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NGX: Applying Next-Generation Sequencing - Day 2


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Tuesday, August 14

7:30 am Breakfast Presentation (Sponsorship Opportunity Available)

8:30 Java and Jive Discussion Groups

Grab a cup of coffee and join one of the discussion groups. These are moderated discussions with brainstorming and interactive problem solving, allowing conference participants from diverse areas to exchange ideas, experiences, and develop future collaborations around a focused topic. 

» Click Here for Discussion Groups «

 

Tips ‘n Tricks 

9:30 Chairperson’s Remarks

Anthony Shuber, Ph.D., CTO, Applied Science, Predictive Biosciences
 

9:35 A Catalog of Loss-of-Function Variants in Healthy Human Genomes: Implications for Clinical Diagnostics

Suganthi Balasubramanian, Ph.D., Associate Research Scientist, Molecular Biophysics and Biochemistry, Yale University

We have obtained a comprehensive catalog of loss-of-function variations in protein-coding genes based on the analysis of 1000 genomes data. This set of variants have been thoroughly examined for sequence artifacts, mapping errors and validated experimentally. This will provide a useful resource for clinical sequencing studies to identify and differentiate potential disease-causing mutations from benign variations. Given that LoF variants are highly likely to be deleterious, this is an invaluable resource.

10:05 Whole-Genome Amplification, Sequencing, and Haplotyping of Single Human Cells

Sijia Lu, Research Scientist in Xie Lab, Department of Chemistry and Chemical Biology, Harvard University

Existing whole genome amplification methods are hindered by non-uniformity across the genome and introduction of spurious sequences. Here we report a new amplification method, which circumvents problems by performing linear pre-amplification with Multiple Annealing and Looping Based Amplification Cycles (MALBAC) before exponential amplification with PCR. We demonstrate sequencing single human cells with ~93% coverage at ~30x depth. We further perform digital whole genome amplification by MALBAC on single human cells from a normal donor, which enables us to determine the haplotype of these cells. Finally, simultaneously determining the genome and transcriptome is possible for single cells.

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

11:15 Sequencing Isolated Chromosomes from Single Cells

Marek Malecki, M.D., Ph.D., Associate Professor of Genetics, Genomics, and Gene Therapy, Western University of Health Sciences

The ultimate goal of our work is to develop targeted, personalized therapy. Therefore, we developed synthetic biotags, targeting specific molecules on the surfaces of cancer cells, which allow us to capture the cancer and cancer stem cells and their clonal expansion. We further developed synthetic probes targeting specific chromosomes, which allow us to isolate spectra of chromosomes from isolated cells. Using liquid FISH and NGS, in addition to native immunoblots and RT qPCR, we characterized molecular profiles of these cells. This novel approach opens new routes for molecular profiling of cancer and cancer stem cells.

11:45 A Cost Effective Assay for Multiplexing Protein and DNA Biomarkers on a Single Analytical Platform

Anthony Shuber, Ph.D., CTO, Applied Science, Predictive Biosciences

To eliminate the need to perform separate procedures for protein and DNA, and to decrease assay complexity and cost, we are developing a method for simultaneous detection of protein (Prot-Seq) and DNA (DNA-Seq) on a NGS platform. We have identified a DNA aptamer that binds Matrix Metalloprteinase-2 (MMP-2) and can be used as template for quantitative protein detection and multiplexed with DNA marker detection using the same NGS platform. Our goal is to simultaneously detect protein and DNA using a single analytical platform (MADR-Seq).

12:15 pm Close of Session

12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

 

Conquering the Cancer Genome 

2:00 Chairperson’s Remarks

Vance Lemmon, Ph.D., Walter G. Ross Distinguished Chair in Developmental Neuroscience; Professor, Neurological Surgery, The Miami Project to Cure Paralysis, Center for Computational Sciences, University of Miami Miller School of Medicine

 

2:05 MI-ONCOSEQ - Experiences in Clinical Cancer Sequencing and the Path to Personalized Cancer Treatment

Dan Robinson, Ph.D., Director, Clinical Sequencing; Assistant Professor, Research, Michigan Center for Translational Pathology, Comprehensive Cancer Center, University of Michigan Health Systems

Presentation will discuss some of the hurdles in establishing next-generation sequencing protocols in a clinical setting.  The utility of various sequencing strategies and the advantages of an integrated approach will be discussed. Examples of results impacting treatment decisions and illuminating tumor progression will be presented.

2:35 Cancer Characterization and Function

Adam Bass, M.D., Assistant Professor, Medicine, Harvard Medical School; Division of Cellular and Molecular Oncology, Dana-Farber Cancer Institute; Associate Member, The Broad Institute 

The advent of NGS technologies has allowed us to perform comprehensive genome-wide surveys of the spectrum of mutations that accumulate in the cancer genome.  I will discuss efforts to catalog and analyze the genomic alterations which exist across several types of gastrointestinal cancers.  These studies have enabled us to identify novel genes which may contribute to these cancers. Additionally, they make us aware of the vast sea of genomic alterations present, creating the need to develop computational and experimental approaches to mine data to identify genes most important for cancer.

3:05 Incorporating NGS into a Gynecologic Cancer Program for Discovery of Novel Diagnostic Biomarkers and Therapeutic Targets - The MSSM Experience

John A. Martignetti, M.D., Ph.D., Associate Professor, Departments of Genetics and Genomic Sciences, Pediatrics, Oncological Sciences, Mount Sinai School of Medicine

3:35 Selected Poster Presentation: Alternative Transcripts: Perspectives on Associating Functions to Genes

Melanie Lehman, Ph.D., Research Fellow, Australian Prostate Cancer Research Centre, Queensland University of Technology

3:50 Refreshment Break in the Exhibit Hall with Poster Viewing

 

RNA-Seq 

4:30 Using NGS Transcriptomic Tools in Non-Model Organisms

Suzy Strickler, Ph.D., Postdoctoral Researcher, Boyce Thompson Institute for Plant Research, Cornell University

Transcriptomic studies can benefit greatly from data generated using next-generation sequencing (NGS), even in non-model organisms. By applying tools developed for NGS to transcriptomic sequence data from non-model species, we can begin to elucidate gene expression in these organisms.  There are various tools currently available for transcriptome assembly and analysis and some of these tools will be reviewed.  Detecting differential expression, identifying SNPs, and performing annotation will be discussed using examples from the literature and data analysis performed in our lab.

FEATURED SPEAKER 

5:00 Using RNA-Seq to Uncover Isoforms and Molecular Networks Involved in Nerve Regeneration

Vance Lemmon, Ph.D., Walter G. Ross Distinguished Chair in Developmental Neuroscience; Professor, Neurological Surgery, The Miami Project to Cure Paralysis, Center for Computational Sciences, University of Miami Miller School of Medicine

Most neurons in the central nervous system (CNS) are unable to re-grow axons that have been cut, yet neurons in the peripheral nervous system (PNS) have this ability. We have used RNA-seq to compare CNS and PNS neurons to identify differentially expressed mRNA isoforms and use this information to explore transcriptional and miRNA regulatory networks for subsequent experimental analysis using over expression and knock-down in neurons, combined with high content analysis.

 

5:30 Close of Day and Dinner Short Course Registration

5:45 – 8:45 Dinner Short Courses

 

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