The reliability, robustness and reproducibility of next-generation sequencing platforms are no longer questioned, making the unstoppable march of genomics into clinical practices a reality. However, many challenges remain for the successful translation of genomic knowledge into health advances and clinical utility.
Bio-IT World and Cambridge Healthtech Institute are again proud to host the Fourth Annual TCGC: The Clinical Genome Conference, inviting stakeholders impacting clinical genomics to share new findings and solutions for advancing the applications of clinical genome medicine.
Final AgendaDay 1 | Day 2 | Day 3 | Download Brochure | Speaker Biographies
Monday, June 22
9:00 am Short Course Registration and Morning Coffee
10:00 am-1:00 pm Short Course
2:00 Conference Registration
3:00 Chairperson’s Opening Remarks
Eric Holland, M.D., Ph.D., Director, Solid Tumor Translational Research, Fred Hutchinson Cancer Research Center
KEYNOTE SESSION
3:15 Through the Keyhole to Genomic Wonderland: Common Sense, Beyond Uncommon Nonsense
Nathaniel Pearson, Ph.D., Senior Director, Scientific Engagement & Public Outreach, New York Genome Center
One hundred fifty years after Gregor Mendel first systematically probed genetic heritability, we
risk forgetting a key insight from his work, in our rush to broaden clinical genomics from urgent
diagnosis for a few to lifelong care for all. By fully embracing that insight now, we can wisely
bolster our health infrastructure for the long haul.
4:00 Integrating the Principles of Preventative and Personalized Medicine to Advance Wellness
Nathan D. Price, Ph.D., Associate Director, Institute for Systems Biology
Future medicine will be more proactive and data-rich than anything before possible – and
will focus on maintaining and enhancing wellness more than just reacting to disease. We
have launched a large-scale 100K wellness project that integrates genomics, proteomics,
transcriptomics, microbiomes, clinical chemistries and wearable devices to monitor wellness
and disease. I will present results from our pilot study of 107 individuals, showing how this data
led to actionable findings for individuals to improve health and reduce risk drivers of disease.
4:45 Big Data in Translational Cancer Genomics
Laura J. van ’t Veer, Ph.D., Director, Applied Genomics and Angela and Shu Kai Chan Endowed Chair, Cancer Research, UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco
Molecular genomics contributes to the knowledge of who is at risk to develop cancer, how
external factors may influence this risk, whether tumors are likely to metastasize or not, and
which subtype of tumors will likely respond to what therapy. Dr. van ’t Veer’s current research
involves integrating various types of genomics data, including next-generation sequencing big
data, and is aimed at understanding the molecular basis for early response to therapy as a
surrogate for long-term survival prediction.
5:30 Welcome Reception in the Exhibit Hall with Poster Viewing
6:30 Close of Day
Day 1 | Day 2 | Day 3 | Download Brochure | Speaker Biographies
Tuesday, June 23
7:30 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee
8:00 Chairperson’s Remarks
Nathaniel Pearson, Ph.D., Senior Director, Scientific Engagement & Public Outreach, New York Genome Center
8:05 FEATURED PRESENTATION: CIViC: CLINICAL INTERPRETATION OF VARIANTS IN CANCER
Malachi Griffith, Ph.D., Associate Director, The Genome Institute; Assistant Professor, Genetics, Washington University School of Medicine
To realize the potential of personalized medicine, genomic aberrations must be placed in the context of therapeutic response and diagnostic or prognostic associations. The evidence for these associations must be captured and characterized so that we can achieve a principled consensus among genomic experts, pathologists and oncologists on how best to interpret a genomic alteration in a clinical context. To this end, we present CIViC as a forum for the clinical interpretation of variants in cancer.
8:35 Identification of Independent Primary Tumors and Intrapulmonary Metastases Using DNA Rearrangements in Non-Small Cell Lung Cancer
George Vasmatzis, Ph.D., Assistant Professor, Laboratory Medicine & Pathology, Mayo Clinic & Foundation
Distinguishing independent primary tumors from intrapulmonary metastases in non-small cell carcinoma remains a clinical dilemma with significant clinical implications. Using next-generation DNA sequencing, we developed a chromosomal rearrangement-based approach to differentiate multiple primary tumors from metastasis. A total of 41 tumor samples were sequenced. Lung tumors predicted to be independent primary tumors based on different histologic subtype did not share any genomic rearrangements. Concordance between histology and genomic data occurred in the majority of cases. Discrepant cases were resolved by genome sequencing.
9:05 Leveraging Germline Genomics to Improve an Individual’s Health
John S. Witte, Ph.D., Professor, Epidemiology & Biostatistics and Urology; Head, Division of Genetic and Cancer Epidemiology; Associate Director, Institute for Human Genetics; Co-Leader, Cancer Center Program in Cancer Genetics, University of California, San Francisco
Vast amounts of germline genomic data have been associated with a large range of diseases and traits. Leveraging this information to improve wellness is a challenge due to the small effect of specific genetic variants. This can be overcome by taking a simultaneous, broader view of many variants. We show by example how incorporating large numbers of variants predictive of prostate specific antigen (PSA) can improve screening for prostate cancer, with the ultimate goal of devising personalized PSA tests for use in the clinic.
9:35 Beyond the Cancer Genome – Computational Enablement of Holistic, Evidence-Driven Patient Care, in a Clinical Oncology Setting
David Jackson, Ph.D., Chief Innovation Officer, Molecular Health
In oncology, the molecular characterization of tumor genes as part of patient care is now synonymous with the concept of precision medicine. Yet, a wealth of other molecular factors, such as patient genetics, co-morbidities and pharmacological constitution are critical to ensuring the clinical utility of this information. In this talk, I describe a computational platform that enables holistic clinical interpretation of multiple clinico-molecular parameters. Case studies will exemplify the real-time clinical necessity of such technology.
10:05 Coffee Break in the Exhibit Hall with Poster Viewing
10:45 Integration of Genetic and Epigenetic Data to Understand Genetic Risk of Prostate Cancer
Bogdan Pasaniuc, Ph.D., Assistant Professor, Pathology & Laboratory Medicine and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles
Although genome-wide association studies have identified over 100 genetic loci that increase risk for developing prostate cancer, their functional effects on risk remain largely unknown. I present new approaches that integrate large-scale genetic data with cell-type-specific epigenetic functional annotation data to gain insights into the genetic architecture of prostate cancer risk.
11:15 Ultrasensitive Detection of Circulating Tumor DNA by Deep Sequencing
Maximilian Diehn, M.D., Ph.D., Assistant Professor, Radiation Oncology, Stanford Cancer Institute, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University
Circulating tumor DNA (ctDNA) represents a promising biomarker for detection and monitoring of cancers. Work on clinical applications of next-generation sequencing-based ctDNA quantitation will be discussed.
11:45 Clinical Laboratory Medicine: From Bench Science to Information Science
Mick Correll, CEO, GenoSpace
Advances in high-throughput molecular profiling technologies have revolutionized clinical laboratory medicine, transforming what was once a bench science into an information science. With limited ability to differentiate on chemistry, the competition among laboratory service providers has shifted to data, where success will be determined by providing the most value from the information that is produced. Here we present a roadmap that will enable molecular labs to focus on their core business and stay ahead of the curve in the IT arms race.
12:15 pm Session Break
12:30 Luncheon Presentation: Seraseq™ Quality Controls for Genomic Analysis
Russell Garlick, Ph.D., CSO, SeraCare
NextGen Sequencing is rapidly moving into clinical diagnostics and with these advances come new quality control challenges. The use of proper controls, standards and reference materials has always been central to all molecular diagnostic laboratory quality management systems in order to ensure accurate results are reported. This presentation will focus on a new generation of NGS controls for genetic, oncology and non-invasive prenatal screening assays.
2:30 Chairperson’s Remarks
Malachi Griffith, Ph.D., Associate Director, The Genome Institute; Assistant Professor, Genetics, Washington University School of Medicine
2:35 An Approach to Whole-Genome Sequence as a Lifelong Health Resource
Sek Won Kong, M.D., Assistant Professor, Medicine/Informatics Program, Harvard Medical School and Boston Children’s Hospital
Accumulated genomic variants provide a foundation of information in the context of precision medicine, and an individual genome can be a resource for lifelong well being. To achieve analytical validity of whole-genome sequence for clinical use, a reproducible and accurate analysis and interpretation pipeline is required. Carrier status of disease-causing mutations and pharmacogenomic variants are of primary interest; however, estimating genetic liability for complex diseases using established risk alleles might be informative. We demonstrate how complex trait risk variants from an individual genome can be summarized and reported for the general clinician and patients.
3:05 Whole-Genome Sequencing of the World’s Oldest People
Kristen Fortney, Ph.D., Research Scientist, Stuart K. Kim Laboratory, Developmental Biology, Stanford University
Supercentenarians (110 years or older) are the world’s oldest people. We sequenced the genomes of 17 supercentenarians to see if we could uncover the genetic basis for their extreme longevity. From this small sample size, we were unable to find rare protein-altering variants significantly associated with extreme longevity. We have made the complete genomes of all 17 supercentenarians available as a resource to assist discovery in future studies.
3:35 Refreshment Break in the Exhibit Hall with Poster Viewing
4:15 Talk Title to be Announced
David Mittelman, Ph.D., CSO, Tute Genomics
4:45 The Role of Genome Sequencing in Personalized Breast Cancer Prevention
Weiva Sieh, M.D., Ph.D., Assistant Professor, Epidemiology, Department of Health Research and Policy, Stanford University School of Medicine
The benefits of genome sequencing for guiding personalized preventive strategies at the population level are uncertain. We evaluated the benefits and harms of targeting preventive efforts to the subpopulation of women whose genomes put them at highest risk of breast cancer using mathematical models for (1) 86 currently known breast cancer susceptibility alleles and (2) assuming complete knowledge of all breast cancer genes. Our findings suggest that genome sequencing has the potential to guide personalized breast cancer prevention, and that the benefits will improve with increased understanding of the genetic etiology of breast cancer.
5:15 Findings from the Critical Assessment of Genome Interpretation, a Community Experiment to Evaluate Phenotype Prediction
Steven E. Brenner, Ph.D., Professor, University of California, Berkeley
The Critical Assessment of Genome Interpretation (CAGI) is a community experiment to objectively assess computational methods for predicting the phenotypic impacts of genomic variation. Participants are provided genetic variants and predict resulting phenotype for ten challenges. These predictions are evaluated against experimental characterizations by independent assessors. CAGI revealed that despite statistically significant predictions, accuracy on the phenotypic impact of any specific variant was of questionable clinical utility. The most effective predictions came for methods honed to the precise challenge. Opportunities for further progress remain.
5:45 Close of Day
Day 1 | Day 2 | Day 3 | Download Brochure | Speaker Biographies
Wednesday, June 24
7:30 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee
8:00 Chairperson’s Remarks
Katherine Tynan, Ph.D., Business Development & Strategic Consulting for Diagnostics Companies, Tynan Consulting LLC (Member, AMP Economic Affairs Committee)
8:05 Estimating the Cost Effectiveness of Returning Incidental Findings from Next-Generation Genomic Sequencing
Caroline Bennette, MPH, Ph.D., K12 Patient-Centered Outcomes Research Scholar, Group Health Research Institute, Fred Hutchinson Cancer Research Center
Our team at the University of Washington recently developed a decision-analytic policy model to evaluate the potential clinical and economic impact of returning ACMG-recommended incidental findings from next-generation sequencing. We found that returning incidental findings is likely cost effective for certain patient populations receiving next-generation sequencing, but that screening of generally healthy individuals is likely not cost effective based on current data and sequencing costs. We describe the development of our policy model, summarize key findings and discuss future research directions.
8:35 Case Studies and Case Series of Genomic/Precision Medicine in a Large Children’s Hospital
Stephen F. Kingsmore, MB, ChB, BAO, D.Sc., FRCPath, Executive Director, Panomic Medicine, Children’s Mercy – Kansas City
Over 5400 single-gene diseases are known, affecting 4-8% of children. Genome and exome sequencing are starting to change the approach to patient management in these diseases, specifically regarding early etiologic diagnosis and “N-of-1-genome” treatment strategies. Six large retrospective case studies have been or soon will be published providing the first measurements of costs and benefits of genomic/precision medicine in neurodevelopmental disorders and acutely ill infants. Two individual patient cases illustrate the transformative potential of genomic/precision medicine.
9:05 The Evaluation of the Patient Presenting with Symptoms of Obstructive Coronary Artery Disease: Clinical Validity, Clinical Utility and Economic Utility of a Blood-Based Test Incorporating Age, Sex and Gene Expression
Mark Monane, M.D., CMO, CardioDx
Patients with symptoms suggestive of obstructive coronary artery disease (CAD) frequently undergo unnecessary testing and procedures. Approximately $6.7 billion/year is spent on non-invasive and invasive testing in the U.S. in the non-diabetic population with no prior revascularization or myocardial infarction, yet some patients continue to be misdiagnosed. We present data on a blood test for use in the evaluation of obstructive CAD among symptomatic patients. Data of clinical validity (96% NPV), clinical utility (multiple change behavior studies) and economic utility (cost implications) will be presented.
9:35 Epigenetic Profiling of DNA Methylation to Identify Breast Tumor Aggressiveness
Adam Marsh, Ph.D., Professor, Center for Bioinformatics and Computational Biology, University of Delaware; CSO, Genome Profiling, LLC
Women with triple-negative genotypes (i.e., normal for the three common marker mutations for breast cancer) are still at risk for developing aggressive breast tumors. We identify a suite of differentially methylated CpG sites between normal and tumor breast tissues using NGS that indicate a high degree of epigenetic conservation among different triple-negative patients who have developed advanced-stage breast tumors. Subtle epigenetic shifts in methylation status may provide a key line of evidence for assessing tumor risk and informing therapy decisions between surgery or non-invasive treatments.
10:05 Coffee Break in the Exhibit Hall with Poster Viewing
10:45 Myths and Realities of Clinical Genomics
David W. Moskowitz, M.D., Chairman, CEO, CMO & CSO, GenoMed, Inc.
Much of what passes for clinical genomics has been a waste of time and money, guided by unrealistic clinical paradigms. This has been fine, because the healthcare system is fundamentally anti-innovative, and is happy to waste the public’s time and money. But for anybody who wants to capture marketshare, it is helpful to review what does and doesn’t work.
11:15 PANEL DISCUSSION: Reimbursement for Genomic Sequencing Services in a Time of Changing Healthcare Business Models
At a time when payers are asking themselves, “Why pay for sequencing services?” come meet the people who are successfully crafting reimbursement arguments for the payers in disease areas as diverse as inherited genetic diseases and oncology. Find out the tactics that are working and why.
Moderator:
Katherine Tynan, Ph.D., Business Development & Strategic Consulting for Diagnostics Companies, Tynan Consulting LLC (Member, AMP Economic Affairs Committee)
Panelists:
Caroline Bennette, MPH, Ph.D., K12 Patient-Centered Outcomes Research Scholar, Group Health Research Institute, Fred Hutchinson Cancer Research Center
Stephen F. Kingsmore, MB, ChB, BAO, D.Sc., FRCPath, Executive Director, Panomic Medicine, Children’s Mercy – Kansas City
David W. Moskowitz, M.D., Chairman, CEO, CMO & CSO, GenoMed, Inc.
Rina Wolf, Vice President, Commercialization Strategies, Consulting & Industry Affairs, XIFIN, Inc.
12:00 pm Session Break
12:15 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
1:30 Chairperson’s Remarks
John E. Mattison, M.D., Chief Medical Information Officer, Assistant Medical Director, Southern California Medical Group, Kaiser Permanente; Co-Chair, eHealth Workgroup, Global Alliance for Genomics and Health GA4GH
1:35 FEATURED PRESENTATION: MAKING SENSE OF BIG DATA - SOME APPLICATIONS AND EMERGING TECHNOLOGIES
Amin Zia, Ph.D., Senior Bioinformatician, Stanford Center for Genomics and Personalized Medicine, Stanford University
Big Data is poised to impact our lives and health. Stanford Center for Genomics & Personalized Medicine is building a transformative platform in Big Data Precision Health by using emerging computational and biological technologies. What are some of the challenges in clinical genomics, population health and personal health profiling that we can address using these emerging technologies?
2:05 Potential Clinical Genomics Applications in China
Bill Zheng, Ph.D., Director, Bioinformatics Section, Institute of Genetic Engineering, Southern Medical University
Next-generation sequencing and microarrays are being extended to clinical diagnosis. Disease can be diagnosed more efficiently and effectively, and the Chinese market has huge innovations in translational medicine. We present the marketing expansion in clinical medicine as well as in health management in China, plus developments in data mining and data management.
2:35 Assessing Allele-Specific Expression across Multiple Tissues from RNA-Seq Read Data
Noah A. Zaitlen, Ph.D., Assistant Professor, Department of Medicine, Lung Biology Center, University of California, San Francisco
Genomic imprinting is an important regulatory mechanism that silences one of the parental copies of a gene. To systematically characterize this phenomenon, we analyze tissue specificity of imprinting from allelic expression data in 1582 primary tissue samples from 178 individuals from the Genotype-Tissue Expression (GTEx) project.
3:05 Refreshment Break in the Exhibit Hall with Poster Viewing
3:45 Whole-Genome Sequences of Two Octogenarians with Sustained Cognitive Abilities
Dorothee Nickles, Ph.D., Computational Biologist, Genentech, Inc.
The genetics of cognitive aging have not been fully defined yet. We sequenced the whole genomes of two octogenarians with sustained cognitive abilities despite being heterozygous for APOEε4, an Alzheimer’s and mortality risk variant. These genomes were neither characterized by an outstanding number of longevity-promoting variants nor an exceptionally low load in disease causing mutations. We identified a number of healthy cognitive-aging candidate genetic loci awaiting confirmation in larger studies.
4:15 FEATURED PRESENTATION: THE ONCOSCAPE APPLICATION IN CANCER BIG DATA ANALYSIS
Eric Holland, M.D., Ph.D., Director, Solid Tumor Translational Research, Fred Hutchinson Cancer Research Center
We have developed a tool for visualization of combined clinical/molecular data for cancer patients. This tool has been used to interrogate multiple public and private datasets for molecular contributions to clinical behavior.
4:45 PANEL DISCUSSION: Analytics and Reality: The Looming Blurring of Boundaries between Genome and Phenome in Health and Disease: Implications for Ontologies and Landing Zones
To maximize the clinical utility of genomic sequencing data, clinicians must ensure that both genomic and phenomic data is successfully integrated into the electronic health record (EHR) and other patient-centered platforms. This in turn requires understanding of technical infrastructure, security issues, policy requirements and the nature of the data itself. Learn about these topics and more from this panel of experts.
Moderator:
John E. Mattison, M.D., Chief Medical Information Officer, Assistant Medical Director, Southern California Medical Group, Kaiser Permanente; Co-Chair, eHealth Workgroup, Global Alliance for Genomics and Health GA4GH
Panelists:
Eric Holland, M.D., Ph.D., Director, Solid Tumor Translational Research, Fred Hutchinson Cancer Research Center
Adam Marsh, Ph.D., Professor, Center for Bioinformatics and Computational Biology, University of Delaware; CSO, Genome Profiling, LLC
Nathaniel Pearson, Ph.D., Senior Director, Scientific Engagement & Public Outreach, New York Genome Center
Becky Swain, Entrepreneur & Founding Member, Cloud Security Alliance
Bill Zheng, Ph.D., Director, Bioinformatics Section, Institute of Genetic Engineering, Southern Medical University
Amin Zia, Ph.D., Senior Bioinformatician, Stanford Center for Genomics and Personalized Medicine, Stanford University
5:30 Close of Conference
Day 1 | Day 2 | Day 3 | Download Brochure | Speaker Biographies
