CHI’s Seventh Annual
DNA-Seq: Advancing Clinical Applications
March 18-20, 2013
Hilton San Diego Resort, San Diego, CA
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Wednesday, March 20
8:00 Morning Coffee
8:15 Chairperson’s Remarks
William Biggs, Ph.D., Senior Director, Genetics & Genomics, Aviir Diagnostic Laboratories
8:20 FEATURED PRESENTATION: Detection of Ultra-Rare Mutations by Duplex Sequencing
Lawrence A. Loeb, M.D., Ph.D., Professor and Director, Department of Pathology, University of Washington School of Medicine
Duplex sequencing offer unprecedented accuracy. It takes advantage of the inherent complementarity of DNA and scores mutants in single DNA molecules only if substitutions are present at the corresponding positions on both strands and are complementary. It eliminates errors due to misincorporation during PCR and errors resultant from copying damaged DNA. This approach is particularly advantageous in identifying rare mutations or in analyzing the multiplicity of mutations in the cancer genome.
8:55 Sample Prep Considerations and Strategies: The Clinical Lab Perspective
Jamie L. Platt, Ph.D., Scientific Director, Advanced Sequencing, Quest Diagnostics, Nichols Institute
In order to achieve maximum results from applying NGS, it is imperative to start from a strong foundation. In nearly all cases, the foundation really is sample prep and the starting sample will readily prove the validity of “garbage in, garbage out.” The importance and key approaches for sample prep will be discussed from a clinical lab perspective.
9:30 Implementation of a Complete Clinical Cardiovascular Exome for the Diagnosis of Heritable Forms of Cardiovascular Disease
William Biggs, Ph.D., Senior Director, Genetics & Genomics, Aviir Diagnostic Laboratories
With the increasing usage of whole and targeted exome sequencing to guide patient care, the goal of achieving near complete coverage of the targeted regions takes on a new importance. We will report on the use of multiple enrichment methods to increase evaluable coverage to greater than 99%.
10:05 Selected Poster Presentation
10:20 Coffee Break in the Exhibit Hall with Poster Viewing
11:00 Genomic Sequencing of Uncultured Bacteria from Single Cells
Roger S. Lasken, Ph.D., Professor, J. Craig Venter Institute
A technology pipeline has been developed for isolating single cells and carrying out genomic sequencing. Uncultured bacteria comprise the majority of complex microbial communities, including the human microbiome. We report on a program for acquisition of MDA-amplified single cell bacterial genomes from the human microbiome for genome sequencing, including high throughput methods for sorting of single cells by flow cytometry, MDA, and 16S PCR for taxonomic identification.
11:35 Sequencing at Ultra-High Resolution: Methods for the Analysis of the Genome and Transcriptome of a Single Cell
Abizar lakdawalla, Ph.D., Associate Director, New Sequencing Technologies, Illumina
Improvements in Illumina sample prep and library prep protocols now allow the sequencing of mRNA and genomic DNA from isolated single mammalian and bacterial cells. The presentation will focus on the specific approaches for successful single cell transcriptome and genome sequencing on the MiSeq and HiSeq 2500 sequencers. Single cell analysis expands the application of Next generation sequencing into the analyses of individual circulating tumor cells, cancer heterogeneity at the level of a few cells and for cellular differentiation and developmental biology from a single cell to a complex organism.
12:10 pm Close of Session
12:15 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own
1:30 Chairperson’s Remarks
Marc Salit, Ph.D., Leader, Multiplexed Biomolecular Science Group, NIST Chemical Science and Technology Laboratory
1:35 Single-Molecule Analysis of DNA Base Modifications Using Protein Nanopores
Cynthia J. Burrows, Ph.D., Distinguished Professor, Chemistry, University of Utah
Moving beyond A, T, C, and G, the ability to sequence DNA for base modifications - including DNA damage sites and methylation patterns - will expand the horizons of genomic discovery. In this work, molecular tagging of abasic sites and oxidative damage sites permits detection of base lesions as single molecules of DNA translocate through the alpha-hemolysin ion channel.
2:10 Toward Sequencing DNA Using Synthetic Nanopore Sensors
Aleksei Aksimentiev, Ph.D., Department of Physics, University of Illinois at Urbana-Champaign
The idea of using a nanopore to sequence DNA continues to generate excitement among scientists and entrepreneurs. The spectacular progress in using biological enzymes to enable nanopore sequencing indicates the imminent arrival of nanopores in practical biomedical applications. Even more exciting are the prospects of creating solid-state devices that can read the nucleotide sequence directly from DNA and RNA molecules. I will describe our recent efforts to model such devices at atomic resolution and develop strategies for electronic readout of the DNA sequence.
2:45 Refreshment Break in the Exhibit Hall with Poster Viewing (Last Chance for Poster and Exhibit Viewing)
3:15 Poster Awards (Announced in Session Room)
3:30 Single Molecule Electronic DNA Sequencing by Synthesis with Tagged Nucleotides and Nanopore Detection
Jingyue Ju, Ph.D., Professor, Chemical Engineering and Pharmacology; Head, DNA Sequencing & Chemical Biology; Director, Center for Genome Technology & Biomolecular Engineering, Columbia University
We have developed a novel single molecule nanopore-based sequencing by synthesis (Nano-SBS) strategy that accurately distinguishes four bases by detecting 4 different sized tags released from 5’-phosphate-modified nucleotides. This produces a unique ionic current blockade signature due to the tag’s distinct chemical structure, thereby determining DNA sequence electronically at single molecule level with single base resolution. This approach coupled with polymerase attached to the nanopores in an array format should yield a single-molecule electronic Nano-SBS platform.
4:05 Fast DNA Sequencing via Tunneling
Massimiliano Di Ventra, Ph.D., Professor, Department of Physics, University of California San Diego
Fast and low-cost DNA sequencing methods would revolutionize medicine; however, this goal of “personalized medicine” is hampered today by the high cost and slow speed of DNA sequencing methods. We suggest a sequencing protocol which requires the measurement of the distributions of transverse currents during the translocation of single-stranded DNA into nanopores. I will support our conclusions with a combination of molecular dynamics simulations coupled to quantum mechanical calculations of electrical current in experimentally realizable systems. I will also discuss recent experiments that confirm these theoretical predictions and show the potential of sequencing via tunneling.
4:40 Conference Wrap-Up
4:45 Close of Conference
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