Author: Ken Rubenstein, PhD
Executive Summary v
Evolution of NGS technologies v
State of the art v
Systems and technologies on the horizon vii
Market dynamics viii
CHAPTER 1
Introduction 1
1.1 Scope and contents of this report 2
CHAPTER 2
Evolution of NGS 3
2.1 Classical sequencing and early applications 3
2.2 The Human Genome Project 5
2.3 First-generation sequencing 6
2.4 The Omics Era and the search for gene-disease associations 7
2.5 Origins and early development of next-generation sequencers 7
CHAPTER 3
State of the Art 10
3.1 Technologies currently on, or very near, the market 10
Illumina 10
Life Technologies 12
Complete Genomics 14
Roche/454 Life Sciences 17
Helicos BioSciences 19
Pacific Biosciences 20
Ion Torrent 25
3.2 Comparative performance of systems currently on the market or nearly so 25
3.3 Bioinformatics 27
3.4 Sample preparation 33
CHAPTER 4
Systems and Technologies on the Horizon 37
4.1 Corporate programs 37
Illumina Avantome 37
Oxford Nanopore Technologies 38
Electronic Bio Sciences 40
General Electric Global Research 43
GnuBio 43
BioNanomatrix 44
Halcyon Molecular 44
IBM 45
Intelligent Bio-Systems 46
Life Technologies Starlight 47
LightSpeed Genomics 47
NABsys 48
NobleGen 49
ZS Genetics 50
4.2 Academic contributions 51
Graphene Nanopores 51
Other nanopore work 52
CHAPTER 5
Market Dynamics 54
5.1 Competitive environment in the sequencing market through 2011 54
5.2 Possible scenario through 2012 56
5.3 Prospects for diagnostic applications of NGS 58
5.4 Deals and deal patterns 59
Instrumentation 59
Informatics 60
Sample preparation 61
5.5 User survey results and discussion 63
Identification of respondents 63
Nature of NGS activities 64
Informatics activities 65
Sequencer attributes 66
5.6 Survey Results from a Recent Bio-IT World Survey 70
CHAPTER 6
Conclusions and Trends 73
6.1 Sequencing—The Next Generation 73
6.2 Translational medicine aspects of NGS 77
Sample handling 79
Data handling 79
CHAPTER 7
Interview Transcripts 81
Geoffrey Barrall, Ph.D., President, Electronic BioSciences 81
Stephen Turner, Ph.D., Founder and CTO, Pacific Biosciences 85
Clifford Baron, Director Biology Product Marketing, Accelrys 89
Clifford Reid, Ph.D., Co-founder, President, CEO, and Chairman, Complete Genomics 94
Jeffery Schloss, Ph.D., Program Director, U.S. National Human Genome Research Institute 99
Todd Smith, CTO, Geospiza 103
References 109
About Cambridge Healthtech Institute 118