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Please click here to download the following podcasts: 

1000 Genomes Project: Cancer, Genetic Variation, and Drug Response

Mapping Genomes in 3D

The Human Microbiome Project: Next-Generation Sequencing and Analysis of the Indigenous Microbiota


Applied Biosystems NEW



Agilent Technologies

Beckman Coulter Genomics



Complete Genomics

Expression Analysis










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The Scientist


Pharm Cast


Sequencing Technologies - The Next Generation by Michael Metzker


Day 1  |  Day 2  |  Day 3  |  Short Courses  

Companion Meeting: Next-Generation Sequencing Data Management 

Wednesday, September 29, 2010

Sponsored by
HP sm 
7:30 am Breakfast Presentation
Enabling World Class Research through Innovative Data Management Strategies
Mark Fahey, Scale Out NAS & Back Up Recovery and Archive Sales Specialist, Hewlett Packard

 Targeted Sample Enrichment

8:15 Chairperson’s Remarks

8:20 Targeted Analysis of DNA Methylation Using Hybrid Capture of Bisulfite Converted DNA

James B. Hicks, Ph.D., Research Professor, Genetics, Cold Spring Harbor Laboratory

Targeted sequencing of bisulfite treated DNA by hybrid capture requires that the array be capable of trapping the converted forms of both methylated and unmethylated sequences. Unmethylated regions will have all C residues converted to T after sequencing, while other regions will have an unknown number of C residues in CpG dinucleotides protected from bisulfite conversion by cytosine methylation. We have published an array capture strategy for detecting DNA methylation at the base pair level using next generation sequencing. We will describe strategies for extending and optimizing the capture of both methylated and unmethylated sequences and the mapping of the resulting information-depleted sequence output.

8:50 Optimization of Sample Preparation for Next-Generation Sequencing

Niall Lennon, Ph.D., Assistant Director, Process Development, The Broad Institute of MIT and Harvard

Long reads and short sequencing run times make the 454 platform a powerful tool for de novo assembly of small genomes, metagenomic profiling and amplicon sequencing. The challenge is that these applications require a small number of reads from large numbers of samples. Overcoming these requires a combination of automation, molecular barcoding and process improvement. Through application of these changes, it is possible to process hundreds of samples in a time and cost effective manner.

9:20 Extending Read Lengths and Accuracy of Next-Generation Sequencing by Molecular Tagging and Subassembly

Joseph Hiatt, M.D., Ph.D. Candidate, Genome Sciences, University of Washington

Major advances in cost and throughput associated with next-generation DNA sequencing are currently offset by significant trade-offs with respect to read length and base-calling accuracy. We have developed a method called subassembly that overcomes these limitations by using unique sequence tags to identify individual sample molecules at the beginning of library construction. These tags then direct grouping of sequencing reads and thereby facilitate accurate reconstruction of a consensus sequence for each sample molecule. Using this approach, we have used the Illumina platform to yield highly accurate (Q40) subassembled reads with effective lengths as long as 700 bp.

9:50 LabChip XT - Advanced Nucleic Acid Fractionation for Next-Generation Sequencing Sample PreparationSponsored by

Isaac Meek, Associate Director of Marketing, Caliper Life Sciences

Reproducible and scalable sizing and isolation has become a bottle neck for many applications of new sequencing technologies. Caliper Life Sciences has developed and commercialized instruments that utilize microfluidics to achieve rapid and high resolution electrophoretic separations. We have now developed a commercial solution, the LabChip XT, that will simplify and improve nucleic acid fractionation. By using intersecting microfluidic channels, optical detection and computer control, we can automatically extract a target band during separation and route the selected material to a collection well. The presented material will describe the fundamentals of our microfluidics-based solution.

10:05 Morning Coffee, Poster and Exhibit Viewing

11:00 Selected Poster Presentation


11:15 MBD-Isolated Genome Sequencing Provides a High-Throughput and Comprehensive Survey of DNA Methylation in the Human Genome

David Serre, Ph.D., Assistant Staff, Genomic Medicine Institute, Cleveland Clinic

We describe a novel technique, MBD-isolated Genome Sequencing, which combines precipitation of methylated DNA by recombinant methyl-CpG binding domain of MBD2 protein and massively parallel sequencing of the isolated DNA. We utilized this approach to study three isogenic cancer cell lines with varying degrees of DNA methylation. We successfully detected previously known methylated regions in these cells and identified hundreds of novel methylated regions. This technique can be applied to any biological settings to identify differentially methylated regions at the genomic scale.

11:45 De novo Variant Detection with Whole Exome Capture

Stephan Sanders, Ph.D., Postdoctoral Associate, Yale University

The number of potentially disease causing variants discovered by whole exome sequencing can be overwhelming. To identify variants with a high likelihood of being deleterious, we sequenced probands along with their parents to detect de novo events. While this strategy drastically reduces the number of variants to consider, detecting de novo events with next generation sequencing poses additional challenges: first, the need to improve specificity due to the rarity of de novo events (approximately two per exome), and second, the need to ensure high quality sequence in every family member.

12:15 pm Close of Session

Sponsored by
Applied Biosystems NEW 
12:25 Luncheon Presentation

Making Whole Human Genome Sequencing Routine
Tim Harkins,Ph.D., Director R&D, SOLiD Collaborations
As sequencing technologies increase their throughput, it is now possible to readily sequence a whole human genome.  As we sequence more human genomes we are learning not only new insights into human biology but also how critical certain technology features are - beyond just shear data mass.  One critical factor is sequencing accuracy.  Although using consensus accuracy can overcome some inherent error rates, a floor is ultimately reached, thereby limiting the ability to identify either low frequency events like somatic mutations or the ability to identify SNV’s when using low coverage techniques to support GWAS based projects.  We have developed a new chemistry that incorporates error-correcting codes that enable the SOLiD platform to achieve up to five 9’s within a single sequencing read.  This improvement will be presented applied to a diverse set of whole human genomes.



NGS Further Elucidates the Genomic Basis of Disease

1:55 Chairperson’s Remarks

2:00 Multiple Approaches for Transcriptome Analysis of a Novel 3D Breast Carcinoma Model

Raymond R. Mattingly, Ph.D., Associate Professor, Pharmacology, Wayne State University

We have applied and cross-validated whole genome microarray, digital gene expression (DGE), and RNA-Seq analyses to explore the networks and pathways that underlie ductal carcinoma in situ (DCIS) of the breast. The analyses have been applied to a novel and tractable model of DCIS in 3D overlay culture.

2:30 Massively Parallel DNA Sequencing to Characterize Cancers of the Head
and Neck

David I. Smith, Ph.D., Consultant and Professor, Laboratory Medicine and Pathology, Mayo Clinic

We have utilized massively parallel ligation-based DNA sequencing to characterize a group of head and neck cancers. We used a methodology to examine the complete transcriptome of a group of matched normal-tumor samples that also preserved the strandedness of each transcript. We also performed mate-pair sequencing of the DNA isolated from these sample normal-tumor pairs. The transcriptome sequencing enabled us to characterize genes with aberrant expression during the development of head and neck cancer. We found that there was allelic expression imbalances associated with copy number alterations.

3:00 Exome Sequencing of Multigenerational Mendelian Families

Stephan Züchner, M.D., Associate Professor, Human Genetics and Neurology; Director, Center for Human Molecular Genomics, University of Miami Miller School of Medicine

Exome sequencing comprises an applicable genomic tool that allows obtaining the majority of coding variation in a given individual with reasonable effort. We have begun to apply the technique to relatively small, dominant, and multigenerational Mendelian families with Axonopathies in order to identify novel causative genes. Results and challenges of this ongoing work will be presented.

3:30 Refreshment Break, Poster and Exhibit Viewing


1000 Genomes Project

(Session shared with Next-Generation Sequencing Data Management Conference)

4:00 Poster Award Sponsored by Oxford Nanopore 

4:00 Detecting Rare Genetic Variants in the Large-Scale 1000 Genomes Exome Resequencing Project

Fuli Yu, Ph.D., Assistant Professor, Human Genome Sequencing Center, Baylor College
of Medicine

The 1000 Genomes Pilot 3 Project aims to generate high coverage data primarily in the coding regions of approximately 1,000 selected genes from ~900 individuals. From this sequencing program we expect to identify essentially all variants present in the targeted exons, using the exome capture technologies combined with different next-generation sequencing platforms. The key challenge in SNP discovery is to distinguish true individual variants from sequencing errors. We have developed Atlas-SNP2 at BCM-HGSC, a computational tool that detects and accounts for systematic sequencing errors caused by context-related variables in a logistic regression model learned from training data sets.

4:30 Impact of the 1000 Genomes Project on the Next Wave of Pharmacogenomic Discovery

M. Eileen Dolan, Ph.D., Professor, Medicine, University of Chicago

The 1000 Genomes Project aims to provide detailed genetic variation data on >1000 genomes from worldwide populations using the next-generation sequencing technologies. Some of the samples utilized for the 1000 Genomes Project are the International Hap-Map samples that are composed of lymphoblastoid cell lines (LCLs) derived from individuals of different world populations. The detailed map of human genetic variation promised by the 1000 Genomes project will allow a more in-depth analysis of the contribution of genetic variation to drug response. Future studies utilizing this new resource can greatly enhance our understanding of the genetic basis of drug response and other complex traits.

5:00 Integrated Analysis of Human Resequencing Data from Multiple Sequencing Platforms

David Craig, Ph.D., Associate Director, Neurogenomics; Investigator, Neurobehavioral Research Unit, TGen

I will present integrated analysis pipelines and software tools for analyzing next-generation sequencing data using multiple sequencing technologies. Specific focus will be on integrating SOLiD and Illumina datatypes, leveraging complementary strengths of both platforms. We will present whole-genome sequence analysis both in the context of 1000 Genomes and within our own whole-genome sequencing studies.

5:30 Close of Conference

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