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Cambridge Healthtech Institute’s Sixth Annual 

Genome and Transcriptome Analysis   

Disease-Relevant Analysis of NGS 'Omics Data 

February 16-18, 2015 | Moscone North Convention Center | San Francisco, CA
Part of the 22nd Annual Molecular Medicine Tri-Conference


The analysis of 'omics data derived from various applications of next-generation sequencing (NGS) has and will continue to radically impact our fundamental understanding of disease biology. As researchers and clinicians more ably harness the power of sequencing technologies, the interrogation of individual and large cross-omics datasets provide broader views of underlying contributors of disease, and insights into the interconnectivity of our underlying genome, and the dynamic, regulatory epigenome and transcriptome. The Genome and Transcriptome Analysis meeting will once again explore how NGS is continuing to shape our understanding human disease, by uncovering biological meaning from analyzing NGS data.

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

Monday, February 16

10:30 am Conference Program Registration


11:50 Chairperson’s Opening Remarks

Todd M. Lowe, Ph.D., CSO, Maverix Biomics, Inc.

12:00 pm Shaping the Blood: Lessons from Chromatin and Single Cell RNA Dynamics

Ido Amit, Ph.D., Associate Professor, Department of Immunology; Principal Investigator, Laboratory for Immuno-Genomics, Weizmann Institute of Science

Chromatin modifications are crucial for development, yet little is known about their dynamics during differentiation. Hematopoiesis provides a well-defined model to study chromatin state dynamics; however, technical limitations impede profiling of homogeneous differentiation intermediates. Using a novel high-sensitivity indexing-first chromatin immunoprecipitation approach we profile the dynamics of four chromatin modifications across 16 stages of hematopoietic differentiation. We find that lineage commitment involves de novo establishment of thousands of lineage-specific enhancers. These enhancer repertoire expansions foreshadow transcriptional programs in the differentiated cells. Combining our enhancer catalog with single cell gene expression profiles, we elucidate the transcription factor network controlling chromatin dynamics and lineage specification in hematopoiesis. Together, our results provide a comprehensive model of chromatin dynamics during development.

12:30 The Biology of CRISPRs: From Genome Defense to Genetic Engineering

Jennifer Doudna, Ph.D., Professor, Molecular and Cell Biology, Chemistry,University of California, Berkeley; Investigator & Professor, Biochemistry, Biophysics & Structural Biology, Howard Hughes Medical Institute

The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. I will present a brief history of CRISPR biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, providing the foundation for remarkable developments using this technology to modify, regulate or mark genomic loci in a wide variety of cells and organisms. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way to both fundamental discoveries in biology, with applications in all branches of biotechnology, and strategies for human therapeutics. Recent results regarding the molecular mechanism of Cas9 and its use for targeted cell-based therapies will be discussed.

1:00 Session Break

1:15 Luncheon Presentation I: Developing Standard Computational Analytic Kits Matched to Sample Preparation Methods for Single Cell Analysis

Todd M. Lowe, Ph.D., CSO, Maverix Biomics, Inc

In spite of the rapid progress in RNA- and DNA-sequencing of single cells, robust standard analytics have yet to be established to meet the needs of the broadening research community.  We have integrated the best methods and visualizations being used today into one, easy to use analytic kit that is accessible to any researcher.  Because multiple technologies exist for sample preparation, we specifically optimize our kits to “match” these methods.

1:45 Luncheon Presentation II (Sponsorship Opportunity Available)

2:15 Session Break


2:30 Chairperson’s Remarks

Cole Trapnell, Ph.D., Assistant Professor, Genome Sciences, University of Washington

2:40 Pseudotemporal Ordering of Single Cells Reveals Regulators of Cell Differentiation and Reprogramming

Cole Trapnell, Ph.D., Assistant Professor, Genome Sciences, University of Washington

Cell differentiation is governed by a vast and mostly unknown gene regulatory program. Each cell makes fate decisions independently by integrating a wide array of signals from other cells, executing a complex choreography of gene regulatory changes. Experiments performed on bulk populations of differentiating cells mask this variation, hiding the inner workings of the cell’s regulatory logic. Single-cell genomics promises to expose this circuitry, revealing the key genes and interactions that determine cell fate. I will discuss our recent efforts to map cell fate circuits through single-cell transcriptomic analysis.

3:10 Expansion of the CRISPR-Cas9 Genome Targeting Space through the Use of H1 Promoter-Expressed Guide RNAs

Donald Jeffrey Zack, M.D., Ph.D., Guerrieri Professor, Genetic Engineering & Molecular Ophthalmology; Professor, Molecular Biology & Genetics, Neuroscience, and the Institute of Genetic Medicine, John’s Hopkins School of Medicine

3:40 Comparative Transcriptomics Analysis Reveals Regulatory and Functional Landscape of RNA Editing

Jin Billy Li, Ph.D., Assistant Professor, Genetics, Stanford University

Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Taking an evolutionary approach to compare transcriptomes of multiple species, we find that the establishment of editing and variation in editing levels are largely explained and predicted by cis-regulatory elements. Furthermore, we are able to identify a large number of editing sites that are very likely functional. Our work illustrates how evolution shapes RNA editing regulatory and functional landscape.

4:10 Selected Poster Presentations

4:40 Break and Transition to Plenary Session

5:00 Plenary Session 

6:00 Grand Opening Reception in the Exhibit Hall with Poster Viewing

7:30 Close of Day

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

Tuesday, February 17

7:00 am Registration and Morning Coffee

8:00 Plenary Session 

9:00 Refreshment Break in the Exhibit Hall with Poster Viewing 


10:05 Chairperson’s Remarks

Dalia Cohen, Ph.D., Head of Research, Beryllium

10:15 About Noam Chomsky, DNA Patterns, Non-CodingRNAs and Cancer Patients

George Calin, M.D., Ph.D., Professor, Experimental Therapeutics, Division of Cancer Medicine, MD Anderson Cancer Center

MicroRNA and other short or long non-coding RNAs alterations are involved in the initiation, progression and metastases of human cancer. Differential expression of non-coding RNAs in malignant compared with normal cells can be explained by the location of these genes in cancer-associated genomic regions, by epigenetic mechanisms and by alterations in the processing machinery. Expression profiling of human tumors has identified signatures associated with diagnosis, staging, progression, prognosis and response to treatment, as well as identification of targets of activated oncogenic pathways.

10:45 Journeys through Space and Time: Ultra High-Resolution Expression Profiling of Long Non-Coding RNAs

Marcel E. Dinger, Ph.D., Head, Clinical Genomics & Genome Informatics, Garvan Institute of Medical Research

Long noncoding RNAs (lncRNAs) are increasingly recognized as having key regulatory roles in development and disease. However, these regulatory molecules often have short half lives and are expressed only in specific tissues or cell types, resulting in the poor representation of lncRNAs in transcriptomic datasets. Using novel detection and sampling approaches, we reveal a high-resolution spatiotemportal view of the long noncoding transcriptome that provides fresh insights into their roles in development and disease.

11:15 Exosomic microRNAs Orchestrate the Biology of the Tumor Microenvironment

Muller Fabbri, M.D., Ph.D., St. Baldrick’s Foundation Scholar; Assistant Professor, Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, University of Southern California- Keck School of Medicine; Children’s Hospital Los Angeles

MicroRNAs (miRNAs) are secreted by cells within microvesicles called exosomes. Cancer cells are selective in defining the miRNA cargo within their exosomes. The function of exosomic miRNAs within the Tumor Microenvironment is currently not completely understood. We discovered that in addition to their “traditional” gene expression regulatory mechanism of action, exosomic miRNAs can also function as ligands of miRNA receptors in surrounding cells, leading to a pro-tumoral response. These findings identify a new mechanism of action of miRNAs and lead to the identification of new targets.


12:15 pm Session Break

12:25 Lunch on Your Own

1:25 Refreshment Break in the Exhibit Hall with Poster Viewing


2:00 Chairperson’s Remarks

Marcel E. Dinger, Ph.D., Head, Clinical Genomics & Genome Informatics, Garvan Institute of Medical Research

2:10 Large-Scale, Cross-Site Sequencing Using Eight NGS Platforms

Christopher E. Mason, Ph.D., Assistant Professor, Computational Biomedicine, Weill Cornell Medical College

Here we will describe the results of the FDA’s SEQC (Seqeuncing Quality Control) study and the ABRF’s NGS study on RNA-seq, where we have examined standardized samples across Illumina’s HiSeq and MiSeq, Life Technologies SOLiD, PGM, and Proton, PacBios RSII, 454, and some newer data from Oxford Nanopore’s MinION system. We show that relative gene quantification is robust across platforms, but that splicing analysis clearly benefits from longer reads. We also present methods for cross-site normalization and quantification. These results suggest that clinical grade RNA-seq is ready for expanded use.

2:40 Integrating Transcriptome and Genome Sequencing to Understand Functional Variation in Human Genomes

Tuuli Lappalainen, Ph.D., Principal Investigator & Core Member, New York Genome Center; Assistant Professor, Systems Biology, Columbia University

Detailed characterization of cellular effects of genetic variants is essential for understanding biological processes that underlie genetic associations to disease. Integration of genome and transcriptome data has allowed us to characterize regulatory and loss-of-function genetic variants as well as imprinting both at the population and individual level, as well as their tissue-specificity and role in disease associations.

3:10 Exploring exRNAs Using Web-Based RNA-Seq Pipelines and Public Data Resources: exRNA Communication Consortium (ERCC)

Matthew E. Roth, Ph.D., Assistant Professor & Co-Director, Bioinformatics Research Lab, Baylor College of Medicine

The NIH funded extracellular RNA Communication Consortium (ERCC) launched in fall 2013. The consortium brings together a wide variety of experts in exRNA biology, human disease, bioinformatics, biomarker discover, and therapeutic development to better understand the basic biology of exRNAs and their potential applications in the clinic. Large-scale RNA-Seq analyses of human exRNAs in the ERCC is a key focus and requires the development of novel analytical pipelines, custom public data sources, and their integration. How these resources are developed and applied to exRNA analyses, and their utility to the broader scientific community will be presented.

Qiagen Bioinformatics3:40 West Nile Virus Case Study —Example of Infectious Disease Research Using Ingenuity Pathway Analysis (IPA) and CLC Cancer Research WorkBench, the Qiagen Bioinformatics Solution

Jean-Noel Billaud, Ph.D., Principal Scientist, QIAGEN Bioinformatics

Discussion will hi-light the application of a high-content and powerful bioinformatics toolset; Ingenuity® Pathway Analysis and CLC Cancer Research Workbench for the characterization of WNV pathogenesis and a resulting mechanism for the mitigation of the pathological consequences of WNV infection. 

4:10 Mardi Gras Celebration in the Exhibit Hall with Poster Viewing

5:00 Breakout Discussions in the Exhibit Hall 

This interactive session provides attendees an opportunity to choose a specific discussion group to join. Each group has a moderator to ensure focused discussions around key issues within the topic. This format allows participants to meet potential collaborators, share examples from their work, vet ideas with peers, and be part of a group problem-solving endeavor. The discussions provide an informal exchange of ideas and are not meant to be a corporate or specific product discussion.

Utilizing Cancer Sequencing Data in the Clinic

Andreas Scherer, Ph.D., President and CEO, Golden Helix

• How long will cancer gene panels remain the bread and butter method of choice to analyze sequencing data of cancer tumors?
• What is the clinical yield of whole exome and genome sequencing in this context? What can we expect in the future?
• Beyond Cosmic: What public or private datasets are needed to annotate sequencing data enabling diagnosis and selection of treatment option?
• As we move beyond gene panels the chances of incidental findings increases. What are the best practices to handle those?
• How do we best structure patient reports to separate results with high degree of certainty from findings that are of uncertain clinical relevance? Who is communicating the results? Are patients open to hearing all findings or are they more selective in their desire to be informed?
• What are best practices to peer-review the diagnosis of a patient utilizing sequencing data in the clinic?

6:00 Close of Day

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure 

Wednesday, February 18

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Plenary Session Panel 

9:45 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall


10:35 Chairperson’s Remarks

Francisco M. De La Vega, D.Sc., Visiting Instructor, Department of Genetics, Stanford University School of Medicine

10:45 FEATURED PRESENTATION: Stable Reference Structures for Human Genome Analysis

David Haussler, Ph.D., Distinguished Professor and Scientific Director, UC Santa Cruz Genomics Institute, University of California Santa Cruz

Currently there are many different ways to map individual patient DNA and call genetic variants relative to the human reference genome GRCh38, and on top of this, when an expanded version GRCh39 arrives, quite a bit of remapping and recalling turmoil will be created. I describe a new scheme being developed with assistance from the Global Alliance for Genomics and Health in which mapping to the reference genome and calling variants would become a precisely defined and relatively stable process, with a well-defined incremental update when the reference genome expands to a more comprehensive version. This will enable a better standardized and more accurate discourse about human genetic variation for science and medicine.

11:15 Supporting a Biomedical Commons with the Bionimbus Protected Data Cloud

Robert Grossman, Ph.D., Chief Research Informatics Officer (CRIO); Director, Center in Data Intensive Science; Professor, Biological Sciences, University of Chicago; Core Faculty and Senior Fellow, Institute for Genomics and Systems Biology (IGSB) and the Computation Institute

11:45 Collaborating and Data Sharing When the Author List Goes Beyond 250 with an Eye to Re-Usability and Reproducibility

Larsson Omberg, Ph.D., Principal Scientist and Head of Data Science, Sage Bionetworks

Life science research projects are getting larger and more integrated across institutional boundaries requiring new paradigms for collaboration and sharing. This has become especially evident when speaking of results and data stemming from genomic technologies where data is often in flux as new samples are processed and existing samples fail quality control. I will discuss methodologies and tools that we have developed in conjunction with several large research communities to evolve active research projects into reusable resources for the broader community.

12:15 pm Session Break

12:25 Lunch on Your Own

1:00 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing


1:40 Chairperson’s Remarks

Francisco M. De La Vega, D.Sc., Visiting Instructor, Department of Genetics, Stanford University School of Medicine

1:50 Cloud Genomics at Scale: The Future of Drug Discovery and Development

Jeffrey Reid, Ph.D., Director & Head, Genome Informatics, Regeneron Pharmaceuticals

The Regeneron Genetics Center (RGC) has partnered with the Geisinger Health System to produce 100,000 exome sequences on patient volunteers over the next five years. Bringing together health-record information and exome sequence data at this scale will provide new insights into biology and genetics that will feed into the drug development pipeline, and deliver on the promise of the genomic medicine revolution. The RGC’s total commitment to cloud computing has been essential in bringing such an ambitious sequence production and analysis project to life in less than a year, and plays a pivotal role in data sharing with research partners.

2:20 Accessible and Reproducible Large-Scale Analysis with Galaxy

James Taylor, Ph.D., Ralph S. O’Connor Associate Professor, Biology; Associate Professor, Computer Science, Johns Hopkins University

I will discuss the Galaxy framework for accessible genomic data analysis. I will particularly highlight new features of Galaxy which are enabling analysis at increasingly larger scales, including UI and backend improvements, as well as other recent improvements to Galaxy.

2:50 Genome Data Aggregation and Exchange across Distributed Genomic Data Repositories

Francisco M. De La Vega, D.Sc., Visiting Instructor, Department of Genetics, Stanford University School of Medicine

As sequencing technologies continue to evolve and the cost of genome sequencing drops, several large-scale population sequencing projects with sizes ranging from tens to hundreds of thousand samples are now being started. In a world where genomic data is distributed across many repositories around the world together with each patient’s phenotype/clinical information, it will become impossible to amass the data in a single location/cloud for analysis. Instead, sharing of genomic data across networks for research and clinical applications will be necessary. We will discuss new paradigms to orchestrate global data sharing while maintaining secure access and privacy for patients.

3:20 Selected Poster Presentations

3:50 Refreshment Break

Advances in Computational
Cancer Genomics

4:00 Chairperson’s Remarks

Andreas Scherer, Ph.D., President and CEO, Golden Helix

4:10 Bioinformatics of Cancer Gene Panels: Challenges to Creating Effective Testing Workflows 

Andreas Scherer, Ph.D., President and CEO, Golden Helix

In the transition of NGS to a clinical setting, the cancer gene panel is leading with a clear value proposition of clinically actionable results in a simple package. Except it’s not so simple. In this presentation I will cover the bioinformatics tools and best practices to achieve the goal of a reproducible workflow for analyzing NGS gene panel data. From amplicon and sample QC, to annotation sources and filtering thresholds, to summary of therapeutic targets and gene level reports, I will cover the methods and edge cases that go into setting up a gene panel test.

4:40 Maximizing the Utility of TCGA Genomic Data: Tools, Analysis and Discovery

Han Liang, Ph.D., Assistant Professor, Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas, MD Anderson Cancer Center

The Cancer Genome Atlas (TCGA) project represents the largest effort to systematically characterize the molecular profiles of human cancers. A central question for the cancer research community is how to use these genomic and proteomic data to guide cancer care. In my talk, I will first introduce two useful bioinformatics tools we recently developed for effectively analyzing and visualizing TCGA data: SurvNet and TCPA. Then I will present a systematic evaluation of the power of diverse TCGA molecular data with or without clinical variables in predicting patient survival and discuss the potential utility of cross-tumor analysis. To facilitate community efforts to make prognostic modeling transparent and reproducible, we established an open-access model evaluation platform. Finally, I will focus on the biomedical significance and clinical relevance of expressed pseudogenes in human cancer.

5:10 Characterization of Cancer Genomes

Sohrab Shah, Ph.D., Assistant Professor, Pathology and Computer Science, University of British Columbia; Scientist, BC Cancer Agency

5:40 Close of Conference Program

Day 1 | Day 2 | Day 3 | Plenary Session | Download Brochure