CHI’s Seventh Annual
DNA-Seq: Advancing Clinical Applications
March 18-20, 2013
Hilton San Diego Resort, San Diego, CA
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Tuesday, March 19
8:00 Java and Jive Discussion Groups
Grab a cup of coffee and join a discussion group. These are moderated discussions with brainstorming and interactive problem solving, allowing conference participants from diverse backgrounds to exchange ideas, experiences, and develop future collaborations around a focused topic:
Table 1: Vetting Clinical Interpretations of SNP Changes
Terry Gaasterland, Ph.D., Director, Genomics, University of California, San Diego
• How do we translate observations from the literature into clinical reports?
• How do we assign levels of evidence to published research papers that associate genome variants with a disease?
• How do we convey to the end user (physician or person)?
• What are the implications of this evidence?
• How do we define and enforce good interpretation of genomes?
Table 2: Utilization of Next-Generation Sequencing for Clinical Microbiology Applications
Andrew Camilli, Ph.D., Associate Professor, Molecular Biology & Microbiology, Tufts University; Investigator, Howard Hughes Medical Institute
• What are the critical limitations for use in diagnosis of infections?
• What measures are being taken to overcome these limitations?
• What are clear-cut and feasible opportunities?
Table 3: Cloud, Desktop Computer, Tablet or Phone – Where is the Best Place to Do My Sequence Assembly and Analysis?
Tom Schwei, Vice President & General Manager, DNASTAR, Inc.
• What tasks or functions are best done on what device?
• What are the major challenges in using each device?
• How do I effectively collaborate with others and share and transfer data?
• What will things look like two years from now?
Table 4: Understanding Non-Canonical DNA Modifications
Terry Kelly, Ph.D., R&D Manager, Active Motif
• Current evidence describing 5hmc, 5caC, 5fc
• What techniques are used to study these modifications?
• Are these modifications stable states or part of a demethylation pathway?
• What is the clinical relevance of these non-canonical DNA modifications?
Table 5: RNA-seq for Gene Expression Profiling
Melanie Lehman, Ph.D., Research Fellow, Australian Prostate Cancer Research Centre, Queensland University of Technology
• What analysis methods are available for RNA-seq analysis and how do they compare?
• Should microarray and RNA-seq data be compared?
• Is the term ‘gene’ useful in RNA-seq analysis given the prevalence of alternative splice variants?
• How can RNA-seq data be used for both clinical application and biological discovery?
9:10 Chairperson’s Remarks
Yijun Ruan, Ph.D., Professor and Director, Genome Sciences, Jackson Laboratory Genomic Medicine
9:15 Tn-Seq: Combining Transposon Mutagenesis and Massively Parallel Sequencing to Generate a Detailed Phenotype-Genotype Map of a Pathogen
Andrew Camilli, Ph.D., Associate Professor, Molecular Biology & Microbiology, Tufts University; Investigator, Howard Hughes Medical Institute
The development of new approaches to battle infectious diseases is hampered by limited knowledge of gene function in pathogens. We developed a high throughput strategy based on the method Tn-seq that can reveal phenotypes associated with virtually all non-essential genes. Our results provide detailed insight into the biology and virulence of pneumococcus, and provide a road map for similar discovery in other microorganisms.
9:50 RRAD-Seq: A Streamlined Method for High-Throughput Genotyping
Paul Etter, Ph.D., Research Associate, Institute of Molecular Biology, University of Oregon
High-density, high-coverage genotyping is increasingly attractive to researchers in the age of next-generation sequencing. Here we present a robust, fully scalable and flexible method for genotyping-by-sequencing that uses amplification rather than digestion by a restriction enzyme to reduce the complexity of the genome. The simplified protocol is designed to allow the high-throughput preparation of very large numbers of samples. We demonstrate the utility of the method in a variety of applications.
10:25 Selected Poster Presentation: The Use of KRAS Deep Sequencing as a Method to Evaluate Tumour Cellularity in Pancreatic Adenocarcinoma Ductal Samples
Ami Panchal, Researcher, Genome Technologies, Ontario Institute for Cancer Research
10:40 Coffee Break in the Exhibit Hall with Poster Viewing
11:15 NOMe-Seq: Single Molecule Mapping of Chromatin Structure
Terry Kelly, Ph.D., R&D Manager, Active Motif
Epigenetic mechanisms work together to determine the transcription potential. We have been developing a method (NOMe-seq) that enables genome-wide mapping of DNA methylation and nucleosome occupancy on individual DNA molecules. Combined high resolution nucleosome occupancy and DNA methylation maps have enabled novel biological insights as well as the identification of promoters with mono-allelic methylation patterns that have not previously been described. NOMe-seq will be useful for assessing changes in chromatin structure that occur in development, disease and in response to treatment.
11:50 ChIA-PET Analysis for 3D Chromatin Interactions, Transcription Regulation, and Diseases
Yijun Ruan, Ph.D., Professor and Director, Genome Sciences, Jackson Laboratory Genomic Medicine
Genomes are organized into 3-dimensional (3D) conformation in vivo through interactions with protein factors for nuclear process such as transcription, and DNA elements separated by long genomic distances are known to functionally interact. However, the details of this view are largely unknown. To study long-range chromatin interactions mediated by protein factors, we developed Chromatin Interaction Analysis using Paired-End-Tag sequencing (ChIA-PET), and applied ChIA-PET analysis to detect chromatin interactions involved in gene transcription regulation that are associated with transcription factors such as Era and RNA polymerase II (RNAPII). Overall, our studies provided new dimension of combinatorial controls of gene transcription within the context of chromatin looping architecture in eukaryotic genomes, provided mechanistic interpretations of non-coding genetic elements involved in diseases, and paved the way towards presenting the 3D maps of the human genomes.
12:25 pm Close of Session
12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own
2:00 Chairperson’s Remarks
Terry Gaasterland, Ph.D., Director, Genomics, University of California, San Diego
2:05 Exome Analysis of Families with Congenital Heart Defects
Neil E. Bowles, Ph.D., Department of Pediatrics, Divisions of Cardiology and Medical Genetics, University of Utah School of Medicine
Congenital heart defects (CHD) constitute a major portion of clinically significant developmental abnormalities with an incidence of 3-6%. Familial cases have been described for nearly all cardiac malformations, suggesting primary genetic etiologies for a subset of non-syndromic CHD. However, mutations are detected in less than 10% of patients, due in part to significant genetic heterogeneity. We are using exome analysis of families with highly penetrant CHD to try to identify variants that cause or modify the phenotypes.
2:40 Discovery and Exploration of Oncogenic Mechanisms in Pediatric Cancer Genomes
Trevor Pugh, Ph.D., Research Fellow, Dana Farber Cancer Institute
Childhood cancers are distinct from many adult cancers due to relatively limited environmental contribution to disease and genetic contributions from inherited, de novo, and somatic variation. Here, I will present whole exome sequence analysis of three cohorts of pediatric solid tumors: medulloblastoma (brain), neuroblastoma (nervous system), and pleuropulmonaryblastoma (lung pleural cavity). Together, these studies illustrate a diversity of oncogenic mechanisms apparent in relatively simple pediatric cancer genomes and identify several new avenues for genome, functional, and clinical study.
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3:15 Rapid Assembly and Analysis of Clinical Sequence Data: Using DNASTAR Software to Identify Disease-Causing Mutations
Tom Schwei, Vice President & General Manager, DNASTAR, Inc.
DNASTAR offers an integrated suite of software for assembling and analyzing clinical sequencing data on a desktop computer. In this example, we align exome data from a disease and control group to the human genome using DNASTAR software. After alignment, the same software package is used to view the results and identify SNPs and genes of interest.
3:30 Refreshment Break in the Exhibit Hall with Poster Viewing
4:00 Application of Next-Generation Sequencing Technologies in a CLIA Certified Laboratory Environment
R. Rajesh Singh, Ph.D., Assistant Professor, Molecular Diagnostic Laboratory, Department of Hematopathology, University of Texas MD Anderson Cancer Center
Next-generation sequencing (NGS) technologies enable massive parallel sequencing of large genomic regions. Application of these technologies in a Clinical Laboratory Improvement Amendments (CLIA) certified clinical setting has been delayed due to lack of adequate validation and guidelines. In our CLIA-certified diagnostic lab, we have validated and applied routine mutation screening assays using two different NGS platforms. An extensive validation of their performance with different tissue isolation/archiving techniques, sequencing accuracy, specificity, sensitivity and feasibility for routine clinical use was undertaken. This talk will highlight the challenges and advantages of implementing these technologies in a diagnostic lab.
4:35 Glaucoma Genomics: Risk Factors for Optic Neuropathy
Terry Gaasterland, Ph.D., Director, Genomics, University of California, San Diego
Primary open angle glaucoma is a leading cause of irreversible blindness and visual impairment worldwide. Some disease-associated genes are known, but none are sufficient to assess disease risk. Since damage is irreversible, early detection of disease and detection of factors that may affect rate of progression is essential to effective disease management. Exons genome-wide (“exomes”) were sequenced in 333 cases with family history of disease and complement a ~5000 subject case-control association study to gain insight into genetic risk factors.
5:10 Close of Day
5:30-8:30 Dinner Short Courses
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