Cambridge Healthtech Institute's Fourth Annual
Genomic Data Analysis: Sequencing's Strategic Step
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
Tom Schwei, Vice President & General Manager, DNASTAR, Inc.
8:20 Moleculo Sequencing for Human Genome Phasing and De Novo Assembly of Complex Genomes
Michael Kertesz, Ph.D., Director, Technology Development, Illumina, Inc.
Moleculo is a novel DNA sequencing approach that delivers synthetic reads up to 10Kb long at an extremely low error rate (Q50) – thus improving the efficiency and accuracy of many existing sequencing applications and enabling a range of new applications, ranging from de novo assembly of complex animal and plant genomes to human genome phasing, cancer genomics and direct measurement of gene isoforms.
8:55 Inference of Transcriptional Networks Based on the Gini Correlation Coefficient
Xiangfeng Wang, Ph.D., Assistant Professor, School of Plant Sciences, University of Arizona
We evaluated the Gini correlation coefficient with an expression dataset containing 8,929 pairs of transcription factors and target genes, in comparison with the Pearson, Spearman, Tukey’s Biweight and Kendall tau correlations. Our analysis showed that the Gini correlation is not only able to derive linear relationships, but also can identify the non-linear relationships and the transient regulations that were missed by the other four methods. Additionally, the robustness of the Gini correlation is reflected from its lesser dependence on the form of data distribution, higher tolerance of outlier data points, and lesser dependence on sample size.
9:30 Accurate de novo Assembly of RNA-Seq Data for Total Analysis of Transcriptome Variance
Hsueh-Ting Chu, Ph.D., Assistant Professor, Department of Biomedical Informatics, Asia University, Taiwan
We introduce a new de novo RNA-Seq assembler, EBARDenovo, which is more accurate than other RNA-Seq de novo assemblers because the EBARDenovo program is based on overlapping of pairs instead of overlapping of reads. Furthermore, it is an assembly algorithm with the powerful functionality of detecting aberrant chimeric sequences without any reference. EBARDenovo is very memory-efficient such that researchers can run the analysis of huge RNA-Seq data (up to 100G) without a reference on a normal PC in their own labs.
10:05 Selected Poster Presentation: A Configurable Pipeline for RNA-Seq Data Analysis
Andrew Oler, Ph.D., Computational Biology Section, Bioinformatics and Computational Biosciences Branch, NIH
10:20 Coffee Break in the Exhibit Hall with Poster Viewing
11:00 Robust Statistical Analysis Methods in RNA-Seq
Zhong Wang, Ph.D., Staff Scientist and Group Lead, Genome Analysis, DOE Joint Genome Institute
RNA sequencing (RNA-Seq) is rapidly replacing microarrays for profiling gene expression with much improved accuracy and sensitivity. One of the most common questions in a typical gene profiling experiment is to identify a set of transcripts that are differentially expressed between different experimental conditions. I will give an in-depth overview of current statistical methods, followed by best practices in choosing the appropriate metrics for performing RNA-Seq statistical analyses.
11:35 The Simple Fool’s Guide to Population Genomics via RNA-Seq: A Streamlined SNP and Gene Expression Pipeline
Daniel Barshis, Ph.D., Assistant Project Scientist, National Marine Fisheries Service, Southwest Fisheries Science Center, NOAA Fisheries Service
We’ve developed a streamlined, non-computer scientist friendly pipeline for the analysis of high-throughput mRNA sequencing data (particularly short read mRNA-Seq). I will present the basic components of the pipeline: data quality control, de novo assembly and annotation, SNP detection, and differential gene expression analysis, and how they were used to investigate the genes and cellular pathways involved in differential susceptibility to climate change in a stress-tolerant and stress-susceptible population of reef building corals in American Samoa. This research provides some of the first insight into the molecular mechanisms that may enable some corals to survive future climate stresses.
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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