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Bio-IT World and Cambridge Healthtech Institute’s Inaugural

Quantitative Digital Detection Technologies
Part of the Fifth International Clinical Genomics & Informatics Europe event
3 December 2013 | Sheraton Lisbon Hotel & Spa | Lisbon, Portugal

Digital enumeration, whether it is done through digital PCR, microfluidics, or next-generation sequencing, is finding growing utility in both basic research and clinical applications. By allowing for detection of nucleic acids at higher resolution and lower target levels, digital detection technologies have the ability to identify diseases earlier in progression, providing an advantage for diagnostics and preventative medicine. Cambridge Healthtech Institute’s Inaugural Quantitative Digital Detection Technologies will cover advances in digital PCR, microfluidics, next-generation sequencing, and single-cell analysis and how these technologies are changing genomic research.

Biographies 

08:30 Registration and Morning Coffee


DIGITAL PCR TECHNOLOGIES AND TECHNIQUES 

09:00 Chairperson’s Opening Remarks

09:10 Clinical Implementation of ddPCR in the Diagnosis, and Management of Myeloproliferative Neoplasms (MPNs)

Christopher Campbell, West Midlands Regional Genetics Laboratory, Birmingham Women’s Hospital, United Kingdom

 

Sensitive quantitative molecular techniques are vital for diagnosis, prognosis and monitoring of minimum residual disease in myeloproliferative neoplasms. Increasingly identification of specific mutations is used to direct treatment options and monitor response to therapy. We present our experience of introducing droplet digital PCR on two platforms, the BioRad QX100 and Raindance technologies RainDrop, as the successor of quantitative real time PCR in a clinical diagnostic laboratory. 

We are currently offering quantitative clinical service for JAK2 V617F mutation analysis for patients with polycythaemia ruba vera, idiopathic myelofibrosis and essential thrombocythaemia, and KIT D816V mutation analysis for patients with systemic mastocytosis.

We have been developing ddPCR for BCR-ABL1 gene fusion quantification in patients with chronic myeloid leukaemia, which in parallel with this laboratories preliminary work on the use of digital PCR in non-invasive prenatal diagnosis, is exploring  the limits of sensitivity of this technology with actionable clinical consequences.

09:40 Value Assignment of Certified Reference Material by dPCR Technologies

Philippe CorbisierPhilippe Corbisier, Ph.D., Scientific and Technical Project Manager, Standards for Innovation and Sustainable Development, European Commission - JRC - IRMM, Belgium

dPCR technologies allow us to quantify nucleic acids without the use of standard curve and are therefore particularly suited to characterize nucleic acids standards used as calibrants in quantitative PCR experiments. A number of parameters that affect the accuracy of the measurements will be discussed and results using commercially available microfluidic chamber based PCR and droplet digital PCR will be discussed.

10:10 Global Detection of BRAF V600 Mutations Using a Wild-Type Negative LNA Probe-Based Droplet Digital PCR Assay

Curtis Hughesman, Ph.D., Post-Doctoral Research Fellow, Michael Smith Laboratories, University of British Columbia, Canada

Here we report a reliable method to collectively detect all known BRAF V600 mutations in a single assay using two LNA probes applied in a droplet digital PCR format. We have used this assay to successful screen cell lines and plasmids bearing 8 unique nucleotide mutations at codon 600 of BRAF with an analytical specificity of <0.05%.

10:40 Coffee Break

11:10 Plasma DNA Digital PCR as a Noninvasive Tool for Detection of Genomic Alterations in Metastatic Breast Cancer

Gaia Schiavon SGaia Schiavon, M.D., Ph.D., Cridlan Fellow in Medical Oncology – Breast Unit, The Royal Marsden NHS Foundation Trust, United Kingdom

Proof of the concept exists that circulating cell-free DNA (cfDNA) carrying tumor-specific alterations is detectable in plasma of these patients and represents a sensitive biomarker of tumor burden. Performing analysis of cfDNA with digital PCR, we screened for the acquisition of HER2 amplification in metastatic breast cancers and this approach could potentially be adapted to the analysis of any locus amplified in cancer.

11:40 The Use of dPCR to Measure Her-2 in Borderline-Amplified Breast Cancer Research Samples

Gabriele ZoppoliGabriele Zoppoli, M.D., Ph.D., Internal Medicine Resident, University of Genova & IRCCS AOU San Martino IST, Italy

Here, we describe the use of dPCR in a set of ERBB2 “equivocal status” BC patients. We also assess TOP2A copy number, and both TOP2A and ERBB2 gene expression intensity, on the described sample set. We discuss dPCR results compared to those obtained by qRT-PCR, IHC, and aCGH methods.

12:10 Sponsored Presentation (Sponsorship Opportunity Available)

12:40 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

13:10 Session Break


IMPROVEMENTS TO TRADITIONAL PCR AND MICROFLUIDICS 

14:00 Chairperson’s Opening Remarks

N. Reginald Beer, Ph.D., Medical Diagnostics Initiative Leader, Center for Micro and Nanotechnologies, Lawrence Livermore National Laboratory, United States

14:05 Preparative Microarrays & Laser Induced Dehybridization: The Intersection of Microarrays, PCR, and Sequencing

Reginald Beer SN. Reginald Beer, Ph.D., Medical Diagnostics Initiative Leader, Center for Micro and Nanotechnologies, Lawrence Livermore National Laboratory, United States

This talk will describe a novel approach using a focused IR laser to dehybridize bound oligos from individual microarray spots. The bound oligos can be 200 bp or longer, providing much more information than just the bases complementary to the short probe sequences. This method has the potential to improve detection and downstream analysis for rare or highly divergent targets in genotyping or microbial discovery applications.

14:35 A Novel Platform for Digital Isothermal Nucleic Acid Amplifications Using BART

Guy Kiddle SGuy Kiddle, Ph.D., Senior Molecular Biologist, IVD Technologies, Lumora Ltd., United Kingdom

Lumora Ltd. has demonstrated that BART technology (a bioluminescent reporter system for isothermal amplification) in conjunction with loop mediated isothermal amplification (LAMP) represent a novel, highly scalable and low-cost platform for digital amplifications based on CCD camera image capture. The LAMP-BART platform has been demonstrated on two applied challenges. This presentation will highlight the potential of dBART, as a commercial alternative to conventional digital PCR.

15:05 Sponsored Presentation (Sponsorship Opportunity Available)

15:35 Refreshment Break


SINGLE-CELL ANALYSIS METHODS 

16:10 Cell Heterogeneity and Single Cell Analysis: A New Paradigm for Translational Medicine

Ferdinando Manello SFerdinando Mannello, Ph.D., Assistant Professor, Cell Biology, Department of Biomolecular Sciences, Section of Clinical Biochemistry and Cell Biology, University “Carlo Bo” of Urbino, Italy

Cellular heterogeneity forms the fundamental principle of cell biology, but the new generation technology of single-cell analysis is able to better characterize cells population, identifying and differentiating outlier cells, and driving beyond the capability of conventional technology. Single-cell analysis is the new frontier in “OMICS”-era, which will become a diffuse and efficient investigational strategy for translational medicine.

16:35 Quantitative High-Resolution Genomic Analysis of Single Cancer Cells

Burkhard Brandt SBurkhard Brandt, Ph.D., Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Germany

We present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyzes by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centered by the therapeutically relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

17:10 Single-Cell Genomics to Study DNA-Mutation, Genetic Heterogeneity and Disease

Thierry Voet SThierry Voet, Ph.D., Head, Laboratory of Reproductive Genomics, KU Leuven, Belgium; Associate Faculty Member, Wellcome Trust Sanger Institute

We have developed various wet-lab and computational methods that allow analyzing a solitary cell. We apply these genome-wide methods to study DNA-mutation, genetic heterogeneity and cancer. Furthermore, we developed novel generic single-cell methods for preimplantation genetic diagnosis (PGD) of human cleavage stage embryos in the clinic.

17:35 Close of Symposium

16:00-18:00 Main Conference Registration


Biographies 

 


 

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Sequencing

Clinical Exome Sequencing 

RNA-Sequencing 

Informatics

High-Scale Computing 

Genome Informatics 

Pre-Conference Symposia:

Clinical Epigenetics 

Digital Detection 


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