8:30 - 9:00 am Pre-Conference Short Course Registration
9:00 am - 12:00 pm Pre-Conference Short Courses*
Short Course One: NGS Sample Prep
9:00 am Chairperson’s Opening Remarks
Kip Harry, Conference Director, Cambridge Healthtech Institute
9:05 
The Importance of Reliable Sample Quality Control in the Next Generation Sequencing Workflow
Melissa Liu, Ph.D., Application Marketing Scientist, Agilent Technologies, Inc.
Assessing the quantity and quality of your experimental starting material and performing essential intermediate checks during sample preparation is key to the success of any assay. Ensuring that genomic DNA, RNA & DNA samples as well as NGS libraries are of sufficient quality to continue with the Next Generation Sequencing (NGS) workflow saves precious time and money further downstream. This course will review the Agilent 2100 Bioanalyzer and introduce the 2200 TapeStation as indispensable tools for sample QC and will provide an overview of protocols, good measurement practices, troubleshooting, tips and tricks to make sure you get the most out of your NGS applications.
9:45 Making SENSE™ of Antisense Transcription - an Exceptionally Strand-Specific mRNA-Seq Library Prep Protocol
Alexander Seitz, M.D., CEO , Lexogen
RNA-Seq has become the method of choice for transcriptome analysis. While sample preparation remains the most challenging step. Lexogen's SENSE mRNA-Seq library prep kit is a fast, simple and complete solution. Its exceptional strand-specificity (>99.9%) empowers the accurate detection of antisense transcripts and overlapping genes.
10:25 Networking Coffee Break
10:45 Development of NGS Library Prep Methods for Standard DNA Samples and 40 kb Long-Span, Mate-Pair Libraries
Curtis Knox, Vice President, Marketing & Sales, Lucigen
Lucigen will present validation data from the NxSeq® DNA Prep Kits and the NxSeq® 40 kb Mate-Pair Cloning kit for de novo genome sequencing. Attendees will learn about the differences between blunt and A-tailed fragment ligation for NGS sample prep and how ligation times affect library quality. In addition, information regarding the use of long-span (40 kb), mate-pair cloning to assemble de novo genomes will be discussed.
11:25 Panel Discussion with Short Course Speakers
11:50 Short Course Wrap-Up
12:00 pm End of Short Course One
Short Course Two: Functional Genomics
9:00 am Chairperson’s Opening Remarks
Mary Ann Brown, Exective Director, Conferences, Cambridge Healthtech Institute
9:05 Scripps Genome ADVISER: Annotation and Distributed Variant Interpretation Server
Ali Torkamani, Ph.D., Director, Genome Informatics and Drug Discovery, The Scripps Translational Science Institute; Assistant Professor, Molecular and Experimental Medicine, The Scripps Research Institute
SG-ADVISER performs holistic, in-depth, annotations and functional predictions on all variants generated from high-throughput sequencing data in multiple arenas of genomic relevance, including coding and regulatory variants as well as the biological processes which connect them. Appropriate annotation of sequence variants is crucial in putting into perspective the overabundance of a particular variant or set of variants in diseased individuals or the belief that a particular variant is likely to have a molecular and/or biological effect. We will demonstrate and describe the different functional annotations produced by SG-ADVISER and demonstrate variant prioritization through annotation based filters through the companion GUI.
9:45 Network-Based Ontologies of Gene Function: Construction and Applications
Janusz Dutkowski, Ph.D., Research Fellow, Ideker Lab, Departments of Medicine and Bioengineering, University of California, San Diego
Ontologies are essential in many domains, capturing knowledge as a hierarchy of concepts and their interrelationships. Most ontologies, including those in biology, are typically developed through manual expert curation - a process that is subjective and limited to well-established knowledge. We have recently shown that the vast amounts of genomic data now available can be transformed to automatically assemble on ontology of gene function that rivals manually curated efforts in coverage and power. Our network-extracted ontology (NeXO) provides a new resource for systems and synthetic biology - i.e. a data-driven multiscale catalog of cellular machinery, from genes to complexes, to pathways and higher-order processes. It also provides a way to systematically update manually constructed ontologies with new terms and relationships derived from high-throughput data. I will discus the construction of data-driven ontologies, as well as major applications including identifying biological components and processes altered in disease.
10:25 Networking Coffee Break
10:45 
Implementation of HGMD and Genome Trax in NGS Analysis Pipeline
Alexander Kaplun, Ph.D., Field Applications Scientist, BIOBASE Corporation
HGMD® Professional is a unique resource providing comprehensive data on human inherited disease mutations. Its compilation of structured, manually curated data from the peer-reviewed literature enables quick access to both single mutation queries and advanced search applications. HGMD® is widely used in human genetics research, diagnostics, and personal genomics applications. Genome Trax™ is a data analysis tool which works with HGMD® and other data sources to enable scientists to identify human genome variations of functional significance by mapping their NGS data to known elements such as disease mutations and regulatory sites.
11:25 Panel Discussion with Short Course Speakers
11:50 Short Course Wrap-Up
12:00 pm End of Short Course Two
5:00 - 5:30 pm Dinner Short Course Registration
5:30 - 8:30 pm Dinner Short Courses*
Short Course Three: Sequencing 101
Sequencing 101
Ryan Kim, Ph.D. Director, UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis
In less than five years, next-generation sequencing has gone from radical to routine. Naturally, in a field moving so fast, newbies can feel overwhelmed. Sequencing 101 is designed to provide definitions of terminology, types of platforms and workflow strategies, as well as current applications and future directions. Learn about the genomic data revolution from data generation to management to analysis and interpretation. This course is perfect for those needing an introduction to next-generation sequencing technology and applications.
Course Outline:
Introduction
- Human Genetics and Genomics
- Conventional sequencing vs. NGS
- Big data and big biology
NGS technology
- Key NGS technology: brief history and technology basics
- NGS applications: de novo sequencing, resequencing, RNA-seq, reduced genome (exome, ChIP-seq, microRNA etc), metagenome, genotyping by sequencing, personalized genomics etc.
- Data analysis 101: assembly and alignment, sequence variation detection, database and IT related consideration
Experimental Design
- Biological question
- Decision tree
- Sample prep
- Data analysis (statistical aspect)
Future Trends of NGS and Genomics
- Emerging technology
- Single cell genomics, synthetic genomics, system biology etc.
- Omics integration
- Cloud computing
Instructor Bio:
Ryan Kim, Ph.D. Director, UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis
Dr. Ryan Kim is leading the implementation of next-generation, emerging sequencing technologies, and data analysis for innovative and large-scale genome studies. Currently, he is the Director of the Genome Center Cores at the University of California, Davis, with his former positions including Deputy Director and Director of Genome Center at National Center for Genome Resources, Director of DNA Services within Biotechnology Center at University of Illinois, Urbana-Champaign, and Senior Research Scientist at Sydney Kimmel Cancer Center at La Jolla, CA. His research has been involved with numerous personal genome projects, comparative genome sequencing projects for agricultural genomics and metagenomes.
Short Course Four: NGS Assembly and Alignment
Knowing Your Upstream: Comparison of Alignment and Variant Callers Used in Production Pipelines and their Limitations
Gabe Rudy, Vice President, Product Development, Golden Helix
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.
In this talk I will compare the performance of the alignment and variant calling tools used by sequencing service providers including Illumina Genome Network, Complete Genomics and The Broad Institute. Using public samples analyzed by each pipeline, we will look at the level of concordance and dive into investigating problematic variants and regions of the genome.
Instructor Bio:
Gabe Rudy, VP, Product Development, Golden Helix
Gabe is a 10-year veteran at Golden Helix, and spends his days collaborating with a diverse set of scientists and building solutions to enable their research. He earned his masters in Computer Science from the University of Utah before setting his sights on the fast-changing field of genomics and bioinformatics. Gabe has been involved in developing various algorithms from copy number segmentation to runs of homozygosity and rare variant association testing. Gabe blogs about the genomics field from the perspective of someone building solutions and curating genomic annotations and public databases. His series "A Hitchhikers Guide to Next Generation Sequencing" has become quite popular as a starter guide for those entering the field.
*Separate Registration Required