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NGX: Applying Next-Generation Sequencing - Day 3

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Wednesday, August 15

7:30 am Breakfast Presentation or Morning Coffee (Sponsorship Opportunity Available)


What’s Next in Sequencing Platforms? 

8:30 Chairperson’s Remarks

Tim Harkins, Ph.D., Director, R&D, Advanced Applications & Collaborations, Life Technologies

Nanopore Sequencing 

8:35 Nanopore Graphene-Based Electronic Devices

Marija Drndic, Ph.D., Department of Physics and Astronomy, University of Pennsylvania

Graphene is an exceptional material for high-speed electronics, as well as a revolutionary membrane material due to its strength and atomic thickness. Nanopores in suspended graphene membranes are currently regarded as candidates for ultrafast DNA sequencing. When a single DNA molecule passes through a nanopore, it blocks the field-driven ions passing through the pore and is detected by measuring the ion current reduction. Due to the thin nature of graphene membranes and reduced pore resistance, we observe larger current signals than in the case of traditional solid-state nanopores. Use of graphene as a membrane material opens the door to a new class of nanopore devices in which electronic sensing and control are performed directly at the pore.

9:05 Noise and Bandwidth Optimization for Nanopore Sensing at Sub-Microsecond Timescales

Jacob Rosenstein, Research Scientist, Department of Electrical Engineering, Columbia University

We describe the integration of solid-state nanopores with custom low-noise complementary metal-oxide-semiconductor (CMOS) circuitry, in which the electronics are directly exposed to the electrolyte. As a result of this close integration and careful design, sub-microsecond temporal resolution has been demonstrated with nanopore recordings.  Speeding up the electronics, complements recent efforts to control and “slow down” DNA translocation, leading to faster and more accurate reads. 

9:35 Solving the Challenges of DNA Sequencing for Molecular Diagnostics

Stefan Roever, CEO & Founder, Genia Technologies

Genia has developed a versatile nanopore-based platform which allows for single molecule, electrical, real-time analysis without the need for complicated optics, labels, amplification, or fluidics.  The sensor itself is truly transformative and allows very small electrical signals (~0.2 pA current levels) to be seen high above the noise floor.  The data shows that with highly accurate analog electronics and clever data analysis techniques, single base discrimination is possible, and adequate SNR can be reached to perform DNA sequencing.

Moving Toward the Clinic 


omixon 10:05 HLA Typing from Genomic Data Using Omixon Target
Attila Berces, Ph.D., CEO, Omixon BiocomputingNext generation sequencing offers inexpensive determination of the HLA type at the highest possible resolution, but the analysis is challenging. I show results obtained with Omixon Target from targeted amplification, HLA-seq kit, exome kits and whole genome data from Illumina, Ion Torrent and Roche454 sequencers and validation on HapMap samples. 

10:20 Coffee Break in the Exhibit Hall with Poster Viewing

Life Technologies

11:00 Scientific Advancements using Ion Torrent's PGM 

Tim Harkins, Ph.D., Director, R&D, Advanced Applications & Collaborations, Life TechnologiesDr. Timothy Harkins will discuss several emerging applications performed using the PGM.  The PGM is a bench top, next generation sequencer that is able to scale in throughput to meet the individual needs of a project.  This presentation will cover several advancements from low frequency variant detection in cancer to shotgun metagenomics to de novo sequencing using long read chemistries.

11:30 Towards Enterprise-Scale Genomics:  The Gene Partnership Project at Boston Children's Hospital

David Margulies, M.D., Executive Director, The Gene Partnership, Children's Hospital Boston

This talk will present the approach, priorities, and early experiences as Boston Children's Hospital and the HMS Center for Biomedical Informatics seek to deploy genomic measurement and interpretive methods to the full array of clinical and research applications.  Policies supporting large scale recruitment of patients and families will be discussed.

12:00 pm Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own


Structural Variation 

1:45 Chairperson’s Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

1:50 Rapid Detection and Characterization of Structural Variation in Hundreds of Human Genomes

Ira M. Hall, Ph.D., Assistant Professor, Department of Biochemistry and Molecular Genetics; Center for Public Health Genomics, University of Virginia

Structural variation (SV) is a major source of genomic diversity in mammals, but accurate detection of SV from NGS data remains a challenge. Here, we present a multi-sample version of our breakpoint detection algorithm, HYDRA, that can simultaneously detect and genotype SV breakpoints in hundreds to thousands of whole genome sequence datasets while using minimal RAM. We further outline a general framework for the characterization of both simple and complex SV in cancer genomes, and present results from an initial study of 64 tumor/normal pairs.

2:20 Discovery and Functional Impact of Structural Variation across 1000 Genomes

Ryan E. Mills, Ph.D., Assistant Professor, Department of Computational Medicine and Bioinformatics; Department of Human Genetics, University of Michigan Medical School

Genomic structural variants (SVs) are a poorly understood class of genetic variation. Through the 1000 Genomes Project, we have analyzed sequence data for 1,092 individuals across 14 populations and have precisely identified many variable regions that have been assessed for functional implications.  We have additionally constructed integrated maps of genetic variation incorporating a subset of high quality SNP, INDEL, and deletion variants in these individuals onto phased haplotypes. These data sets will help further our understanding of the formation and prevalence of common and rare chromosomal rearrangements, informing future studies investigating the impact of such variation in human health and disease phenotypes.

2:50 Refreshment Break, Last Chance for Exhibit and Poster Viewing

Quantum3:15 Poster Awards Sponsored by Quantum

3:30 Combining Effects from Rare and Common Genetic Variants in Exome-Wide Association Study of Sequence Data

Hugues Aschard, Ph.D., Research Fellow, Department of Epidemiology, School of Public Health, Harvard University    

Next-generation sequencing has the potential to revolutionize complex trait genetics by directly measuring common and rare genetic variants within a genome-wide context. Strategies that model the effects of both common and rare variants could enhance the power of identifying disease-associated genes. We evaluated various strategies for association of rare, common, or a combination of both rare and common variants on quantitative phenotypes in unrelated individuals using the Genetic Analysis Workshop 17 data.

4:00 Taking NGS into the Clinic

Gholson J. Lyon, M.D., Ph.D., Assistant Professor, Human Genetics, Cold Spring Harbor Laboratory; Research Scientist, Utah Foundation for Biomedical Research; Adjunct Assistant Professor, Psychiatry, New York University Child Study Center

For the implementation of genomic analysis in the clinic, it will be critically important to optimize and standardize pipelines with high sensitivity and specificity for variant calling. This includes having sufficient sequencing depth as well as high quality of sequencing data. One way to reduce false positives could be to use variants called by two or more variant calling approaches on one set of sequencing data. We are using various tools such as ANNOVAR and VAAST to prioritize variants from various families for follow-up in case-control and biological studies.


4:30 Tools for Processing Next-Generation Sequencing Data

Mark Gerstein, Ph.D., Albert L. Williams Professor of Biomedical Informatics, Molecular Biophysics and Biochemistry, Computer Science, Yale University - Download Podcast 

A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes. My talk will focus on annotating the bulk of the genome that does not code for canonical genes, concentrating on intergenic features such as TF binding sites and non-coding RNAs (ncRNAs) and structural variations and pseudogenes. Much of this work has been carried out within the ENCODE and 1000 Genomes projects.

5:15 Close of Conference

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