Sequencing

chicorporate.com
  • No tags were found...

Next-Generation Sequencing - CHI Corporate - Cambridge ...

Next-Generation

June 2009

Sequencing:

Solving the Genome

Ken Rubenstein, PhD

Next-generation sequencing (NGS) technologies are

advancing in quality and applications diversity at a

breathtaking pace. The market is diversifying strongly into

labs without previous involvement in sequencing. This

report examines:

• Current NGS platforms and how they compare

• Market dynamics and competitive landscape for

new entrants

• Next-generation systems in development

• Bioinformatics issues

• Applications of NGS

• User survey results and views of

interviewees

Continued on next page

Exploring the

depths of the

human

genome

Insight Pharma Reports, a division of Cambridge Healthtech Institute

250 First Avenue • Suite 300 • Needham, MA 02494 •781-972-5444 • InsightPharmaReports.com


Overview

The first generation of DNA sequencing can be said to have

ended when the first few human genomes were sequenced

and a large number of genetic variations were detected in

a relatively few individuals. Sequencing throughput is rising

dramatically as costs per unit of sequence are falling equally

dramatically. Now it has become possible to sequence a sufficiently

large number of human genomes to explore the extent

and medical meaning of genetic variations in statistically

meaningful ways. The race to the “$1,000 genome” is well

underway, and the number of entrants is surprisingly large, as

are the ingenuity and inventiveness that have been brought

to race.

Next-Generation Sequencing: Solving the Genome provides

a detailed overview of the technologies involved in

next-generation sequencing, starting with the four systems

currently on the market and continuing with those now in

Source: Insight Pharma Reports

development. A number of companies have technologies that

promise some advantage over existing systems, but whether

those advantages will be great enough to merit significant

market share remains an open question. We also provide

an overview of bioinformatics issues in next-generation sequencing

and a comparative analysis of currently available

platforms.

Applications of next-generation sequencing discussed in this

report include whole-genome sequencing, RNA resequencing,

ChIP-seq, disease prediction and diagnosis, and personal

genomics. Next-generation sequencing is starting to impinge

on DNA microarray usage and should continue to do so as

costs drop. Existing next-generation sequencing users are

striving to expand the case for personal genomics and for

personalized medicine in general. Next-generation systems

are currently enabling the genome-wide association studies

needed to identify the genome variants central to deeper understanding

of the molecular basis of genetically complex diseases

and predicting individual risk of developing them.

Next-Generation Sequencing: Solving the Genome examines

market dynamics and includes discussions of key issues

relating to the competitive position of various technologies

and companies. Next-generation sequencing instruments

and consumables are selling rapidly and contributing nicely

to growth rates of the market leaders. Second-round players

must offer significant improvements over current market

entrants in order to merit viable market share. Third-round

technologies, particularly those involving nanopores, remain

speculative at present, but could serve to accelerate market

decentralization by virtue of extremely low costs and high

speeds.

About the Author: Ken Rubenstein, PhD, a biochemist and molecular biologist, received his PhD at the University of Wisconsin

and postdoctoral training at the University of Pennsylvania School of Medicine. He was a key innovator and research manager

for Syva Company, the diagnostics branch of Syntex Corporation. During his 13 years with Syva, Dr. Rubenstein became

vice president, scientific affairs, a function that included strategic planning. Since 1983, he has served as a technology and

marketing consultant to biomedical companies and an industry analyst, with more than 40 published studies to his credit.

Tables and Figures

Figures

Sanger Sequencing Methodology

Roche/454 Sequencing Concept

The Illumina Genome Analyzer Sequencing Concept

The Applied Biosystems SOLiD Sequencing Concept

The Complete Genomics cPAL Sequencing Concept

The Pacific Bioscience Sequencing Concept

Tables

Relative Performance of Applied Biosystems, Illumina, and 454

Sequencers

Comparison of Applied Biosystems, Illumina, and 454 Sequencers

with Sanger Sequencing

Selected Deals in the Next-Generation Sequencing Space

SURVEY EXHIBITS

Chief Application of DNA Sequencing, Industry Respondents

Chief Application of DNA Sequencing, Academic Respondents

Main Organism for Next-Generation Sequencing, Industry Sector

Main Organism for Next-Generation Sequencing, Academic Sector

User Experience with Next-Generation Platform, Industry Sector

User Experience with Next-Generation Platform, Academic Sector

Next-Generation Platform Predicted to Dominate in 2–3 Years, Industry

Sector

Next-Generation Platform Predicted to Dominate in 2–3 Years,

Academic Sector

Most Exciting Third-Generation Platform, Industry Sector

Most Exciting Third-Generation Platform, Academic Sector

Applications to Benefit Most from Next-Generation Sequencing,

Industry Sector

Applications to Benefit Most from Next-Generation Sequencing,

Academic Sector

To order a report, e-mail rlaraia@healthtech.com, call Rose LaRaia at 781-972-5444, or order on-line


Tables and Figures (cont.)

Research Areas to Benefit Most from Next-Generation Sequencing,

Industry Sector

Research Areas to Benefit Most from Next-Generation Sequencing,

Academic Sector

Biggest Technical Concern about Next-Generation Sequencing

Platforms, Industry Sector

Biggest Technical Concern about Next-Generation Sequencing

Platforms, Academic Sector

Biggest Computational/IT Concern, Industry Sector

Biggest Computational/IT Concern, Academic Sector

Adequate Cost/Benefit from Next-Generation Sequencing, Industry

Sector

Adequate Cost/Benefit from Next-Generation Sequencing, Academic

Sector

Cost of Full Human Genome Sequence by 2010, Industry Sector

Cost of Full Human Genome Sequence by 2010, Academic Sector

Opinion on Platform Market Dominance, Industry Sector

Opinion on Platform Market Dominance, Academic Sector

Does Sanger Sequencing (Capillary) Play a Role after 2010, Industry

Sector?

Does Sanger Sequencing (Capillary) Play a Role after 2010, Academic

Sector?

Most Important Factors in Selecting a Next-Generation System,

Industry Sector

Most Important Factors in Selecting a Next-Generation System,

Academic Sector

Buy Sequence from a 3rd-Party Service Provider, Industry Sector?

Buy Sequence from a 3rd-Party Service Provider, Academic Sector?

Table of Contents

Chapter 1: INTRODUCTION

1.1. Background

1.2. Scope and Nature of the Report

Chapter 2: HISTORY AND EVOLUTION OF SEQUENCING

TECHNOLOGY

2.1. Frederick Sanger & Early DNA Sequencing

2.2. Leroy Hood Pioneers Semi-Automated Sequencing

2.3. The Human Genome Project and

Celera Genomics: Race On

2.4. The $1,000 Genome & Next-Generation Systems

Chapter 3: SEQUENCING TECHNOLOGIES:

NEXT-GENERATION AND BEYOND

3.1. Current Next-Generation Sequencers

Roche/454 Life Sciences

Illumina

Applied Biosystems

Helicos

3.2. Sequencers Currently in Development

Complete Genomics

BioNanomatrix

VisiGen

Pacific Biosciences

Dover Systems

Intelligent Bio-Systems

ZS Genetics

Reveo

LightSpeed Genomics

3.3. Nanopore-Based Systems

NABsys

Oxford Nanopore Technologies

3.4. Performance Comparisons

3.5. Bioinformatics

3.6. Sample Preparation

3.7. National Human Genome Research Institute (NHGRI)

Funding

3.8. Intellectual Property Issues

Chapter 4: APPLICATIONS OF NEXT-GENERATION

SEQUENCING TECHNOLOGIES

4.1. Whole-Genome Sequencing

The 1,000 Genomes Project

Exon Sequencing

Accuracy and Precision in Genetic Variation Studies

4.2. RNA Sequencing

4.3. Gene Regulation and Control Analysis

4.4. Disease Diagnosis and Prediction

Cancer Genomics

Personal Genomics

4.5. Metagenomics

Chapter 5: MARKET DYNAMICS

5.1. Deals

5.2. User Survey Results

Chief Application for Next-Generation DNA Sequencing

Main Organism for Next-Generation Sequencing

User Experience with Next-Generation Platform, Industry Segment

Next-Generation Platform Predicted to Dominate in 2–3 Years

Most Exciting Third-Generation Platform

Applications to Benefit Most from Next-Generation Sequencing

Research Areas to Benefit Most from Next-Generation Sequencing

Greatest Technical Concern about Next-Generation Sequencing

Platforms

Greatest Computational/IT Concern

Adequate Cost/Benefit from Next-Generation Sequencing

Cost of Full Human Genome Sequence by 2010

Opinion on Platform Market Dominance

Future of Sanger Sequencing

Most Important Factors in Selecting a Next-Generation System

Opinion on Acquiring Sequence from a Service Provider

5.3. The Competitive Environment

Chapter 6: OBSERVATIONS AND CONCLUSIONS

CHAPTER 7: INTERVIEW TRANSCRIPTS

7.1. Clifford Reid, PhD, Chairman, President, & CEO, Complete

Genomics

7.2. Patrice Milos, PhD, VP & Chief Scientific Officer, Helicos

BioSciences

7.3. Steven Salzberg, PhD, Director, Center for Bioinformatics

and Computational Biology, University of Maryland

7.4. Todd Smith, PhD, Chief Science Officer, Geospiza

7.5. Anonymous Academic Researcher Active in Next-

Generation Sequencing

7.6. Stephen Naylor, PhD, CSO & Chairman, Predictive

Physiology and Medicine (PPM)

References

Company Index with Web Addresses

InsightPharmaReports.com


Related Conference

CO-LOCATED SEQUENCING CONFERENCES

CHI’s Second Annual

Next-Generation Sequencing Data Analysis

September 21–23, 2009

Rhode Island Convention Center | Providence, RI

and

CHI’s Third Annual

Exploring Next-Generation Sequencing

September 21–23, 2009

For details and to register, visit: www.healthtech.com

Related Report

Bioinformatics and Computational Biology:

Bottlenecks and Options

The interdisciplinary fields of Bioinformatics and Computational Biology are

locked in a high stacks race with analytical instrument developers and innovators.

The pace and scope of change in many fields of biomedical research

rivals what we once associated only with semiconductor devices. This report

explores the interlocking challenges facing instrumentation advances,

computational demands and our evolving systems biology knowledge. Key

challenges presented in this report include:

• Instrumentation capable of generating terabytes of raw data daily

• Storage requirements for human gene sequences

• Need for cross-platform data analysis standards

• Appropriateness of analysis and modeling applications

• Database data quality and annotation protocols

Get FREE sample pages, view full details and order this report

at InsightPharmaReports.com

About Insight Pharma Reports

CHI Insight Pharma Reports are written by experts who collaborate

with CHI to provide a series of reports that evaluate the salient trends

in pharmaceutical technology, business, and therapy markets.

Insight Pharma Reports are used by senior decision makers at life

science companies to keep abreast of the latest advances in pharmaceutical

R&D, their potential applications and business impacts. Our

clients include the top 50 pharmaceutical companies, top 100 biotechnology

companies, and top 100 vendors of life science products

and services. Typical purchasers are managers, directors, and VPs

in business development, discovery research, clinical develop ment,

strategic planning, portfolio management, new product planning,

and marketing.

Insight Pharma Reports offer:

• Current information and analysis of R&D technologies, therapeutic

markets, and critical business issues.

• Analysis of the probability of success for various applications of

each technology.

• Expert insight based on interviews with key personnel in companies

at the forefront of technological advances who share their

views on their technology’s current status, applications, future

direction, and market environment.

Barnett Educational Services Leading Industry Publication

New Drug Development: A Regulatory Overview: A critical resource that addresses

the most cutting-edge developments redefining how new drugs are developed and regulated

today. For more information, visit www.barnettinternational.com or call 800-856-2556

Yes! I would like to receive a FREE subscription to:

r

r

r

Innovative management in clinical trials

Informatics tools and strategies driving decisions

The latest industry news, commentary, and highlights from

Bio•IT World

Next-Generation Sequencing: Solving the Genome

Print

Single-Site/Operational Unit License*

Next-Generation Sequencing: Solving the Genome — June 2009 (164 pages) c $2,995.00 c $3,750.00

Bioinformatics and Computational Biology — May 2009 (134 pages) c $2,995.00 c $3,750.00

Purchase both reports and receive a 10% discount

*Single-site licenses are multi-user, searchable, cut-and-paste ready PDFs

Call for global license pricing; contact David Cunningham at 781-972-5472 or cunningham@healthtech.com

Total: $_________________

Choose a payment option:

1. c Enclosed is a check order payable to Cambridge Healthtech Publishing, in U.S. currency. (In Massachusetts, add 5% sales tax.)

2. c Purchase order number ____________________________

3. Credit card: c Amex c Visa c MC ___________________________________________________Exp. Date:__________Sec. Code:____________________

Cardholder: ________________________________________________________ Signature____________________________________________________________

c Mr. c Ms. c Mrs. c Dr. First Name:_______________________Last Name__________________________________________________________

Job Title:__________________________Div./Dept.________________________ Company____________________________________________________________

Address (please include Mail Stop, Room or Bldg. #):_________________________________________________________________________________________

City/State/Postal Code:______________________________________________ Country:_____________________________________________________________

Telephone:___________________________Fax:__________________________ E-Mail:______________________________________________________________

Please refer to the key code below

TO ORDER:

Web: InsightPharmaReports.com

Phone: 781-972-5444

Fax: 781-972-5425

E-mail: rlaraia@healthtech.com

Mail: Rose LaRaia

250 First Avenue, Suite 300

Needham, MA 02494

More magazines by this user
Similar magazines