2017 Archived Content

Track 7: Next-Gen Sequencing Informatics

Tremendous advancements have been made to broaden NGS applications from research to the clinic, especially as genomics becomes more integrated with precision medicine initiatives. In spite of this, enormous challenges for NGS still exist, including real time sequencing, data storage, processing, scaling, quality control management, security and compliance in the cloud, and interpretation. Track 7 presents case studies on these challenges.

Tuesday, May 23

7:00 am Workshop Registration and Morning Coffee

8:0011:30 Recommended Morning Pre-Conference Workshops*

12:304:00 pm Recommended Afternoon Pre-Conference Workshops*

(W13) Proteogenomics: Integration of Genomics and Proteomics Data

* Separate registration required.

2:006:00 Main Conference Registration Open


GeneData logo  5:007:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Wednesday, May 24

7:00 am Registration Open and Morning Coffee


9:50 Coffee Break in the Exhibit Hall with Poster Viewing


10:50 Chairperson’s Remarks
Bhanu Bahl, Ph.D., Director, Clinical and Translational Science Centre, Harvard Medical School

11:00 Deep Analytics of Cancer Genomics Data

Nicholas Camarda, Bioinformatics Analyst I, Carter Group, Dana-Farber Cancer Institute

The very large collection of cancer genomic data within Foundation Medicine allows us to see not only breadth of mutational variation, but re-occurring and significant patterns in many different cancers. These different mutational modes potentially have great relevance to more actionable diagnoses, as well as providing deeper insights for cancer research and drug development. We are exploring a new method to map each case into a statistically-defined multidimensional space along with functional and response associations.

11:30 Building a Harmonized Clinical Data Resource for Cancer Research and Translational Medicine: Challenges, Goals and Progress

John Methot, Director, Health Informatics Architecture, Dana-Farber Cancer Institute

Oncology’s pioneering role in precision medicine has led to routine tumor sequencing. However, the incompleteness and inconsistency of data from EMRs and other sources presents significant challenges to building the patient-specific diagnosis, treatment and outcome “stories” that are required as correlates to genomic data to inform outcomes and clinical quality research. At DFCI, we are striving to improve the quality and coverage of clinical data for research and translational medicine, including decision support in the clinic. We are leveraging this data resource, using modern software architectures, to accelerate research and improve patient outcomes.

12:00 pm Graph Genome Tools for Precision Medicine

Jack DiGiovanna, Senior Scientist, Director of Program Management, Seven Bridges

Constructing a genome graph captures variations within a population as branches which diverge from the common reference but later rejoin it. This approach is fundamentally different than alignment and variant calling against a single linear reference, but does it matter for precision medicine? Here, we explore two key features of graph technology - improved variant calling and capturing distributions of variations in a population. We project these features onto the current state of precision medicine.

12:30 Session Break

12:40 Luncheon Presentation I: NGS in the Fast Lane: How a Collaborative Approach between the Mayo Clinic and Illumina is Advancing Genetic Testing

Michael Ball, Vice President, EIBU Commercial, Illumina

Despite progress in sequencing technologies, obstacles still prevent a systematic method for deriving actionable information from an individual’s genome. The BaseSpace® Suite from Illumina was designed to eliminate obstacles and enable users to easily store, manage, and aanalyze genomic data. In this session, learn how the Mayo Clinic is using BaseSpace Suite to expedite the delivery of its genomic expertise, and how Illumina is applying feedback from the Mayo Clinic to make the BaseSpace Suite even more efficient.

WuXi Nextcode  1:10 Luncheon Presentation II: Making TCGA Tumor Datasets Accessible for Real-Time Multiomics Analysis and Visualization
Jim Lund, Ph.D., Director, Tumor Product Development, WuXi NextCODE 
The collection of cancer datasets in The Cancer Genome Atlas (TCGA) dataset has provided a wealth of insight into cancer biology; however, analyzing such a complex dataset is challenging for most investigators. This talk will demonstrate the Wuxi NextCODE approach using our proprietary genomically ordered relational (gor) database architecture to rapidly and simultaneously explore the diverse data types in TCGA. 

1:40 Session Break


1:50 Chairperson’s Remarks

Shanrong Zhao, Ph.D., Director, Computational Biology, Early Clinical Research, Pfizer Worldwide Research and Development

1:55 QuickMIRSeq: A Strand-Aware Pipeline for Quick and Accurate Quantification of Known miRNAs and isomiRs from Large-Scale Small RNA Sequencing

Shanrong Zhao, Ph.D., Director, Computational Biology, Early Clinical Research, Pfizer Worldwide Research and Development

Genome-wide miRNA expression data can be used to study miRNA dysregulation comprehensively. We designed and implemented a pipeline called QuickMIRSeq (https://sourceforge.net/projects/QuickMIRSeq/) for quick and accurate quantification of known miRNAs and miRNA isoforms (isomiRs) from large-scale sequencing experiments. QuickMIRSeq considers the unique nature of miRNAs and combines many important features into its implementation for the sake of computational efficiency and quantification accuracy.

2:25 Creating and Executing Large-Scale, Reproducible Genomics Analysis Pipelines Using Globus Genomics

Ravi K. Madduri, Ph.D., Scientist, Mathematics and Computer Science, Argonne National Laboratory; Senior Fellow, Computation Institute, University of Chicago

2:55 Transforming Data Storage for life Sciences Research

Paul Jeffreys, Professor, Digital Operations, Programme Lead, The Institute of Cancer Research; Keble College Fellow, University of Oxford Digital Operations, The Institute of Cancer Research

Jon Lockley, Head of Scientific Computing, The Institute of Cancer Research

In the context of a leading cancer research institute working in close partnership with a world-leading cancer hospital, we will present an innovative approach to storing and managing research data through its life-cycle.

3:10 Sponsored Presentation (Opportunity Available)

3:25 Refreshment Break in the Exhibit Hall with Poster Viewing

4:00 Democratize Public Genomic Data Analysis through WebMeV

Yaoyu Wang, Ph.D., Associate Director, Center for Cancer Computational Biology, Dana-Farber Cancer Institute

WebMeV is a robust, open-source cloud based scalable data analysis software tool developed at the Dana-Farber Cancer Institute that uses intuitive visual interfaces to provide users with access to advanced data analysis methods. It will allow researchers and biotechnology companies considering tools for large scale genomic data analysis an additional option to all the proprietary software.

4:30 An Analysis of Cancer Genome Large-Scale Variation

Jeffrey Rosenfeld, Ph.D., Assistant Professor, Pathology and Laboratory Medicine, Rutgers Cancer Institute of NJ

Large-scale sequencing has been done on cancer genomes through projects such as TCGA, but there is still a lot to learn about genomics variation in cancer. Most of the current studies have looked at SNPs and other base-level variants in the genome. We have used advanced techniques and novel sequencing platforms to explore structural variation in cancer both at a DNA and a RNA level.

 Intel Logo 5:00 Democratizing NGS Analytics with HPE Purpose-Designed Solutions

Michael J. McManus, Ph.D. Senior Health & Life Sciences Solution Architect Intel

Haruna Cofer, Ph.D., Senior Applications,Engineer, Domain Expertise Group, HPE

Genomics is the key to unlocking the power of precision medicine. As the demand for genome sequencing grows in areas like pediatric medicine and oncology, so does the amount of data that must be processed, stored and managed.

5:30 – 6:30 15th Anniversary Celebration in the Exhibit Hall with Poster Viewing and Best of Show Awards

Thursday, May 25

7:00 am Registration Open and Morning Coffee


8:05 Benjamin Franklin Awards and Laureate Presentation

8:35 Best Practices Awards Program

8:50 Plenary Keynote

9:45 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced


10:30 Chairperson’s Remarks
Jeffrey Rosenfeld, Ph.D., Assistant Professor, Pathology and Laboratory Medicine, Rutgers Cancer Institute of NJ

10:40 KEYNOTE PRESENTATION: Integrating Multiple High Content Technologies for Precision Immunology

Mario Roederer, Ph.D., Senior Investigator, ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH

11:10 Subtyping Cancer Patients Using Immune Gene Expression

Jurriaan Brouwer, Ph.D., Data Science and Oncology, Roche Innovation Center, NY

We will present a novel method of identifying cancer patients that may respond to cancer immunotherapy using immune-related gene expression. By establishing the balance between immune activating and inhibiting signatures, we can suggest more personalized treatment options than classical subtyping methods.

11:40 Analysis and Exploration of n-Dimensional Single Cell-Data from Cytometry and Single Cell Sequencing

Michael Stadnisky, Ph.D., CEO, FlowJo, LLC

The single cell is the basic unit of disease, but emerging technologies in cytometry and single cell sequencing are held back by time-consuming, sequential manual steps or computationally expensive, non-deterministic data reduction. Herein, we describe a powerful nonlinear, deterministic data reduction technique which we use to drive insight in single cell phenotyping and single cell sequencing of whole melanoma metastases.

12:10 pm Session Break

12:20 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:20 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing

1:55 Chairperson’s Remarks

Yuval Itan, Ph.D., MRes, Research Assistant Professor, Human Genetics of Infectious Diseases, The Rockefeller University

2:00 Management, Analysis, and Interpretation of DNA and RNA Sequencing To Aid in the Interpretation of Variants of Unknown Significance for Studies of Rare Inherited Disease and in Oncology

David Wesley Craig, Ph.D., Professor of Translational Genomics, Keck School of Medicine, University of Southern California; Co-Director, USC Institute of Translational Genomics
With the emergence of DNA and RNA sequencing (RNA-seq) technologies, RNA-based biomolecules hold expanded promise for their diagnostic, prognostic and therapeutic applicability in various diseases, particularly in the context of variants of unknown significance. Beyond, detection of gene fusions and differential expression of known disease-causing transcripts by RNA-seq, it is the diversity of RNA species and measurements that holds new promise for the multi-faceted clinical applicability of RNA-based measures, including examining allele specific expression, non-sense mediated decay, exon skipping, gene silencing, among others. In this talk we describe ongoing efforts towards the establishment of benchmark standards, assay optimization for clinical conditions and demonstration of assay reproducibility are required to expand the clinical utility of RNA-seq. We examine application of integrated RNA and DNA analysis within research studies in two major very different clinical paradigms - rare inherited diseases with a pediatric neurological component and in late stage metazoic oncology. We highlight both the promise and the challenges faced from informatics framework of integrating effectively two sets of tests within a singular reporting structure. We describe the development of the LIMS and database framework supporting both independent analysis and joint analysis within CLIA/CAP reporting frameworks. Finally, we describe necessary efforts towards providing reference standards aiding in the analytical validation of these tests.

2:30 Estimating Genotypic Heterogeneity Underlying Human Disease

Yuval Itan, Ph.D., MRes, Research Assistant Professor, Human Genetics of Infectious Diseases, The Rockefeller University

3:00 Challenges and Implications of RNA-Seq Quantification at the Transcript Level

Chi Zhang, Ph.D., Post Doc, Computational Biology, Early Clinical Research, Pfizer Worldwide Research and Development

3:30 NGS Informatics for Mouse Cancer Avatars

Govindarajan Kunde Ramamoorthy, Associate Director, Computational Sciences – Scientific Computing, Jackson Lab for Genomic Medicine
Vinod Yadav, Application Computational Scientist, The Jackson Laboratory

Mouse cancer avatars provide a power platform for rapidly investigating therapies for treatment resistant cancers. Patient tumors are engrafted into mice, and various treatment approaches can be evaluated in the context of their genomic and transcriptomic profiles. JAX has developed cutting edge approaches to assist preclinical oncology in the effort to understand tumor response or resistance to treatment, including sequencing and analysis for genomic, transcriptomic, and expression data. This talk will cover the bioinformatics associated with detecting a variety of molecular alterations in patient tumors as well as the unique challenges associated with working with animal avatars.

4:00 Conference Adjourns

Exhibit hall pass

Modern Data Platforms and Storage Infrastructure