Posts Tagged ‘Atul Butte’

The Stanford Center for Clinical and Translational Research and Education, or Spectrum – NIH Awards Stanford $45.3M

Reporter: Aviva Lev-Ari, PhD, RN

NIH Awards Stanford $45.3M for Translational Research

October 07, 2013

NEW YORK (GenomeWeb News) – The Stanford Center for Clinical and Translational Research and Education, or Spectrum, is being awarded $45.3 million over four and a half years by the National Institutes of Health to push forward translational research in medicine.

Spectrum is one of 15 institutions to receive such an award being funded as part of the Clinical and Translational Sciences Awards, which were launched in 2006 by NIH “to help meet the nation’s urgent need to provide better healthcare to more people for less money,” the Stanford School of Medicine said.

Stanford won a first round of CTSA funding in 2008 of $30 million.

The new funding will be used to support two new programs at Stanford, one in disease diagnostics and one in population health sciences.

The diagnostics program seeks to develop new methods of testing and preventing disease through advances in omics, immune monitoring, molecular imaging, single-cell analysis, computation, and informatics, the school said. Atul Butte, chief of systems medicine and associate professor of pediatrics and genetics, will lead the program.

The Population Health Sciences Initiative will design systems to serve as a new source of practice-based evidence. The systems will be based on the daily experiences of practicing physicians and information drawn from clinical data warehouses, Stanford said.

This initiative is led by Robert Harrington, professor and chair of medicine; Mark Cullen, professor of medicine and chief of the Division of General Medical Disciplines; and Douglas Owens, professor of medicine and director of the Stanford Center for Primary Care and Outcomes Research and the Center for Health Policy.

The new CTSA award also will be used to address the shortage of qualified clinical and translational researchers across the US by funding new training programs and online courses in clinical research, Stanford said.

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Reporter: Aviva Lev-Ari, PhD, RN


Track 5

Next-Gen Sequencing Informatics

NGS, Genome-Scale Screening, and HTP Proteomics

Track 5 is dedicated to advances in analysis and intepretation of next-gen data. Topics to be covered include analysis of

sequence variants related to cancer research from NGS data, instruments facilitate a cloud approach for NGS, analysis tools

and workflows, and network biology/network medicine.


7:00 am Workshop Registration and Morning Coffee

8:00 Pre-Conference Workshops*

*Separate Registration Required

2:00 – 7:00 pm Main Conference Registration

4:00 Event Chairperson’s Opening Remarks

Cindy Crowninshield, RD, LDN, Conference Director, Cambridge

Healthtech Institute

4:05 Keynote Introduction

Kevin Brode, Senior Director, Health & Life Sciences, Americas Hitachi

Data Systems


Do Network Pharmacologists Need Robot Chemists?

Andrew L. Hopkins, DPhil, FRSC, FSB, Division of Biological Chemistry

and Drug Design, College of Life Sciences, University of Dundee

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

Drop off a business card at the CHI Sales booth for a chance to win 1 of 2

iPads® or 1 of 2 Kindle Fires®!*

*Apple ® and Amazon are not sponsors or participants in this program


7:00 am Registration and Morning Coffee

8:00 Chairperson’s Opening Remarks

Phillips Kuhl, Co-Founder and President, Cambridge Healthtech Institute

8:05 Keynote Introduction

Sanjay Joshi, CTO, Life Sciences, EMC Isilon


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

8:55 Benjamin Franklin Award & Laureate Presentation

9:15 Best Practices Award Program

9:45 Coffee Break in the Exhibit Hall with Poster Viewing

Best Practices for Genomic Data Interpretation & Analysis

10:50 Chairperson’s Remarks

Steve Dickman, Founder & CEO, CBT Advisors, Inc.

11:00 CLARITY Challenge

Shamil Sunyaev, Ph.D., Associate Professor, Division of Genetics,

Department of Medicine, Brigham and Women’s Hospital/Harvard

Medical School

11:30 HLA and KIR Typing from NGS Reads with

Omixon Target

Attila Berces, Ph.D., CEO, Omixon

HLA is the most polymorphic region of the human genome

with several segmental duplications and its analysis is a computational

challenge. In this presentation I will show examples including validation

studies of HLA typing from various sources of genomic data: whole genome,

whole exome, targeted amplicon sequencing with Illumina, Ion Torrent and

Roche sequencer.

11:45 Comparison of Genome Analysis Tools

Jason Wang, Co-founder & CTO, Arpeggi, Inc.

A major impediment to clinical sequencing is the paucity of

analysis standards and comparison metrics. We present our

progress towards developing analysis standards, as well an open-access

collaborative tool that enables anyone to define comparison metrics and

compare tool performance. We hope that in making available this resource

we can help fuel a community-driven solution for standardizing genome

analysis pipelines.

12:00 Case Study: Sequencing Informatics System to Profile Genetic

Changes in Tumors

Long Phi Le, M.D., Ph.D., Department of Pathology, Massachusetts

General Hospital

This presentation will discuss the development of a sequencing informatics

system to profile genetic changes in tumors that is in collaboration between

PerkinElmer with Massachusetts General Hospital. This system, based on

PerkinElmer’s Geospiza platforms, will allow genotype analysis to define

key targets.

12:30 Ion Torrent Informatics Enables

Semiconductor Sequencing

Darryl León , Ph.D., Associate Director, Product

Management, Ion Torrent, Life Technologies

Data generated by the Ion Torrent Personal Genome Machine Sequencer or

the Ion Torrent Proton Sequencer are analyzed by Torrent Suite Software.

An overview of the data analysis steps will be provided. Torrent Suite offers

a flexible plug-in system allowing software developers the ability to deliver

custom analysis solutions using the compute resources associated with the

local Torrent Server. For researchers with need for either rich annotations

or controlled data analysis, the Ion Reporter Software offers a streamlined

data analysis and decision engine for use with amplicons, exomes,

or genomes.

1:40 Chairperson’s Remarks

Jeffrey Rosenfeld, Ph.D., IST/High Performance & Research Computing,

University of Medicine & Dentistry of New Jersey (UMDNJ)

Sponsored by

Sponsored by

Sponsored by

Bio-ITWorldExpo.com 18

1:45 Data Intensive Academic Grid (DIAG): A Free Computational Cloud

Infrastructure Designed for Bioinformatics Analysis

Anup Mahurkar, Executive Director, Software Engineering and IT, Institute

for Genome Sciences, University of Maryland School of Medicine

We have deployed the NSF funded Data Intensive Academic Grid (DIAG),

a free computational cloud designed to meet the analytical needs of

the bioinformatics community. DIAG has 200+ registered users from 130

institutions worldwide who conduct large-scale genomics, transcriptomics,

and metagenomics data analysis. Learn about the grid’s architecture, how

to access this free resource, and success stories.

2:15 Performance Comparison of Variant Detection Tools for Next

Generation Sequencing (NGS) Data: An Assessment Using a Pedigree-

Based NGS Dataset and SNP Array

Ming Yi, Ph.D. IT Manager, Functional Genomic Group, Advanced

Biomedical Computing Center, SAIC-Frederick at Frederick National

Laboratory for Cancer Research (formerly National Cancer Institute)

There is an urgent need for the NGS community to be able to make the

right choice out of a large collection of available SNP detection tools. Our

methodology offers a great example of comparing SNP discovery tools and

paving a way to expand such methods in more global scope for comparison.

2:45 Informatics in the Cloud

Karan Bhatia, Ph.D., Solutions Architect, Amazon

Web Services

Learn about how to easily create sophisticated, scalable,

secure pipelines to accelerate life science research with Amazon Web

Services. In this presentation, you will learn how to drive scale out, tightly

coupled and Hadoop based workflows on Amazon EC2, a utility computing

platform that provides a perfect fit for data management and collaboration.

3:15 Refreshment Break in the Exhibit Hall with Poster Viewing

Gene Mapping & Expression

3:45 InSilico DB Genomic Datasets Hub: An Efficient Starting Point for

Managing and Analyzing Genomewide Studies in GenePattern, Integrative

Genomics Viewer, and R/Bioconductor

David Weiss, Ph.D., CEO, InSilico Genomics

Alain Coletta, Ph.D., Co-Founder and CTO, InSilico Genomics

The InSilico DB platform is a powerful collaborative environment, with

advanced capabilities for biocuration, datasets subsetting and combination,

and datasets sharing. InSIlico DB solution architecture will be presented

along with a live demo of the InSilico DB online platform. Learn how more

than 1000 users from top academic and research institutions are using

InSilico DB in their daily research.

4:15 Constructing a Comprehensive Map for Molecules Implicated in

Obesity and Its Induced Disorders

Kamal Rawal, Ph.D., Faculty, Biotechnology and Bioinformatics, Jaypee

Institute of Information Technology

We have constructed a comprehensive map of all the molecules (genes,

proteins, and metabolites) reported to be implicated in obesity. This map

paves the way to understanding the pathophysiology of obesity and identify

drug targets and off-targets for existing drugs. This talk discusses the

integrated approach we used in combining public resources, abstracts, and

research articles to construct this map.

4:45 Quality Assurance: An Essential Step for Gene

Expression Analysis Using Deep Sequencing

Dan Kearns, Director, Software Development, Maverix

Biomics, Inc.

Dave Mandelkern, CEO & Co-Founder, Maverix Biomics, Inc.

With the advancement of deep sequencing technologies, researchers

expect to obtain high quality results from their studies. However, this cannot

be obtained solely by successful sequencing runs. Multiple data checks

and pre-processing must be performed before downstream analysis. In this

case study, we will present an automated quality assurance pipeline that

helps improve gene expression analysis results.

5:00 DDN LS Appliance – Simple Platform for NGS

Analysis, Data Distribution and Collaboration

Jose L. Alvarez, WW Director Life Sciences,

DataDirect Networks

With this unique approach the DDN LS appliance can deliver flexible data

ingest options, optimized data analysis resources, a policy based data

tiering/archive solution and a geo-distributed secure collaboration platform.

The appliance delivers 1.46X better performance on popular LS applications

like Bowtie when compared to NFS based solutions.

5:15 Best of Show Awards Reception in the Exhibit Hall

6:15 Exhibit Hall Closes


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

Morning Coffee

Gene Mapping & Expression

8:45 Chairperson’s Opening Remarks

8:50 Network Biology and Personalized Medicine in Multiple Sclerosis

Mark Chance, Ph.D., Vice Dean for Research, Proteomics, Case Western

Reserve University

Almost nothing is known about biological factors underlying the remarkable

disease heterogeneity observed across multiple sclerosis (MS) patients,

and there are no accurate biological predictors of disease severity that

can be used for guiding clinical treatment options. Learn about the network

biology methods we are using to analyze blood cell gene expression and

understand good and poor responders to therapy.

9:20 GeneSeer: A Flexible, Easy-to-Use Tool to Aid Drug Discovery by

Exploring Evolutionary Relationships between Genes across Genomes

Philip Cheung, Bioinformatics Group Leader, Scientific Computing,

Dart Neuroscience

GeneSeer is a publicly available tool that leverages public sequence data,

gene metadata information, and other publicly available data to calculate

and display orthologous and paralogous gene relationships for all genes

from several species, including yeasts, insects, worms, vertebrates,

mammals, and primates such as human. This talk describes GeneSeer’s

underlying methods and the user-friendly interface.

9:50 Sponsored Presentations (Opportunities Available)

10:20 Coffee Break in the Exhibit Hall and Poster Competition

Winners Announced

10:45 Plenary Keynote Panel Chairperson’s Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

10:50 Plenary Keynote Panel Introduction

Yury Rozenman, Head of BT for Life Sciences, BT Global Services

Niven R. Narain, President & CTO, Berg Pharma

»»Plenary Keynote Panel

11:05 The Life Sciences CIO Panel


Remy Evard, CIO, Novartis Institutes for BioMedical Research

Martin Leach, Ph.D., Vice President, R&D IT, Biogen Idec

Andrea T. Norris, Director, Center for Information Technology (CIT)

and Chief Information Officer, NIH

Gunaretnam (Guna) Rajagopal, Ph.D., VP & CIO – R&D IT, Research,

Bioinformatics & External Innovation, Janssen Pharmaceuticals

Cris Ross, Chief Information Officer, Mayo Clinic

Matthew Trunnell, CIO, Broad Institute of MIT and Harvard

Sponsored by

Sponsored by

Sponsored by

19 Bio-ITWorldExpo.com

12:15 Luncheon in the Exhibit Hall with Poster Viewing

Panel Session: Building the IT Archetecture of the New York

Genome Center

2:00 Panel Session: Building the IT Architecture of the New York

Genome Center

Moderator: Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

Christopher Dwan, Acting Senior Vice President, IT, New York

Genome Center

Kevin Shianna, Senior Vice President, Sequencing Operations, New York

Genome Center

Sanjay Joshi, CTO, Life Sciences, EMC Isilon Storage Division

Robert B. Darnell, M.D., Ph.D., President & Scientific Director, New York

Genome Center

George Gosselin, CTO, Computer Design & Integration LLC

In 2011, a consortium of 11 major academic and medical organizations in

and around New York announced the creation of the New York Genome

Center (NYGC). Under the direction of Nancy Kelley, the NYGC aspires to

be a world-class genomics and medical research center, and is currently

undergoing construction in the heart of Manhattan. NYGC management

has the opportunity to design and create a state-of-the-art IT and data

management infrastructure to handle, store and share the output from

what will rapidly become one of the world’s foremost genome sequencing

facilities. This series of talks will describe the thinking that went into the

design, creation and construction of the NYGC’s IT infrastructure and entire

data management strategy.

4:00 Conference Adjourns


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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


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.

Table 1. Performance values for genome sequenc...

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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