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Please click here to download the following podcasts: 

In the Wake of the Flood 

Using VAAST to Identify Causative Mutations 

Taking NGS into the Clinic 

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 

Building a Genome Sequencing Center: Managing and Mining Two Years of NGS Data 

Short Courses

Sunday, September 25 (afternoon) *

Short Course One: Gene Sequence to Gene Function


Sequencing of whole genomes is advancing exponentially. While these genome sequencing efforts reveal the basic building blocks of life, a genome sequence alone is insufficient for elucidating biological function. In addition, there is a real opportunity and clear need to generate associated functional genomic data. This short course is designed provide the scientific basis of bridging the gap between gene sequence and gene function.

2:00 pm Short Course Registration

2:30 Opening Remarks

2:40 Illuminating Evolutionary Constraints by Systematic Mutation and Deep Sequencing

Daniel Bolon, Ph.D., Assistant Professor, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School

We have exploited deep sequencing technology to experimentally determine the fitness of all possible individual point mutations for a gene. The approach is very general and can be applied to any genetically tractable biological system that grows rapidly including yeast, bacteria, viruses, and cancer cells. Potential applications include exhaustive screening of mutations that confer drug resistance. Proof of principle work will be presented for a nine amino acid region of yeast Hsp90.

3:10 Functional Annotation of Single Nucleotide Variants in Cancer

Michael Krauthammer, Ph.D., Associate Professor, Pathology, Yale University School of Medicine

This talk will highlight current strategies for assessing the functional consequences of Single Nucleotide Variants (SNVs) in cancer. The discussed topics include: computational challenges when mapping genomic variant positions to transcript positions, codon-level machine-learning strategies for identifying deleterious amino acid substitutions, and gene-level statistics for identifying driver genes from whole-exome sequencing.

3:40 Refreshment Break

4:00 A Computational Approach to Detect Chimeric Transcripts with Paired-End RNA-Seq Experiments: FusionSeq

Andrea Sboner, Ph.D., Associate Research Scientist, Computational Biology and Bioinformatics, Molecular Biophysics and Biochemistry, Yale University

Recent advances in sequencing technologies have enabled the analysis of genomes and transcriptomes at an unprecedented level of resolution. Here we present a computational approach to identify chimeric transcripts using paired-end (PE) RNA-Seq data. The approach, called FusionSeq, first detects all possible chimeric candidates, then filters artifacts caused by several sources of noise, and finally identifies the sequence of the junction. FusionSeq was able to identify known and new candidates in a set of prostate cancer samples.

4:30 Using the Probabilistic Disease-Gene Finder, VAAST, to Identify a New and Very Rare Mendelian Syndrome

Gholson Lyon, M.D., Ph.D., Research Scientist, Pediatrics, Center for Applied Genomics, Children’s Hospital of Philadelphia

We identified a family with a previously undescribed lethal X-linked disorder. We used X-chromosome exome sequencing on an affected newborn individual and his relatives, followed by analysis with a new software program, VAAST, to identify the causative mutation, a gene that encodes the catalytic subunit of the major human N-terminal acetyltransferase (NAT). Surprisingly, mutations in the NAT genes have never before been linked to human genetic disease. Functional analysis of proteins demonstrated significantly impaired biochemical activity, confirming that this mutation causes this disease.

5:00 Panel Discussion 

5:00-5:30 Short Course Dinner


Sunday, September 25 (evening) *


5:30-8:30 Short Course Two: Developing and Managing Your NGS Pipeline

Managing and developing a successful NGS pipeline includes pre-sequence planning; experimental design, sample procurement, DNA/RNA sample preparation; the sequence platform runs; and post-sequence data analysis, management, and storage. NGS has revolutionized biological research but sequences cannot be accomplished without supporting technologies, managed resources, efficient workflows, and enthusiastic researchers. Learn from the practical experiences of experts who have developed their NGS pipelines for peak performance.

5:00-5:30 Short Course Dinner 

5:30 Opening Remarks 

Podcast5:40 Next-Generation Sequencing and Its Impact on Clinical Practice: The Mayo Experience

David Smith, Professor, Lab Medicine & Pathology, Mayo Clinic and Foundation

In this talk, we will discuss the impact of a terrabase sequencer on clinical practice. This presentation will summarize how Mayo Clinic got into next-gen sequencing and how we’ve attempted to implement the technology directly into our Department of Laboratory Medicine and Pathology. The first clinical tests are now being developing to capitalize on existing next-gen capabilities. We will discuss implications for the future, especially when patients start showing up with their genomes already completely sequenced.

6:10 Comparison of Commercially Available In-Solution Target Enrichment Methods for Next Generation SequencingKip Lord Bodi, Genomics Core Director, Tufts University Core Facility, Tufts University School of MedicineSeveral commercial methods exist for the targeted capture of genomic DNA in Next-Generation Sequencing (NGS) libraries. Isolating subsets of genomes greatly enhances the efficiency of NGS by allowing researchers to focus on their regions of interest and increase the level of multiplexing. For the 2010-11 ABRF DNA Sequencing Research Group (DSRG) study, we compared in-solution products from two leading companies that offer custom enrichment methods. Both companies were provided with the same genomic DNA and genomic locations of the targeted regions. The targeted region totalled 3.5 Mb and included 31 individual genes and a 2Mb continuous interval. Each company was asked to design the best assay, perform the capture in replicates and return the captured material to the DSRG. Sequencing was performed in two different laboratories. Sequencing data were analyzed for sensitivity, specificity and coverage of the targeted regions. SNP calling was compared for each platform, and the bait designs of each targeted capture were compared with the overall results.

6:40 Refreshment Break 

7:00 High-Throughput Sample Preparation and Sequencing at the Broad InstituteMaura T. Costello, Process Development Scientist, Operations and Process Development, Genome Sequencing Platform, Broad Institute of MIT and HarvardDramatic increases in data produced by next-generation sequencing technologies demand robust, high throughput sample preparation pipelines, the ability to multiplex samples, and tools for efficient data monitoring and troubleshooting. This talk will provide an overview of the Broad Institute Sequencing Platform’s high-throughput sequencing pipeline, which is capable of producing and sequencing >2000 libraries per week.

7:30 Setting Up and Running Sequencers in Core Laboratories for the NCIMichael W. Smith, Ph.D., Vice President, Director, Genetics and Genomics Group, Advanced Technology Program, SAIC-Frederick, National Cancer Institute at FrederickIn March 2009, the Center for Cancer Research Sequencing Facility opened from the ground up.  Today it operates two Genome Analyzers. The sister Laboratory of Molecular Technology operates four  Progress, lessons learned, challenges and opportunities for the future will be discussed in regards to serving numerous NCI investigators and bringing these sequencers into routine operation for a diverse set of projects and experimental designs.

8:00 Discussion Panel 

8:30 Close of Short Course 


Tuesday, September 27 *


Sponsored by
Partek New 
6:00-9:00 Dinner Short Course Three: Start-to-Finish Analysis of a Multi-Assay Next Generation Sequencing Study

Instructors:Jean Jasinski, Ph.D., Field Application Scientist, Partek
Ryan Peters, M.Sc., Field Application Specialist, Partek
In this workshop, we present a comprehensive start-to-finish of a multi-assay NGS study. The data comes from 8 breast cancer cell lines, each assayed using the  Illumina GA including DNA, small RNA, RNA, and bisulfite methylation sequencing. With the individual assays, we will  analyze copy number changes, examine microRNA’s regulatory effects, detect differentially expressed genes, and uncover  methylated CpG islands and CpG sites. Finally, we will discuss how to integrate the results to establish  biological relationships across multiple genomic mechanisms. Learn how these exciting new technologies can be used along with advanced statistics and dynamic visualizations to get the most biological relevant results from Next Generation Sequencing data.


*Separate registration required


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