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Next-Generation Sequencing Data Management - Day 2

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Tuesday, September 27


Sponsored by
Genomatix Software 
7:30 am Breakfast Presentation
Results Matter: Examples of NGS Data Interpretation in Personalized Medicine 

Martin Seifert, Ph.D., CEO, Genomatix Software & Thomas Langmann, Ph.D., Professor, University Hospital RegensburgPersonalized Medicine aims to provide medical treatment specific to an individual's genomic makeup. A biologically intelligent interpretation of genomic NGS data is critical to this process. The presentation is split into two sections, a general introduction and application examples of medically meaningful results obtained from NGS data.

8:15 Successful Sequencing Discussion Groups
Grab a cup of coffee and join a facilitated discussion group focused around specific themes. This unique session allows conference participants to exchange ideas, experiences, and develop future collaborations.

Challenges of Detecting Structural Variants in Tumor SamplesMartina Mijuskovic, Ph.D., Postdoctoral Associate, Center for Health Informatics and Bioinformatics, New York University Langone Medical CenterDiscussion topics include:
• Mate pair vs. paired end sequencing: Which method to use?
• How to predict necessary coverage: effect of repetitive genomic sequences, effect of tumor heterogeneity
• Experiences with different structural variant calling algorithms

NGS Technology AssessmentDavid I. Smith, Ph.D., Professor, Laboratory Medicine and Pathology, Mayo ClinicDiscussion topics include:
• Evaluate advances in sequencing technology, including molecular sequencers
• Discuss supportive technologies such as capture and robotics to make libraries

Alleviating the NGS Bottlenecks Created by Sample PreparationSteven R. Kain, Ph.D., Director, Product Marketing, NuGEN Technologies, Inc.Discussion topics include:
• What are the bottlenecks limiting your ability to process more samples by NGS?
• How significant is the challenge of working with different sequencing platforms?
• How important is it to standardize protocols?
• Is automation the answer?

Handling the Opportunities and Challenges of Diverse Platforms and Projects in a Core EnvironmentMichael W. Smith, Ph.D., Vice President, Director, Genetics and Genomics Group, Advanced Technology Program, SAIC-Frederick, National Cancer Institute at FrederickDiscussion topics include:
• Overview of current NGS platforms experience
• Finding suitable projects
• Matching projects to platforms
• Managing investigator expectations

Using Next-Gen Sequencing for Genome Wide Association Studies (GWAS)Stephanie Costello, Director of Sales, Distribution and Technical Support, DNASTAR Discussion topics include:
• Benefits of using sequencing
• How to analyze the data?
• SNPs and other structural variations
• Integration of existing data (previous studies and databases)

NGS Data Analysis and Medical Applications: From Data to Results – How Much Is Enough?Peter Grant, CEO, Genomatix Software, Inc.Discussion topics include:
• How much Information is provided by genomic variants?
• How do we extract biological/medical KNOWLEDGE from this information?
• What are the building blocks needed to build the road to medically relevant knowledge?

QA and QC During Secondary Analysis:  What are You Doing Now and What Do You Wish Software Could Do for You?Jean Jasinski, Ph.D., Field Application Scientist, Partek, Inc.Discussion topics include:
• What parameters do you examine before aligning reads to the reference? 
• What parameters do you examine after alignment?
• Which operations should be used to deal with poor quality reads (filter, trim, remove, repair, etc.)?
• If you had a programmer in your pocket, which features would you request?

Using Whole Genomes and Exomes for Drug DevelopmentNathan Pearson, Director of Research, Knome, Inc.Discussion topics include:
• What phase(s) of drug development can benefit most from comprehensive sequence analysis? 
• In-house or outsource analysis?
• Can we understand efficacy?  Dosage?  Adverse events?

Open-Source Versus Commercial SoftwareHarsha Rajasimha, Ph.D., Consultant, Bioinformatics and Next-Generation Sequencing, NIHDiscussion topics include:
• Where do you see the field of NGS software going… toward open-source, commercial, or in-between?
• How would the NGS software look differently 3-5 years from now (web-based, cloud-based or desktop workbenches)?

Assembly and Annotation

9:15 Chairperson’s Remarks

Robert M. Stephens, Ph.D., Director, Bioinformatics Support Group, Advanced Biomedical Computing Center, Information Systems Program, SAIC‐Frederick/NCI Frederick

9:20 Extending The Human Reference Sequence - What Are We Doing with the Reads and Contigs That Do Not Map?

Robert M. Stephens, Ph.D., Director, Bioinformatics Support Group, Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick/NCI-Frederick

While new human genomes are becoming available almost daily, most of the released information is limited to short indels and SNVs and is relative to a reference sequence that is incomplete. This presentation will be aimed at launching a discussion of how to best capture the additional information of unmapped reads and contigs so that we extend the “reference” to include this additional material in subsequent analysis.

9:50 Sequencing Chromosomal Rearrangements Reveals Single Gene Disruptions in Otherwise Complex Developmental Disorders

Michael E. Talkowski, Ph.D., Research Fellow, Neurology, Harvard University Program in Medical and Population Genetics, Broad Institute of MIT and Harvard

Delineation of balanced chromosomal rearrangements (BCRs) offers a powerful route to discovery of genes underlying complex disorders, but remains a relatively untapped reservoir of high penetrance alterations because cytogenetic resolution is low and BCRs are not detected by genome-wide microarrays. Here, we show that sequence based characterization of BCRs using optimizations in paired-end sequencing can be leveraged to identify individual loci contributing to otherwise complex genetic disorders. We have applied these methods uncover novel genes and pathway contributing to human neurodevelopmental disorders, as well as a complex genetic architecture associated with human chromosomal alterations. These studies significantly expand the set of known genes and pathways responsible for NDD and will have significant implications for autism research, mechanistic studies of genomic rearrangements, and future interpretation in clinical diagnostics.

Sponsored by
10:20 The Next, Next Generation of Sequencing - From Semiconductor to Single Molecule

Justin H. Johnson, Director, Bioinformatics, EdgeBioThis generation of sequencer holds the promise to revolutionize and democratize sequencing through unprecedented scale and flexibility. However, this promise largely hinges on choosing the appropriate technology for the application of interest (targeted resequencing, de novo sequencing, metagenomics, etc) and gaining the expertise of a rapidly changing technology.  EdgeBio will present case studies highlighting and comparing information, methods, challenges and opportunities in realizing the potential of this latest generation of sequencers, specifically focusing on Ion Torrent, Miseq, and PacBio.

10:35 Networking Coffee Break in the Exhibit Hall with Poster Viewing

11:15 Next-Generation Sequencing Approach to Search for Off-Target Drug Resistance Variants in Three Bacterial Whole Genomes

Sara Dempster, Ph.D., Bioinformatics Scientist – External Resource, R&D, AstraZeneca Pharmaceuticals

11:45 Jellyfish, a Fast Hash Based k-mer Counter

Guillaume Marçais, Ph.D., Postdoctoral Associate, Applied Mathematics & Statistics, Scientific Computation, University of Maryland

From error correcting sequencing read to annotating genomes, counting k-mer frequencies is an important step in many biological application. Jellyfish is a fast and memory efficient software package to count k-mer frequencies. It uses current multi-core computer architecture to handle the very large data set generated by second generation sequencing.

12:15 pm Close of Session


Sponsored byPerkinElmer NEW 2009 12:30 pm Luncheon Presentation
Data Analysis for Next Generation Sequencing: Challenges and Solutions
N. Eric Olson, Ph.D., Senior Leader, Product Development, GeospizaThe presentation will include an overview of Whole Transcriptome Sequencing, Small RNA sequencing and Exome Resequencing and the specific data analysis needs and challenges for each application. Topics covered will include Secondary Analysis (alignments, gene models, etc.) as well as Tertiary Analysis (multi-sample comparisons, biological annotation, etc.) for each application. Geospiza’s cloud-based GeneSifter Analysis Edition software will be used to present best-practice analysis workflows using sample data sets from NCBI’s GEO and SRA.


From Populations to Personalized Medicine 

2:00 Chairperson’s RemarksMichael W. Smith, Ph.D., Vice President, Director, Genetics and Genomics Group, Advanced Technology Program, SAIC-Frederick, National Cancer Institute at Frederick 

2:05 Data Processing and Analysis of Genetic Variation Using Next-Generation Sequencing in the 1000 Genomes Project

Mark A. DePristo, Ph.D., Manager, Medical and Population Genetics Analysis, Broad Institute of MIT and Harvard

Recent advances in sequencing technology make it possible to comprehensively catalogue genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. I discuss a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. We discuss the application of these tools, instantiated in the Genome Analysis Toolkit (GATK), to deep whole-genome, whole-exome capture, and to the multi-sample low-pass (~4x) 1000 Genomes Project datasets.

Podcast 2:35 Using VAAST to Discover the Genetic Basis of Both Rare "Mendelian" Disorders and More Common "Complex" DisordersGholson Lyon, M.D., Ph.D., Research Scientist, Pediatrics, Center for Applied Genomics, Children’s Hospital of PhiladelphiaThis presentation will summarize the efforts of Mark Yandell, Martin Reese and Gholson Lyon to use a newly developed disease-variant finding algorithm, called VAAST, to discover the genetic basis of several rare "Mendelian" disorders, along with applying the algorithm to some "complex" disorders. There is an ongoing blurring of the boundary between Mendelian and complex disorders, given that recent evidence indicates that a certain portion of the heritability of certain "complex" disorders like autism might result from multiple rare mutations exhibiting an oligogenic mode of inheritance, with markedly incomplete penetrance of each variant.

Sponsored byNuGen3:05 Transcriptome Profiling Solutions for Eukaryotes and ProkaryotesSteve Kain, Ph.D., Director, Product Management, NuGEN TechnologiesAdvances in Next-Generation Sequencing (NGS) have increased both the throughput and capacity of sequencing platforms, calling for increased efficiency in cDNA preparation and the ability to work with small, degraded, and heterogeneous samples. NuGEN’s portfolio of NGS products meets this challenge by enabling simple, rapid and affordable workflows with a broad range of sample types. Data will be presented for RNA-Seq studies in diverse areas of research such as oncology, viral assembly, immunology and metagenomics with the common thread of enabling studies with the most precious RNA samples.
3:20 Networking Refreshment Break in the Exhibit Hall with Poster Viewing 

Sponsored by
DNA Star
4:15 Methodology and Analysis Workflow for Next‐Gen Population Genomics without a Reference Genome

Thomas L. Parchman, Postdoctoral Scientist, University of Wyoming

4:45 Establishment of a Library of Repetitive Element (RE) Arrays Unique to the Human Genome: Implication of RE Arrays’ Involvement in Phenotype Determination

Kiho Cho, Ph.D., Associate Professor, Department of Surgery, University of California, Davis; Shriners Hospitals for Children Northern California

The vast majority of mammalian genomes are occupied by a plethora of repetitive elements (REs). Our studies identified a diverse population of complex RE arrays in the human and mouse genomes. Importantly, the genome-wide RE array profiles of mouse and human were unique for each species, which is consistent with the obvious phenotypic differences between the mouse and human. We postulate that the unique sets of RE arrays in the genomes of different species, or even individuals within the same species, may play a role in the determination of species/individual-specific phenotypes.

5:15 Sequencing Frameworks for Rare Variations

Yaniv Erlich, Ph.D., Principal Investigator, Whitehead Institute for Biomedical Research

In this presentation, we will describe frameworks for sequencing and annotating rare variations in genetic diseases. In the first part, we will present DNA Sudoku, a highly efficient strategy to find rare variations in large cohorts. In the second part, we will present two exome sequencing studies for identifying rare neurological disorders in Ashkenazi Jews and Palestinians.

5:45 Close of Day

Sponsored byPartek New 6:00-9:00 Dinner Short Course Three: Start-to-Finish Analysis of a Multi-Assay Next Generation Sequencing StudyInstructors:
Jean Jasinski, Ph.D., Field Application Scientist, Partek
Ryan Peters, M.Sc., Field Application Specialist, Partek

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