2017 Archived Content

Track 11: Clinical Genomics

As genomic testing becomes more routine, the data generated are more complete, but also more complex. Applications for analyzing, storing, processing, exploring, and sharing these dynamic data must keep pace with a variant landscape that is constantly being refined by new information and new classifications. Track 11 continues its tradition of exploring ways we are analyzing genome variant data to improve researchers’ understanding of human health and disease leading to medically actionable results.

Tuesday, May 23

7:00 am Workshop Registration and Morning Coffee

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

(W2) An Intro to Blockchain in Life Sciences

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

(W12) Leveraging Cloud Technologies to Enable Large-Scale Integration of Human Genome and Clinical Outcomes Data

(W13) Proteogenomics: Integration of Genomics and Proteomics Data

* Separate registration required.

2:006:00 Main Conference Registration Open

4:00 PLENARY KEYNOTE SESSION

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

8:00 PLENARY KEYNOTE SESSION

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

CLASSIFYING VARIANTS: PERSONAL > POPULATION GENOMICS

10:50 Chairperson’s Remarks

Narges Bani Asadi, Ph.D., Vice President and Life Cycle Leader, Roche Sequencing Solutions

11:00 KEYNOTE PRESENTATION: Analysis of Personal Genomes

Mark Gerstein, Ph.D., Albert L. Williams Professor, Biomedical Informatics, Molecular Biophysics & Biochemistry, and Computer Science; Co-Director, Computational Biology & Bioinformatics, Yale University

I discuss how we interpret and prioritize the many variants in a personal genome. I concentrate on rare and somatic variants and discuss ways of assessing their impact in coding regions using protein structure. For non-coding regions, I present ways to analyze the overall burden of mutations, finding allelic elements differentially affected by variants in paternal and maternal chromosomes and using network connectivity to prioritize variants.

11:30 The Clinical Cloud: An Industry View

Pamela Duffy, MS, Director, Core Clinical Solutions, IT, Pfizer

Aggregation of clinical data in the cloud to create a single source of the truth is here and maturing. Is it hype or is the business case for savings and insights proving out?

12:00 pm Clinical Genomics for Research Questions

Alan Martin, Head, Innovation & Data Science, Congenica

Bringing high throughput DNA sequencing into clinical practice presents an opportunity to analyse aggregate patient data to find new biological understanding. Potential analyses will be presented as well as the pitfalls of working with heterogeneous data sources and some data integration methods used by Congenica.

12:15 Sponsored Presentation (Opportunity Available)

12:30 Session Break

12:40 Luncheon Presentation I: Low Abundance Calls: Using Group Variant Calling to See Through the Noise and Find Value that Drives Translational Discovery  

Zachary Pitluk, Ph.D., Vice President, Life Sciences and Healthcare, Paradigm4
Large-scale group-based somatic mutation calling using tunable ROC curves produces high quality identification of low abundance calls. These low abundance calls support accurate determination of genomic and transcriptional heterogeneity, providing a window into cell population changes from cell line cloning, disease progression, treatment response and adaptation, and biomanufacturing environmental factors. New scalable computational platforms like SciDB enable computationally efficient and validatable support for executing this method over groups of thousands of aligned sequences, as well as for other common variant analyses on a million whole exomes.

1:10 Luncheon Presentation II (Sponsorship Opportunity Available)

1:40 Session Break

CLASSIFYING VARIANTS: ADVANCING INTO THE CLINIC

1:50 Chairperson’s Remarks

Leonard Lipovich, Ph.D., Associate Professor, Center for Molecular Medicine and Genetics, Wayne State University

1:55 Taking the Next Step: Computational Challenges Overcome in Rapidly Scaling Output from a Carrier Screening Program within 6 Months

Andrew McLellan, Ph.D., Assistant Professor, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai

The Genetic Testing Laboratory at MSSM has increased its volume of carrier-screening five-fold this past year. Ramping up to processing data from over 200 HiSeq2500 rapid run flow cells per month has presented numerous challenges regarding data analysis, storage, automation and development of the tools required to provide a timely service without compromising quality. This talk documents our journey of discovery as we embraced high-throughput NGS-based genetic testing.

2:25 A Holistic Approach to Pediatric Rare Disease: Integration of Genomic Data for Research, Diagnostics, and Therapy

Timothy Yu, M.D., Ph.D., Instructor, Pediatrics, Harvard Medical School; Medicine Research, Division of Genetics and Genomics, Boston Children’s Hospital

The talk will explore how genomic systems can be applied to manage unsolved rare disease cases. Whole exome sequencing has a diagnostic yield of 20-40% in complex genetic cases which leaves up to 80% of the cases unsolved. To address this challenge, it requires new genomic medicine systems that create an integration between laboratory diagnostics, clinical care and ongoing collaborative clinical research.

2:55 Big-Data Analytics and Genomics to Optimize Infertility Treatment

R. Mark Adams, Ph.D., CIO, Celmatix Inc.

Dr. Adams will discuss how Celmatix Inc., a next-generation company focused on women's health, is leveraging genomics and big data to explore the underlying biological causes of infertility. Celmatix has leveraged these capabilities to create and market an industry-leading genetic test that reveals how DNA may influence a woman's ability to have a baby today and in the future.

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

CLASSIFYING VARIANTS: UNDERSTANDING AND TREATING COMPLEX DISEASE

4:00 Genetic Data Sharing to Advance Complex Disease Research for Type 2 Diabetes

Jason Flannick, Ph.D., Senior Group Leader, Medical and Population Genetics, Broad Institute of Harvard and MIT

I focus on our efforts to understand the genetic and biological basis of type 2 diabetes. I describe progress from large-scale sequencing studies to characterize the genetic basis of T2D, as well as to translate association signals to biological or clinical insights. I discuss a forward paradigm to maximize the utility of these data: through data sharing via a public and broadly accessible knowledge portal of T2D genetics.

4:30 From GWAS to Post-Genomic Personalized Therapeutics: Integrated Variant Annotation and Validation Reveals a Functional and Targetable Long Non-Coding RNA in Type 2 Diabetes

Leonard Lipovich, Ph.D., Associate Professor, Center for Molecular Medicine and Genetics, Wayne State University

We report computational discovery and experimental validation of an exonic polymorphism in a novel, primate-specific, evolutionarily non-conserved, long non-coding RNA (lncRNA), a leading type 2 diabetes direct causal candidate from GWAS. This lncRNA is expressed in the liver, where it regulates glycogen storage and hence fasting glucose levels. Since in vivo liver delivery of therapeutic oligonucleotides targeting this lncRNA is feasible, our results herald a new treatment for type 2 diabetes.

5:00 KEYNOTE PRESENTATION: Using Networks to Link Genotype to Phenotype

John Quackenbush, Ph.D., Professor, Biostatistics, Harvard T.H. Chan School of Public Health; Professor, Biostatistics and Computational Biology, Dana-Farber Cancer Institute

Network and systems methods, combined with unprecedented large-scale data sets, are providing us with a unique opportunity to explore the associations between genotype and phenotype. Using data from the Genotype-Tissue Expression project (GTEx), we will explore the factors that influence the manifestation of complex traits.

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

8:00 PLENARY KEYNOTE SESSION & AWARDS PROGRAM

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

Classifying Variants: Cancer Biomarker Interpretation
and Classification

10:30 Chairperson’s Remarks

Honey Reddi, Ph.D., FACMG, Clinical Laboratory Director, The Jackson Laboratory

10:40 Fusion RNAs and Their Implications in Cancer Diagnosis

Hui Li, Ph.D., Associate Professor, Pathology, University of Virginia

Gene fusions and fusion products have been thought to be cancer-unique features. However, our recent work on intergenic splicing challenged this prevailing view. These findings complicate the usage of fusion RNAs as a whole for cancer diagnosis and treatment. On the other hand, the novel mechanism represents a new repertoire for the discovery of new biomarkers and drug targets.

11:10 Somatic Variants – Approaches to Predicting Actionability

Honey Reddi, Ph.D., FACMG, Clinical Laboratory Director, The Jackson Laboratory

There are currently no defined algorithms in place for the interpretation and classification of somatic variants, unlike the ACMG guidelines for germline variants. We are currently evaluating a series of steps that can be implemented for the interpretation and classification of somatic cancer variants keeping in mind the factors that define actionability.

11:40 Unlock Asian Giant’s Precision Medicine Computing Potential – Intel’s Bio-IT Know-How and Footprints in China

Jian Li, Ph.D., Life Science Business Lead, Intel Health & Life Science, Greater Asia

Chang Yu, Life Science Solution Architect, Intel Health & Life Science, Greater Asia

China has become a new battlefield for global precision medicine, which could be largely attributed to it having the largest patient population in the world, the government’s endorsement and huge funding support, the booming market needs on NIPT and cancers, and also the emerging genomics giant players, e.g., Beijing Genomics Institute and Novogene.

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

Classifying Variants: Analyzing > Interpreting > Storing >
Sharing Dynamic Data

1:55 Chairperson’s Remarks

Liz Worthey, Ph.D., Faculty Investigator & Director, Software Development and Informatics, HudsonAlpha Institute for Biotechnology

2:00 Community-Driven Approaches to Gene Curation

Marina DiStefano, Ph.D., Variant Scientist, Laboratory for Molecular Medicine, Partners HealthCare

As precision medicine expands and whole exome sequencing becomes standard, it is critical to define a common framework to assess the evidence for gene-disease associations. Testing this framework involves reaching out to the experts in various specialties for validation. With input from the genetic community, genes can be transparently and systematically evaluated and prioritized for analysis in various clinical contexts.

2:30 FEATURED PRESENTATION: A Comprehensive Approach to Rare Disease Interpretation: Moving beyond Identification of a Causal Variant

Liz Worthey, Ph.D., Faculty Investigator & Director, Software Development and Informatics, HudsonAlpha Institute for Biotechnology

We discuss application of methods for analyzing, storing, and interpreting variant data that allows us to move beyond MDx related to a single variant to support a refined understanding of human health and disease. The discussion includes methods to: 1) support increased definitive diagnosis rates, 2) explore genotype to phenotype associations that can be used to predict disease course in a particular individual, and 3) identify modifiers that alter clinical presentation.

3:00 A Curated Database of 150,000 Variants from Clinical Whole-Genome Sequencing: What Does It Take to Maintain and Donate to ClinVar?

Aditi Chawla, Ph.D., Senior Scientist, Clinical Services Laboratory, Illumina

We present the workflow for variant classification, including an autoscore system that calculates a variant’s potential to have caused the associated disease, search for literature on variants, and manual clinical curation based on ACMG guidelines. We discuss strategies for maintaining and updating variant classifications over time, laboratory policy for updating clinical reports as variant classification changes, process for donating to ClinVar, and summary of our ClinVar donation.

3:30 Conference Adjourns



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