment’ has been the use of large-scale biological models such as cancer cell lines to correlate mutations in cancer genes with drug sensitivity, such that one could begin to develop rationale clinical trials to begin to test these hypotheses. It is at this intersection of cancer genomes and biological models that there exists the opportunity to completely transform how we stratify cancer patients in the clinic for treatment.


Genome Sequencing for Molecular Stratification of Cancers
Holger Sultmann, Head, German Cancer Research Center, Germany

Genome sequencing has provided deep insights into mutational patterns of many cancers. The presentation will focus on how to exploit this knowledge in order to understand the underlying biological processes as well as to implement genome sequencing for cancer diagnosis, prognosis, and prediction.


Lunch & Networking in Exhibition Hall


Poster Viewing Session

NGS: Insights into Cancer Development


Comprehensive Cancer Genome Analysis Using Sequencing
Ivo Gut, Director, Centro National de Análisis Genomico, Spain

2nd generation sequencing is a powerful tool in cancer genome analysis. Apart from the identification of somatic variants, it allows high resolution analysis of the transcriptome and the epigenome. Streamlined pipelines for somatic variant identification, transcriptomic and epigenomic analysis as well as their data integration will be discussed.


NGS of Bladder Cancer, the Genomic Landscape Driving Progression
Torben Orntoft, Professor, Aarhus University Hospital, Denmark

We have analyzed early and late lesions of bladder cancer by NGS, and defined sub populations and driving mutations.


Coffee & Networking in Exhibition Hall


Deep Sequencing to Rebuild Tumor Evolution
Francesca Ciccarelli, Group Leader, European Institute of Oncology Milan, Italy

Deep sequencing provides a digital count of DNA segments that mutate during cancer progression. We used this feature to rebuild the evolutionary tree of single tumors starting from their collection of somatic mutations.

Small-RNA Sequencing


Michael PfafflKeynote Presentation

Biomarker Development in Translational Research using Small-RNA Seq
Michael Pfaffl, Professor, Technical University of Munich, Germany

Small RNAs, in particular microRNAs, regulate gene expression by post transcriptional binding and thereby suppressing protein translation. They are present in most eukaryotic cells and play an important role in nearly all physiological and regulative processes. Small RNAs were detected in various extracellular locations such as blood plasma and urine. However, very less information is available about the small RNA composition in biofluids such as milk and whether milk possesses its own defined small RNA profile differing from blood. To generate a holistic overview of all present small RNAs in bovine blood and milk and to identify shifts in their profiles, small RNA NGS was performed on whole blood and milk samples during the progressing lactation period. Small RNA-Sequencing was performed using an Illumina HiSeq and subsequent data analysis was done independently using either the GGS and GGA stations from Genomatix Software GmbH (Munich, Germany) or using freely available python scripts and R-packages (Bioconductor).


End of Day One

Thursday, 17 October 2013

Single Cell qPCR


Mikael KubistaKeynote Presentation

High throughput mRNA and Protein qPCR Profiling
Mikael Kubista, Professor/Founder, TATAA Biocenter AB, Sweden

In my talk I will present high throughput single cell multiway expression profiling of astrocytes, studying their activation upon induced brain trauma in mice, and high throughput protein profiling in serum samples collected from breast cancer patients.


Multi-analyte Analysis in Single-cells using qPCR
Anders Stahlberg, Senior Scientist, University of Gothenberg, Sweden

The single cell represents the basic unit of all organisms. Most investigations have been performed on large cell populations, but understanding cell dynamics and heterogeneity requires single-cell analysis. We will discuss how DNA, RNAs and proteins can  be analyzed in the same single-cell using qPCR.


Coffee & Networking in Exhibition Hall

qPCR in Cancer Diagnosis


DiSSeCT Technology Provides Mutation Enrichment Prior to PCR or COLD-PCR and Enables Detection of Traces of Rare Mutations in Cancer Samples
Mike Makrigiorgos, Professor, Dana-Farber Cancer Institute/Harvard Medical School, United States of America

Multiplex detection of low-level mutant alleles in the presence of wild-type DNA is useful for several fields of medicine including cancer, pre-natal diagnosis and infectious diseases. We present DiSSeCT, a new technology that enables detection of traces of mutations in cancer and circulating DNA when combined with LNA-PNA-enhanced real time PCR or COLD-PCR.


Using High Throughput qPCR for DNA Methylation Biomarker Validation
Andreas Weinhaeusel, Senior Scientist, Austrian Institute of Technology GmbH, Austria

Elucidation of genome wide epigenetic changes has become a routine application, and is of utmost interest for the development of biomarkers. Along the biomarker developmental chain upon discovery of candidate markers, confirmation and validation are indispensable steps. For nucleic acids based markers the method of choice is qPCR. Focusing on DNA methylation based biomarker development, we have established methylation sensitive restriction enzyme (MSRE) based qPCR analyses for DNA methylation analyses. Efficient assay design tools have been developed enabling high throughput sequence manipulation and qPCR design. Several hundred assays for human DNA methylation targets have been designed and setup. Analytical validation according MIQE guidelines has been conducted using a standard qPCR and Fluidigm’s Biomark system. These assays have been used for validation of DNA-methylation biomarkers of cancerous and non cancerous disease. Results from the high throughput MSRE-qPCR Biomark runs were successfully used for confirmation of DNA methylation changes elucidated by Illumina’s bisulfite deamination based 450k genomic methylation arrays.  From our experience the MSRE high throughput qPCR enables reliable and very efficient validation of DNA methylation changes derived from genome-wide analyses.


Lunch & Networking in Exhibition Hall


Poster Viewing Session

Improving Accuracy & Reliability


Azure PCR Technology enables Automated Data-Analysis for Real-Time PCR and Melt Curves
Ze'ev Russak, CTO, Azure PCR Limited, United Kingdom

To assess cost-savings and demonstrate the performance delivered by the Azure PCR automated qPCR data-analysis technology in a routine diagnostics setting, at NHS Greater Glasgow & Clyde. Azure PCR’s technology for automating analysis of melt-curve data will also be presented.


The Use of Heat-labile Enzymes in qPCR and Next-Gen-Sequencing Sample Preparation
Morten Elde, Head, ArcticZymes AS, Norway

In qPCR and Next-Generation-Sequencing the final results are dependent on the quality of the sample used in the reaction. In this presentation we will discuss how the use of heat-labile enzymes in sample preparations before qPCR and Next-Generation-Sequencing can improve efficiency and give reliable results.


Coffee & Networking in Exhibition Hall

qPCR Analysis


A Unified Censored Normal Regression Model For qPCR Differential Gene Expression Analysis
Olivier Thas, Professor in Biostatistics & Honorary Professor, Ghent University, Belgium

We propose a method that unites qPCR preprocessing and differential expression analysis in a single statistical method that provides a rigorous way for handling undetermined Cq values.


In-vivo Single Cell Transcript Analyses for Systems Modelling
Philip Day, Reader, The University of Manchester, United Kingdom

Single cell measurements of DNA, mRNA and protein for bcr-abl was measured in K562 cells to produce a steady state model of BCR.ABL protein abundance per mRNA molecule. Impact of heterogeneity and development of in-vivo transcript measurements will be discussed.


Close of Conference

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