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Third Annual TCGC: The Clinical Genome Conference, San Francisco, June 10-12, 2014 by Bio-IT World and Cambridge Healthtech Institute

Posted in Biological Networks, Gene Regulation and Evolution, CANCER BIOLOGY & Innovations in Cancer Therapy, Computational Biology/Systems and Bioinformatics, Genome Biology, Genomic Expression, Genomic Testing: Methodology for Diagnosis, Reproductive Andrology, Embryology, Genomic Endocrinology, Preimplantation Genetic Diagnosis and Reproductive Genomics, tagged Biotechnology and Pharmaceuticals, Data management, gene expression, Medical genetics on December 4, 2013| Leave a Comment »

Third Annual TCGC: The Clinical Genome Conference, San Francisco, June 10-12, 2014 by Bio-IT World and Cambridge Healthtech Institute

Reporter: Aviva Lev-Ari, PhD, RN

 

UPDATED on 5/1/2014

Register by May 2 for

Hotel Kabuki, San Francisco, CA

June 10 – 12, 2014

FINAL AGENDA

CLINICAL GENOME

conference

THE 3rd ANNUAL

Mining the Genome for Medicine Clinical Genome Conference.com

TCGC

The unstoppable march of genomics into clinical practice continues. In an ideal world, the expanding use of genomic tools will identify disease before the onset of clinical symptoms and determine individualized drug treatment leading to precision medicine. However, many challenges remain or the successful translation of genomic knowledge and technologies into health advances and actionable patient care. Join vital discussions of the applications, questions and solutions surrounding clinical genome analysis.

KEYNOTE SPEAKERS

Atul Butte, M.D., Ph.D.

Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics, Lucile Packard Children’s Hospital

David Galas, Ph.D.

Principal Scientist, Pacific Northwest Diabetes Research Institute

Gail P. Jarvik, M.D., Ph.D.

Head, Division of Medical Genetics, Arno G. Motulsky Endowed Chair in Medicine and Professor, Medicine and Genome Sciences, University of Washington Medical Center

John Pfeifer, M.D., Ph.D.

Vice Chair, Clinical Affairs, Pathology and Immunology; Professor, Pathology and Immunology, Washington University

John Quackenbush, Ph.D.

Professor, Dana-Farber Cancer Institute and Harvard School of Public Health; Co-Founder and CEO, GenoSpace

Topics Include:

• Working with the Payer Process

• Genome Variation and Clinical Utility

• NGS Is Guiding Therapies

• NGS Is Redefining Genomics

• Interpretation and Translation to the Client

• Integrating Genomic Data into the Clinic

ClinicalGenomeConference.com

Cambridge Healthtech Institute

250 First Avenue, Suite 300

Needham, MA 02494

www.healthtech.com

 

TUESDAY, JUNE 10

7:30 am Conference Registration and Morning Coffee

Working with the Payer Process

8:30 Chairperson’s Opening Remarks

»»KEYNOTE PRESENTATION

8:45 Case Study on Working through the Payer Process

John Pfeifer, M.D., Ph.D., Vice Chair, Clinical Affairs, Pathology; Professor,

Pathology and Immunology; Professor, Obstetrics and Gynecology, Washington

University School of Medicine

If next-generation sequencing (NGS) is to become a part of patient care in routine clinical practice (whether in the setting of oncology or in the setting of inherited genetic disorders), labs that perform clinical NGS must be reimbursed for the testing they provide. Genomics and Pathology Services at Washington University in St. Louis (GPS@WUSTL) will be used as a case study of a national reference lab that has been successful in achieving high levels of reimbursement for the clinical NGS testing it performs, including from private payers. The reasons for GPS’s success will be discussed, including NGS test design, clinical focus of testing, use of different models for reimbursement and payer education.

9:30 Implementation of Clinical Cancer Genomics within an Integrated

Healthcare System

Lincoln D. Nadauld, M.D., Ph.D., Director, Cancer Genomics, Intermountain Healthcare

Precision cancer medicine involves the detection of tumor-specific DNA alterations followed by treatment with therapeutics that specifically target the actionable mutations. Significant advances in genomic technologies have now rendered extended genomic analyses of human malignancies technologically and financially feasible for clinical adoption. Intermountain Healthcare, an integrated healthcare delivery system, is taking advantage of these advances to programmatically implement genomics into the regular treatment of cancer patients to improve clinical outcomes and reduce treatment costs.

10:00 PANEL DISCUSSION:

Payer’s Dilemma: Evolution vs. Revolution

As falling genome sequencing costs help clinicians refine patient diagnoses and therapeutic approaches, new complexities arise over insurance coverage of such tests, classification by CPT codes and other reimbursement issues. Experts on this panel will discuss payer challenges and changes—both rapid and gradual—occurring alongside these advances in clinical genomics.

Moderator: Katherine Tynan, Ph.D., Business Development & Strategic Consulting for Diagnostics

Companies, Tynan Consulting LLC

Panelists:

Tonya Dowd, MPH, Director, Reimbursement Policy and Market Access, Quorum Consulting

Mike M. Moradian, Ph.D., Director of Operations and Molecular Genetics Scientist, Kaiser

Permanente Southern California Regional Genetics Laboratory

Rina Wolf, Vice President of Commercialization Strategies, Consulting and Industry Affairs, XIFIN

Additional Panelists to be Announced

10:45 Networking Coffee Break

11:15 Beyond Genomics: Preparing for the Avalanche of Post-Genomic

Clinical Findings

Jimmy Lin, M.D., Ph.D., President, Rare Genomics Institute

Whole genomic and exomics sequencing applied clinically is revealing newly discovered genes and syndromes at an astonishing rate. While clinical databases and variant annotation continue to grow, much of the effort needed is functional analysis and clinical correlation. At RGI, we are building a comprehensive functional genomics platform that includes electronic health records, biobanking, data management, scientific idea crowdsourcing and contract research sourcing.

11:45 The MMRF CoMMpass Clinical Trial: A Longitudinal Observational

Trial to Identify Genomic Predictors of Outcome in Multiple Myeloma

Jonathan J. Keats, Ph.D., Assistant Professor, Integrated Cancer Genomics Division, Translational

Genomics Research Institute

12:15 pm Luncheon Presentation: Sponsored by

Big Data & Little Data – From Patient Stratification

to Precision Medicine

Colin Williams, Ph.D., Director, Product Strategy, Thomson Reuters

Molecular data has the power, when unlocked, to transform our understanding of disease to support drug discovery and patient care. The key to unlocking this potential is ‘humanising’ the data, through tools and techniques, to a level that supports interpretation by Life Science professionals. This talk will focus on strategies for extracting insight from ‘big data’ by shrinking it to ‘little data’, with a focus on applications to support patient stratification in drug discovery and for practising precision medicine in a clinical setting.

Genome Variation and Clinical Utility

1:45 Chairperson’s Remarks

»»KEYNOTE PRESENTATION

1:50 Lessons from the Clinical Sequencing Exploratory

Research (CSER) Consortium: Genomic Medicine

Implementation

Gail P. Jarvik, M.D., Ph.D., Head, Division of Medical Genetics, Arno G. Motulsky Endowed Chair in Medicine and Professor, Medicine and Genome

Sciences, University of Washington Medical Center

Recent technologies have led to affordable genomic testing. However, implementation of genomic medicine faces many hurdles. The Clinical Sequencing Exploratory Research (CSER) Consortium, which includes nine genomic medicine projects, was formed to explore these challenges and opportunities. Dr. Jarvik is the PI of a CSER genomic medicine project and of the CSER coordinating center. She will focus on the frequency of exomic incidental findings, including those of the 56 genes recommended for incidental finding return by the ACMG. The CSER group has annotated the putatively pathogenic and novel variants of the Exome Variant Server (EVS) to estimate the rate of these in individuals of European and African ancestry. Experience with consenting and returning incidental findings will also be reviewed.

2:35 Decoding the Patient’s Genome: Clinical Use of Genome-Wide

Sequencing Data

Elizabeth Worthey, Ph.D., Assistant Professor, Pediatrics & Bioinformatics Program, Human & Molecular Genetics Center, Medical College of Wisconsin

Despite significant advances in our understanding of the genetic basis of disease, genomewide identification and subsequent interpretation of the molecular changes that lead to human disease represent the most significant challenges in modern human genetics.

Starting in 2009 at MCW, we have performed clinical WGS and WES to diagnose patients coming from across all clinical specialties. I will discuss findings, pros and cons in approach, challenges remaining and where we go next.

3:05 Analyzing Variants with a DTC Genetics Database

Brian Naughton, Ph.D., Founding Scientist, 23andMe, Inc.

Sequencing a genome results in dozens of potentially disease-causing variants (VUS). I describe some examples of using the 23andMe database, including quick recontact of participants, to determine if a variant is disease-causing.

3:35 Refreshment Break in the Exhibit Hall with Poster Viewing

 

Genome Interpretation Software Solutions: Software Spotlights

(Sponsorship Opportunities Available)

Obtaining clinical genome data is rapidly becoming a reality, but analyzing and interpreting the data remains a bottleneck. While there are many commercial software solutions and pipelines for managing raw genome sequence data, providing the medical interpretation and delivering a clinical diagnosis will be the critical step in fulfilling the promise of genomic medicine. This session will showcase how genome data analysis companies are streamlining the genomic diagnostic pipeline through:

• Transferring raw sequencing data

• Interpreting genetic variations

• Building new software and cloud-based analysis pipelines

• Investigating the genetic basis of disease or drug response

• Integrating with other clinical data systems

• Creating new medical-grade databases

• Reporting relevant clinical information in a physician-friendly manner

• Continuous learning feedback

4:15 Software Spotlight #1

4:30 Copy Number Variant Detection Using Sponsored by

Next-Generation Sequencing: State of the Art

Alexander Kaplun, Ph.D., Field Applications Scientist, BIOBASE

This talk will provide a short review about the current state of the art in detection of larger variants that have an important role in many diseases such as haplotypes, indels, repeats, copy number variants (CNVs), structural variants (SVs) and fusion genes using NGS methods, and an outlook to their use for pharmacogenomic genotyping.

4:45 Software Spotlight #3

5:00 Software Spotlight #4

5:15 Software Spotlight #5

5:30 Pertinence Metric Enables Hypothesis-Independent Sponsored by

Genome-Phenome Analysis in Seconds

Michael M. Segal, M.D., Ph.D., Chief Scientist, SimulConsult

Genome-phenome analysis combines processing of a genomic variant table and comparison of the patient’s findings to those of known diseases (“phenome”). In a study of 20 trios, accuracy was 100% when using trios with family-aware calling, and close to that if only probands were used. The gene pertinence metric calculated in the analysis was 99.9% for the causal genes. The analysis took seconds and was hypothesis-independent as to form of inheritance or number of causal genes. Similar benefits were found in gene discovery situations.

6:00 Welcome Reception in the Exhibit Hall with Poster Viewing

7:00 Close of Day

WEDNESDAY, JUNE 11

7:30 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

NGS Is Guiding Therapies

8:30 Chairperson’s Opening Remarks

8:35 Next-Generation Sequencing Approaches for Identifying Patients

Who May Benefit from PARP Inhibitor Therapy

Mitch Raponi, Ph.D., Senior Director and Head, Molecular Diagnostics, Clovis Oncology

The following questions will be addressed: What biomarkers should we be focusing on to identify appropriate patients who will likely benefit from PARP inhibitors? How can we apply next-generation sequencing technologies to identify all patients who will respond to the PARP inhibitor rucaparib? What regulatory challenges are we faced with for approval of NGS companion diagnostics?

9:05 Whole-Genome and Whole-Transcriptome Sequencing to Guide

Therapy for Patients with Advanced Cancer

Glen J. Weiss, M.D., MBA, Director, Clinical Research, Cancer Treatment Centers of America

Treating advanced cancer with agents that target a single-cell surface receptor, up-regulated or amplified gene product or mutated gene has met with some success; however, eventually the cancer progresses. We used next-generation sequencing technologies (NGS) including whole-genome sequencing (WGS), and where feasible, whole-transcriptome sequencing (WTS) to identify genomic events and associated expression changes in advanced cancer patients. While the initial effort was a slower process than anticipated due to a variety of issues, we demonstrated the feasibility of using NGS in advanced cancer patients so that treatments for patients with progressing tumors may be improved. This lecture will highlight some of these challenges and where we are today in bringing NGS to patients.

9:35 The SmartChip TE™ Target Enrichment System for Sponsored by

Clinical Next-Gen Sequencing

Gianluca Roma, MS MBA, Director, Product Management, WaferGen Biosystems

10:05 Coffee Break in the Exhibit Hall with Poster Viewing

Data Mining

»»KEYNOTE PRESENTATION

10:45 Translating a Trillion Points of Data into

Therapies, Diagnostics and New Insights into Disease

Atul Butte, M.D., Ph.D., Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics,

Lucile Packard Children’s Hospital; Co-Founder, Personalis and Numedii

There is an urgent need to translate genome-era discoveries into clinical utility, but the difficulties in making bench-to-bedside translations have been well described. The nascent field of translational bioinformatics may help. Dr. Butte’s lab at Stanford builds and applies tools that convert more than a trillion points of molecular, clinical and epidemiological data— measured by researchers and clinicians over the past decade—into diagnostics, therapeutics and new insights into disease. Dr. Butte, a bioinformatician and pediatric endocrinologist, will highlight his lab’s work on using publicly available molecular measurements to find new uses for drugs, including drug repositioning for inflammatory bowel disease, discovering new treatable inflammatory mechanisms of disease in type 2 diabetes and the evaluation of patients presenting with whole genomes sequenced.

11:30 DGIdb – Mining the Druggable Genome

Malachi Griffith, Ph.D., Research Faculty, Genetics, The Genome Institute, Washington University School of Medicine

In the era of high-throughput genomics, investigators are frequently presented with lists of mutated or otherwise altered genes implicated in human disease. Numerous resources exist to generate hypotheses about how such genomic events might be targeted therapeutically or prioritized for drug development. The Drug-Gene Interaction database (DGIdb) mines these resources and provides an interface for searching lists of genes against a compendium of drug-gene interactions and potentially druggable genes. DGIdb can be accessed at dgidb.org.

12:00 pm Sponsored Presentation (Opportunity Available)

12:30 Luncheon Presentation (Sponsorship Opportunity Available)

 

The unstoppable march of genomics into clinical practice continues. In an ideal world, the expanding use of genomic tools will identify disease before the onset of clinical symptoms and determine individualized drug treatment leading to precision medicine. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances and clinical practice.

Bio-IT World and Cambridge Healthtech Institute are again proud to host the Third Annual TCGC: The Clinical Genome Conference, inviting stakeholders from all arenas impacting clinical genomics to share new findings and solutions for advancing the application of clinical genome medicine.

TCGC brings together many constituencies for frank and vital discussion of the applications, questions and solutions surrounding clinical genome analysis, including scientists, physicians, diagnosticians, genetic counselors, bioinformaticists, ethicists, regulators, insurers, lawyers and administrators.

Topics addressing successful translation of genomic knowledge and technologies into advancement of clinical utility (medicines and diagnostics) include but are not limited to:

Scientific Investigation and Interpretation

• Technologies/Platforms
• WGS/Exome/Single-Cell Sequencing

• Variation
  . Deletions and Amplifications
  . Gene Expression
  . Epigenetic Regulation
  . Structural Changes
  . Chromosomal Alterations
  . Molecular Networks

• Drug and Diagnostic Targets
• Interpretation and Analysis Pipelines
• Case Studies

Clinical Integration and Implementation

• Mechanisms to Monitor Genomic Medicine
• Determining Clinical Utility
• Standardization/Regulation/Certification
• Reimbursement
• Data Management
• Diagnostic Lab Infrastructure
• HIT/Data Integration
• Reporting Results to Patients/Physicians

Call for Speakers
For a limited time, we are inviting researchers and clinicians applying genome analysis tools in clinical settings, as well as regulators and administrators implementing genomics into the clinic, to submit proposals for platform presentations. Please note that due to limited speaking slots, preference is given to abstracts from those within pharmaceutical and biopharmaceutical companies, regulators and those from academic centers. Additionally, as per CHI policy, a select number of vendors/consultants who provide products and services to these genomic researchers are offered opportunities for podium presentation slots based on a variety of Corporate Sponsorships.

All proposals are subject to review by the organizers and Scientific Advisory Committee.

Please click here to submit a proposal.

Submission deadline for priority consideration: November 15, 2013

For more details on the conference, please contact:
Mary Ann Brown
Executive Director, Conferences
Cambridge Healthtech Institute
250 First Avenue, Suite 300
Needham, MA 02494
T:  781-972-5497
E:  mabrown@healthtech.com

For exhibit and sponsorship opportunities, please contact:
Jay Mulhern
Manager, Business Development, Conferences & Media
Cambridge Healthtech Institute
250 First Avenue, Suite 300
Needham, MA 02494
T: 781-972-1359
E: jmulhern@healthtech.com

SOURCE

http://www.clinicalgenomeconference.com/

 

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Genome Sequencing of the Healthy

Posted in Cell Biology, Signaling & Cell Circuits, Chemical Genetics, Computational Biology/Systems and Bioinformatics, Genome Biology, Health Law & Patient Safety, tagged Atul Butte, Aviva Lev-Ari, benefits, Biology, DNA, Eric Topol, ethical issues, Eukaryotic, Full genome sequencing, genetics, genome, healthy individuals, issues, Medical genetics, New England Journal of Medicine, Plant, Whole genome sequencing on March 2, 2013| 3 Comments »

Genome Sequencing of the Healthy

Curators: Larry H. Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

 

Key Issues in Genome Sequencing of Healthy Individuals
Eric Topol, MD, Genomic Medicine

I briefly review 3 important articles that recently appeared, each touching on important controversies in the use of whole genome sequencing
http://www.linkedin.com/…/Key-Issues-in-Genome-Sequencing-218

http://boards.medscape.com/.2a38676f!comment=1

I briefly review 3 important articles that recently appeared, each touching on important controversies in the use of whole genome sequencing:

1. Should Healthy People Have Their Genomes Sequenced At This Time? Wall Street Journal, February 15, 2013.

2. A Genetic Code for Genius? Wall Street Journal, February 15, 2013.

3. Francke U, Djamco C, Kiefer AK, et al. Dealing with the unexpected: consumer responses to direct-access BRCA mutation testing. PeerJ. 2012;1:e8. DOI 10.7717/peerj.8

Welcome to another segment on genomic medicine. Today, I want to get into 3 different articles: 2 from the Wall Street (“Medical”) Journal and the other from a new open access journal, PeerJ. All of them are related to the issues of genome sequencing.

First, there was a debate about whether all healthy people should have their genomes sequenced. It was a debate between Atul Butte from Stanford and Robert Green from Harvard. In this debate, they made a number of really good points, and I have linked you to that article if you’re interested.

Basically, is it too early to get sequencing because we need millions of people to have whole genome sequencing who are healthy in order for that information to be truly informative. The price continues to drop. So even though the sequencing that is done today would still be valid if it’s done accurately, the problem we have, of course, is a lack of enough people who are phenotyped with a particular condition to extract all the best information that is truly informative from whole genome sequencing.

 it’s unlikely that even 2000 individuals with high IQ will be particularly informative but also, of course, what this could do from a bioethical standpoint. I’ll leave that to your imagination and thoughts as to where this could go – that is, trying to understand, even with limited power, the genomics of intelligence.

The third article, which is also very interesting, comes from this new journal called PeerJ. I’m on the editorial board of that journal, and I think it’s terrific to see open access, high-quality biomedical articles.

This one comes from the company 23andMe. From a very large number of individuals – now over 200,000 and rapidly approaching 1 million – who have had genome scans, a large number of women had information about the BRCA gene and whether they had a significant mutation. From these women who volunteered to participate in this study, we learned that they had no serious psychological repercussions from knowledge of this highly actionable BRCA pathogenic mutation.

This goes along with the previous study that we had done at Scripps led by my colleague Cinnamon Bloss in the New England Journal of Medicine, where, in thousands of individuals who had genome scans and had such data as ApoE4 status known to them for the first time, there were no significant negative psychological repercussions.

Should Healthy People Have Their Genomes Sequenced At This Time?

‘Patients in Waiting’

Injecting so much uncertain genetic information into the doctor-patient relationship could create legions of “patients in waiting” leading to unnecessary tests, harmful outcomes and lifelong anxiety. As private software companies compete to provide more genomic “findings” to a medical culture that is trained to search for diagnostic fire when they smell the smoke of disease risk, there are potential benefits. But there is also a real possibility that medical resources will be squandered and patients could be harmed.

Perhaps we all underestimated how complicated it would be to move genomic knowledge into the practice of medicine and public health. Now is the time to make sure we get this right through rigorous basic and clinical studies that define which mutations are dangerous, and distinguish useful from unnecessary interventions. Soon, genomic insights will give us early warnings about life-threatening illnesses that we may be able to prevent. Soon, standards will be available to guide doctors about which findings are meaningful and which are not.

Soon, there may be evidence to support the benefits of screening healthy individuals. But not today.

SOURCE:

http://online.wsj.com/article/SB10000872396390443884104577645783975993656.html

Related articles

• Should you Get Your Genome Sequenced? (simplerna.com)
• Whole-Genome Sequencing Data will be Stored in Coriell’s Spin off For-Profit Entity (pharmaceuticalintelligence.com)
• 2013 Genomics: The Era Beyond the Sequencing Human Genome: Francis Collins, Craig Venter, Eric Lander, et al. (pharmaceuticalintelligence.com)
• Personal Tale of JL’s Whole Genome Sequencing

Table 1. Performance values for genome sequencing technologies including Sanger methods and Massively Parallel Seqeuncing methods. Sinville, R. and Soper, S. A. High resolution DNA separations using microchip electrophoresis. J. Sep. Sci. 2007, 30, 1714 – 1728 Morozova,O. and Marra, M. A. Applications of next-generation sequencing technologies in functional genomics. Genomics. 92 (2008) 255–264 (Photo credit: Wikipedia)

 

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