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Sample Preparation and Library Preparation for DNA Sequencers
(Results of The Kalorama Survey of Labs)
January 1, 2011
Sample preparation and library preparation are important steps in the DNA sequencing
process with specialized products and companies. Based on a survey of labs worldwide
conducted by Kalorama's biotech analyst Justin Saeks, this report provides detailed
information on the current state of DNA sequencing sample preparation and library
preparation for next-generation systems, as well as sample preparation, cycle
sequencing and sequencing reaction cleanup with capillary systems. The report's
perspective is demand-side, focusing on what labs are doing today.
The information in the report from survey results includes:
Number of Sequencers and Models Owned
Typical Applications and Libraries Run (by percentage)
How Often or How Many Samples (runs, samples, slides, flow cells, plates,
multiplexed or not) and Typical Output (reads, read length)
Changes Sought in Sequencer Features, or Steps in the Sequencing Process
Main Bottlenecks in Sequencing Process
Sources of the Samples (human, bacteria, plant)
Types of Targeted Enrichment Products Used
Systems Used for Checking Concentration, Size, and/or Quality
Importance of Cost, Throughput, Flexibility, Reproducibility, Robustness, User-
Friendliness, Accuracy and other factors
Brands Used for DNA or RNA Extraction and Purification
Brands Used for Fragmentation and Library Preparation
Brands Used for Amplification/ Polymerases, Dyes, and Sequencing Cleanup
Third Party Liquid Handlers Used
Barriers to 2nd- and 3rd-generation Sequencer Use
Analyst Findings
The study focuses on a survey of 120 laboratories which was carried out from July to
September of 2010, with the majority in the latter portion. Along with questions about
the specific sequencers used in the labs, the respondents were asked about the sample
preparation and library preparation kits, reagents, and other consumables used for
sequencing.

2. The survey effort targeted any lab that uses sequencing for any application, but with the
goal of achieving as close as possible a representative breadth of labs. Due to the
increasing importance of 2nd- and 3rd-generation systems in the market, the scope
leans towards these types of sequencers.
However, the market inevitably also includes capillary sequencers, as 47 of the 87
surveyed labs with next-generation systems also have capillary sequencers. Around a
third of the systems in the respondents’ labs overall are capillary systems. The mix of
labs reached in the survey provides both diverse industry segments, as well as groups
of labs with both types of systems, only capillary systems, or only next-generation
systems.
Table of Contents
TABLE OF CONTENTS
CHAPTER ONE: INTRODUCTION & DEMOGRAPHICS
Introduction
Scope
Methodology
Outline
Demographics
Industrial Distribution of Respondents’ Labs
o Laboratory Function of Respondents’ Labs
o Distribution by Number of Sequencers
o Total Numbers of Systems in Labs
o Numbers of 2nd and 3rd Generation Systems
o Numbers of Capillary/ Gel Systems
o Brand(s)/ Types(s) of Sequencers Owned, Overall
o Position/ Role of Respondents
Analyst Findings
CHAPTER TWO: SYSTEM INSTALLATIONS
Overall Installed Base
o Distribution of Sequencer Models
o Overall Totals
o Versions of 2nd-Generation Systems
Installed Base by Region
o Overall Brand/ Type
o Next-Generation Systems
o Capillary / Gel Systems
Installed Base by Industry Segment
o Overall Brand/ Type
o Next-Generation Systems

3. o Capillary / Gel Systems
o Overall Brand/ Type
o Next-Generation Systems
o Capillary / Gel Systems
o Distribution by Next-Generation vs Capillary
o Distribution by Next-Generation Model
CHAPTER THREE: APPLICATIONS AND USAGE TRENDS
Applications
o Applications / Libraries Run, Overall and by Brand/ Type
o Applications Run; Next-Generation Systems Only
o Applications Likely to Increase the Most
o Overall
Next-Generation vs Capillary Systems
o by Brand of Next-Generation System Owned
o Types of Sample Being Studied
o Frequency of Sequencer Runs
o Next-Generation Systems
o Capillary Systems
o Kits/ Products Used for DNA and RNA Extraction and Purification
o Overall
o By Next-Generation Sequencing vs Capillary/ Gel Sequencing
o By Brand of Next-Generation Sequencer
o Fragmentation Systems/ Products Used for Next-Generation Sequencing
o Overall
o By Brand of Next-Generation Sequencer
Library Preparation Kits/ Products Used for Next-Generation Sequencing
Targeted Enrichment Systems Being Used
Polymerase/ Amplification Kits Used in Sequencing Reaction for Capillary/ Gel
Systems
Dye(s) Used in the Sequencing Reaction for Capillary/ Gel Systems
Sequencing Reaction Cleanup Products Used for Capillary/ Gel Sequencing
Liquid Handlers/ Robotics Used for Sequencing
CHAPTER FOUR: PREFERENCES AND EVALUATIONS
Overall
By Next-Generation Sequencing vs Capillary/ Gel Sequencing
By Brand of Next-Generation Sequencer
CHAPTER FIVE: FUTURE PURCHASE PLANS
Time Frame
Models
Barriers to Next-Gen Use

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