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August 19-20

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RNA-Seq Experimental Design and Bioinformatics

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Short Courses* 

Monday, August 19

9:00 am - 12:00 pm

SC1: Mapping Genomes in 3D

Genomes are organized into 3-dimensional (3D) conformation in vivo through interactions with protein factors. In addition, DNA elements separated by long genomic distances are known to functionally interact. However, the details of these 3D structures and their role in gene transcription are largely unknown. This course is designed to provide an overview of sequencing strategies and analysis for probing the 3D structure of genomes.

9:00 am Introduction and Opening Remarks

Mary Ann Brown, Executive Director, Conferences, Cambridge Healthtech Institute

9:20 Analyzing Three-Dimensional Organization of Epigenomes

Jennifer E. Phillips-CreminsJennifer E. Phillips-Cremins, Ph.D., Research Scientist, Job Dekker Laboratory, Program in Systems Biology, University of Massachusetts Medical School  Biography  

Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cellular function. Here I will compare and contrast the utility of various molecular Chromosome-Conformation-Capture methodologies (e.g., 3C, 4C, 5C, Hi-C) in mapping 3-D organization of genomes. I will provide an overview of computational strategies used to analyze “C"” data and discuss the chromatin organizing principles that have emerged from the integration of 3-D architecture maps with genome-wide maps of epigenetic modifications.

10:00 From One-Dimensional Mapping to Three-Dimensional Genome Structure and Function

Yijan Ruan SYijun Ruan, Ph.D., Professor and Director for Genome Sciences, Jackson Laboratory for Genomic Medicine, The Jackson Laboratory  Biography 

It has been viewed that distant DNA elements functionally interact with one another via protein factors. However, the details of this view are largely missing. To explore in this direction, we developed the Chromatin Interaction Analysis using Paired-End-Tag sequencing (ChIA-PET) strategy for de novo detection of genome-wide long-range chromatin interactions, and applied this approach to elucidate whole-genome chromatin interactions mediated by a number of protein factors including RNA polymerase II (RNAPII) that involves transcription activities and transcription facts that modulate specific regulations. Such analyses in human and mouse cells revealed the general landscape of chromosomal organization and the topological framework for transcription coordination and regulation. Overall, ours and others’ studies are starting to pave the way towards presenting the 3D topographic maps and functional architecture of the human genomes. Experimental and computational strategies will be discussed in this course.

10:40 Refreshment Break

10:55 High-Order Chromatin Structure and Transcription Regulation

Chia-Lin WeiChia-Lin Wei, Ph.D., Group Lead, Sequencing Technologies, DOE Joint Genome Institute Biography 

In multicellular organisms, expression regulation is the central theme modeling lineage differentiation and development. Transcription regulation is involved in the dynamic interactions between components of the “transcription factory,” including the binding of RNA polymerases and their distal regulatory elements (DREs) in three-dimensional nuclear space. Despite being efficient and precise, the efforts in global identification of DREs have been focused on linear genomic organization. In this talk, we will discuss the approaches used to construct spatial genomic organization and examine the influence of chromatin structure on lineage-specific transcription. The current knowledge of chromatin conformation sets the stage for the full-scale dissection of spatial and temporal genome structures and their roles in orchestrating development.

11:35 Panel Discussion with Speakers

12:00 pm Close of Short Course


SC2: Sample Prep

The emergence of next-generation sequencing technologies has revolutionized genomic research. This dramatic advancement, however, still involves complicated and labor-intensive workflows for upstream sample preparation, library construction, and template amplification. Instructors share their solutions to prepare for sequencing runs (including the specific requirements of sequencing platforms) by addressing customizability, compatibility, and cost effectiveness.

9:00 am Introduction and Opening Remarks

An-Dinh Nguyen, Associate Conference Producer, Cambridge Healthtech Institute

9:20 Rapid Conservative DNA Shearing for Long-Paired End Library Construction

Stacey M. BroomallStacey M. Broomall, MS, Laboratory Manager, ECBC Genomic Sciences Team, U.S. Army, BioSensors Branch, Edgewood Chemical Biological Center  Biography 

Sample preparation for paired-end library construction in genome finishing, a process necessary for microbial forensic applications, relies on the use of commercial hydrodynamic shearing platforms. This method can be cumbersome as the available instruments have been subject to frequent clogging, air bubble formation and substantial loss of DNA (up to 50%). Sonication and nebulization of DNA for PE purposes is not an option as they are only amenable for fragments up to 5kb and 1.5kb, respectively. ECBC functioned as a beta test bed for the Covaris g-TUBE and provided feedback for the PE library preparation process and sequencing data on the Roche 454 FLX Titanium sequencing platform. Results are presented here.

9:50 Improved FFPE Nucleic Acid Extraction for NGS

John-David HerlihyJohn-David Herlihy, Ph.D., Product Manager, Covaris, Inc.  Biography  

Adaptive Focused Acoustics (AFA) technology offers a versatile solution to simplify and improve pre-analytical sample preparation workflows and enhance bioanalytical assay performance. The precision, accuracy and robustness of AFA technology has established Covaris as the DNA Shearing solution of choice for research and clinical labs. The versatility of AFA is enabling new methods in the extraction of nucleic acids from formalin-fixed, paraffin-embedded (FFPE) tissues. The inclusion of FFPE samples in genomics and transcriptomics studies requires higher-quality starting material for integration with Next-Generation Sequencing library preparation. Covaris’s new method for DNA extraction from FFPE tissue samples eliminates the need for organic solvents and high-heat, and provides seamless integration of high-quality DNA in NGS library prep and genomic analysis workflows.

10:20 Library Preparation for RNA Sequencing

Alexander SeltzAlexander Seitz, M.D., CEO, Lexogen  Biography 

Library preparation is an essential step for RNA sequencing. Appropriately chosen protocol will not only improve quality of the sequencing results but also save your time and money. In this presentation I will review existing methods for RNA-Seq library preparation and present SENSE protocol for a fast and very reproducible generation of exceptionally strand-specific RNA libraries.


10:50 Refreshment Break


11:05 Making Targeted Sequencing Simple with SmartChip TE System

Michael VishnevetskyMichael Vishnevetsky, Ph.D., Vice President, WaferGen Biosystems, Inc.  Biography 

Whole exomes or targeted panels? Large panels or just a few relevant genes? And what about a workflow that will prompt clinicians to broadly adopt Next-Gen Sequencing? The clinical sequencing community has been challenged with the transfer of NGS tests from research and development into the clinic. To meet this challenge, WaferGen has developed the high-density SmartChip TE System for targeted sequencing. Practical benefits of this methodology include flexibility in panel development, improved accuracy and precision with a simple, intuitive, lab-friendly workflow.

11:35 Panel Discussion with Speakers

12:00 pm Close of Short Course



Tuesday, August 20

6:00 - 9:00 pm

SC3: Assembly and Alignment

The most important first step in understanding next-generation sequencing data is the initial alignment or assembly. This course is designed to provide an overview of alignment and assembly algorithms, and comparisons for various applications.

Knowing Your Upstream: Comparison of Alignment and Variant Callers Used in Production Pipelines and Their Limitations

Gabe RudyGabe Rudy, Vice President, Product Development, Golden Helix and Author,  “A Hitchhiker’s Guide to Next Generation Sequencing”  Biography 

Alignment algorithms are not just about placing reads in best-matching locations to a reference genome. They are now being expected to handle small insertions, deletions, gapped alignment of reads across intron boundaries and even span breakpoints of structural variations, fusions, and copy number changes. At the same time, variant-calling algorithms can only reach their full potential by being intimately matched to the aligner's output or by doing local assemblies themselves. Knowing when these tools can be expected to perform well and when they will produce technical artifacts or be incapable of detecting features is critical when interpreting any analysis based on their output.


*Separate Registration Required