PCR & Next-Gen Sequencing Agenda

Registration

Extreme PCR: Efficient Amplification in Less than One Minute
Carl Wittwer, Professor, University of Utah, United States of America

Extreme PCR combines higher primer and polymerase concentrations with cycle times of less than 2s, resulting in specific, high-yield amplification as demonstrated by gels, melting curves and real time analysis. Monovalent cations and dsDNA dyes inhibit, while DMSO enhances, polymerase extension.

Coffee and Networking in Exhibiton Hall

Digital PCR goes COLD: Application of COLD-PCR in Digital Format Enables Quantitative and Multiplexed Mutation Scanning
Mike Makrigiorgos, Professor, Dana-Farber Cancer Institute/Harvard Medical School, United States of America

As currently applied, digital PCR can only be used to detect known mutations at single sequence positions. By merging COLD-PCR and digital -PCR technologies we enable digital mutation scanning, a new frontier for digital-PCR. A single reaction can now interrogate numerous mutations, and replaces multiple individual digital-PCR reactions.

Opening New Dimensions in Diagnostics with Hybridization Probes
Kenneth Pierce, Senior Research Scientist, Brandeis University, United States of America

Probes that signal upon hybridization offer advantages over hydrolysable probes for digital PCR multiplexing.  Ratios of fluorescent signals from different probes can identify many specific mutations per probe, even if measured only at ambient temperature.  If melting analysis is added, detection capability greatly increases.  Large genes can be interrogated for rare mutations and identified in a background of normal DNA.

Lunch and Networking in Exhibition Hall

Free Workshop
Introduction of miRNA Research Reagents and Development of Novel Transfection Reagents using Combinatorial Chemistry and High-Throughput Cell Screening
Taku Funakoshi, Leader

Poster Viewing Session

Simple, Sensitive Protein Quantification by Proximity Ligation and Real-time PCR
Mark Shannon, Senior Staff Scientist, Applied Biosystems, United States of America

The proximity ligation assay (PLA^TM) extends the utility of quantitative PCR to the analysis of proteins.  With its simple workflow and exquisite sensitivity, PLA enables a broad range of applications including the detection of post-translational modifications, protein-protein interactions, and the quantification of proteins from blood samples, tissues, and single cells.

Coffee and Networking in Exhibiton Hall

Systems Biology Using Single Cells
David Ruff, Visiting Senior Research Fellow/ Principal Scientist , Oxford University/Fluidigm Corporation, United States of America

Systems biology endeavors to unravel biological complexity using multidimensional approaches. Cells use DNA, RNA, and proteins to power biological networks. Recent advances in single-cell analytical technology using the Fluidigm® C1TM Single-Cell Auto Prep System are providing profound insights into the dynamic elements used in biological response-signaling pathways.

Novel Methods of Detecting Mutations and Copy Number Variation with Single Color Digital PCR
Hanlee Ji, Assistant Professor/Senior Associate Director, Stanford University School of Medicine, United States of America

We have developed a number of high performance assays for determining copy number and point mutations in clinical samples such as cancer with single color digital PCR. We have demonstrated the high sensitivity and specificity of these assays in control experiments and also in the context of clinical colorectal cancer samples.

End of Day One

Coffee and Networking in Exhibiton Hall

Peripheral Whole Blood Transcriptomes of Asthmatic Individuals Undergoing Allergen Inhalation Challenge
Scott Tebbutt, Associate Professor, University of British Columbia, Canada

Allergen inhalation challenge can be a suitable model to explore the dynamics of immune cells and to elucidate the mechanism of allergic asthma in humans.  We performed RNA-seq transcriptomic analysis on Illumina rRNA/globin-depleted stranded cDNA libraries generated from blood leukocyte samples donated by asthmatic individuals undergoing allergen inhalation challenge.

Molecular Indexing For Improved RNA-Seq Quantitation and Analysis
Leah Matzat, Senior Scientist, Bioo Scientific, United States of America

Most modern methods for NGS library prep require the use of enzyme processing, such as DNA polymerase reactions, which can introduce errors in the form of incorrect sequence and misrepresented copy number. Conventional RNA sequencing library construction involves the ligation of a population of cDNA molecules with adapters prior to amplification and sequencing. With Molecular Indexed™ libraries, each molecule is tagged with a molecular index randomly chosen from ~10,000 combinations so that any two identical molecules become distinguishable (with odds of 10,000/1), and can be independently evaluated in later data analysis. Analysis using molecular indexing information provides an absolute, digital measurement of gene expression levels, irrespective of common amplification distortions observed in many RNA-Seq experiments.

Lunch and Networking in Exhibition Hall

Poster Viewing Session

Challenges and Opportunities in Automation for NGS Sample Preparation
Robin Coope, Group Leader and CoDirector, British Columbia Cancer Agency Genome Sciences Centre, Canada

The British Columbia Cancer Agency's Genome Sciences Centre has processed about 12,500 libraries in the last 12 months, and these range from large mRNA and miRNA research sample cohorts to clinical amplicons sets and whole genomes and transcriptomes for personalized onco-genomics. This has produced a range of challenges including the need to automate difficult processes such as poly-A capture and gel based size selection, the need to handle sample sets of variable size in the same pipeline, and the ever present need for robust, fast and actionable QC. This talk will describe several of these areas where what was thought to be easy turned out to hard, and highlight some of our novel solutions automation solutions.

Identification of Clinically Significant Genetic Variants by Exome Sequencing of DNA Extracted from Dried Blood Spots: A Model for Newborn Screening
Toumy Guettouche, Director, Sequencing, Children’s Hospital of Philadelphia , United States of America

Here we present a protocol that allows WES from as little as 75ng of genomic DNA extracted from a dried blood spot.

Coffee and Networking in Exhibiton Hall

Towards Precision Medicine with Integrative Personal Omics Profiles – To Genomics and Beyond
Rui Chen, Post Doctor Research Fellow, Stanford University, United States of America

Personalized profiling of quantifiable molecules collected in the human body conveys comprehensive information of our health, which sheds light on future health care transformation towards data-driven precision medicine.

Close of Conference