Sample Preparation and Library Preparation for DNA Sequencers (Results of The Kalorama Survey of Labs)

Report Summary

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.

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

CHAPTER ONE: INTRODUCTION & DEMOGRAPHICS

Introduction
Scope
Methodology
Outline
Demographics

Industrial Distribution of Respondents’ Labs
           Laboratory Function of Respondents’ Labs
           Distribution by Number of Sequencers
           Total Numbers of Systems in Labs
           Numbers of 2nd and 3rd Generation Systems
           Numbers of Capillary/ Gel Systems
           Brand(s)/ Types(s) of Sequencers Owned, Overall
           Position/ Role of Respondents
Analyst Findings

CHAPTER TWO: SYSTEM INSTALLATIONS

Overall Installed Base
           Distribution of Sequencer Models
           Overall Totals
           Versions of 2nd-Generation Systems

Installed Base by Region
           Overall Brand/ Type
           Next-Generation Systems
           Capillary / Gel Systems

Installed Base by Industry Segment
           Overall Brand/ Type
           Next-Generation Systems
           Capillary / Gel Systems
           Overall Brand/ Type
           Next-Generation Systems
           Capillary / Gel Systems
           Distribution by Next-Generation vs Capillary
           Distribution by Next-Generation Model

CHAPTER THREE: APPLICATIONS AND USAGE TRENDS

Applications
           Applications / Libraries Run, Overall and by Brand/ Type
           Applications Run; Next-Generation Systems Only
           Applications Likely to Increase the Most
           Overall

Next-Generation vs Capillary Systems
           by Brand of Next-Generation System Owned
           Types of Sample Being Studied
           Frequency of Sequencer Runs
           Next-Generation Systems
           Capillary Systems
           Kits/ Products Used for DNA and RNA Extraction and Purification
           Overall
           By Next-Generation Sequencing vs Capillary/ Gel Sequencing
           By Brand of Next-Generation Sequencer
           Fragmentation Systems/ Products Used for Next-Generation Sequencing
           Overall
           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

TABLE OF EXHIBITS

CHAPTER ONE: INTRODUCTION & DEMOGRAPHICS

Exhibit 1: Regional Distribution of Labs (North America, Europe, Asia-Pacific, R.O.W)
Exhibit 2: Industrial Distribution of Labs (Academia, Hospital, Indep. Research/ Non-profit, Contract Rsch/ Svcs, Gov’t, Other)
Exhibit 3: Industrial Distribution of Labs, by Region (# of Labs)
Exhibit 4: Industrial Distribution of Labs, Cross-Referenced by Region (% of Labs)
Exhibit 5: Major Function(s) of Labs (Core Lab, Service Provider, Research, Genome Center, Diagnostics, Teaching, Bioinformatics, Overall)
Exhibit 6: Major Function(s) of Labs, by Region (# of Labs)
Exhibit 7: Major Function(s) of Labs, Cross Referenced by Region (% of Labs)
Exhibit 8: Distribution of Total Number of Sequencers in Respondent Labs
Exhibit 9: Distribution of Number of Next-Generation Sequencers in Labs
Exhibit 10: Distribution of Number of Capillary/ Gel Sequencers in Labs
Exhibit 11 Brands/ Types of Sequencers Owned Overall in Respondent Labs (Next gen., ABI/Life Tech., ABI Capillary/ Gel, Illumina, 454, ABI SOLiD, No sequencer)
Exhibit 12: Average Number of Sequencers in Respondent Labs, by Brand/ Type
Exhibit 13: Distribution of Positions/ Roles of Respondents

CHAPTER TWO: SYSTEM INSTALLATIONS

Exhibit 14: Installed Base of Respondent Labs, by Model
Exhibit 15: Distribution of ABI SOLiD System Versions in Respondents’ Lab
Exhibit 16: Average Number of Systems Installed in Respondent Labs, by Region (N. America, Europe, Asia, R.O.W.)
Exhibit 17: Sequencer Models in Respondent Labs, by Region (# of Systems)
Exhibit 18: Sequencer Models in Respondent Labs, by Region (% of Systems)
Exhibit 19: Next-Gen Sequencer Models in Respondent Labs, by Region (# of Systems)
Exhibit 20: Next-Gen Sequencer Models in Respondent Labs, by Region (% of Systems)
Exhibit 21: Capillary and Gel Sequencer Models in Labs, by Region (# of Systems)
Exhibit 22: Capillary and Gel Sequencer Models in Labs, by Region (% of Systems)
Exhibit 23: Average Number of Sequencers Installed by Industry/ Segment (Academic, Hospital, Indep. Rsch/ Non-profit, Contract Research/ Svcs, Government, Other)
Exhibit 24: Industrial Distribution of Systems, by Brand/ Type (# of Systems)
Exhibit 25: Industrial Distribution of Systems, by Brand/ Type (% of Systems)
Exhibit 26: Brand/ Type of Sequencer System Installed, Cross-Referenced by Industry/ Segment (% of Systems)
Exhibit 27: Number of Next-Generation Systems in Labs Owning, by Industry/ Segment (Academic, Hospital, Indep. Rsch/ Non-profit, Contract Rsch/ Svcs, Gov’t, Other)
Exhibit 28: Industrial Distribution of Next-Generation Sequencers, by Model (# of Systems)
Exhibit 29: Industrial Distribution of Next-Generation Sequencers, by Model (% of Systems)
Exhibit 30: Next-Generation Models in Respondent Labs, by Industry/ Segment (% of Systems)
Exhibit 31: Capillary/Gel Systems Installed in Lab Owning, by Industry/Segment (Academic, Hospital, Indep. Rsch/ Non-profit, Contract Rsch/ Svcs, Gov’t, Other)
Exhibit 32: Industrial Distribution of Capillary/Gel Sequencers, by Model (# of Systems)
Exhibit 33: Industrial Distribution of Capillary/Gel Sequencers, by Model (% of Systems)
Exhibit 34: Capillary/ Gel Sequencer Models in Labs, by Industry/ Segment (% of Systems)
Exhibit 35: Average Number of Systems Installed by Laboratory Function
Exhibit 36: Distribution of Systems by Lab Function, by Brand/ Type (# of Systems)
Exhibit 37: Distribution of Systems by Lab Function, by Brand/ Type (% of Systems)
Exhibit 38: Brand/Type of System Installed, Cross-Referenced by Lab Function (% of Systems)
Exhibit 39: Average Number of Next-Generation Systems in Labs Owning, by Lab Function
Exhibit 40: Next Generation Models in Respondent’s Labs, by Lab Function (# of Systems)
Exhibit 41: Distribution of Next-Generation Systems by Lab Function, Cross-Referenced by Model (% of Systems)
Exhibit 42: Next Generation Models in Respondent Labs, by Lab Function (% of Systems)
Exhibit 43: Average Number of Capillary/ Gel Systems in Labs Owning, By Lab Function
Exhibit 44: Distribution of Capillary/ Gel Sequencers by Lab Function, by Model (# of Systems)
Exhibit 47: Age of Next-Generation and Capillary Systems Installed in Labs, Q1 2000 - Q4 2004
Exhibit 48: Age of Next-Generation and Capillary Systems Installed in Labs, Q1 2005 - Q3 2010
Exhibit 49: Age of Next-Generation Systems in Respondent Labs by Model, Q3 2005 - Q3 2010

CHAPTER THREE: APPLICATIONS AND USAGE TRENDS

Exhibit 50: Distribution of Runs/ Libraries by Application, by Brand/ Type (% of Samples)
Exhibit 51: Applications Expected to Increase the Most
Exhibit 52: Applications Expected to Increase the Most, for Next-Generation Systems
Exhibit 53: Applications Expected to Increase the Most, Capillary/Gel System Owners
Exhibit 54: Applications Expected to Increase the Most, by Brand/ Type Owned (# of Labs)
Exhibit 55: Applications Expected to Increase the Most, by Brand/ Type Owned (% of Labs)
Exhibit 56: Main Types of Samples Being Sequenced in Labs (Human, Bacteria, Plant, Agricultural, Animals, Variety, Other)
Exhibit 57: Frequency that Next-Generation Systems are Running (# of Systems)
Exhibit 58: Frequency that Next-Generation Systems are Running (% of Systems)
Exhibit 59: Distribution of Number of Plates Run per Week, for Capillary Systems
Exhibit 60: Brand(s) of DNA/ RNA Extraction and Purification Products Used, Overall
Exhibit 61: Brand(s) of DNA/RNA Extraction and Purification Products; Next-Generation vs. Capillary/ Gel Systems (# of Labs)
Exhibit 62: Brand(s) of DNA/RNA Extraction and Purification Products; Next-Generation vs. Capillary/ Gel Systems (% of Labs)
Exhibit 63: Brand(s) of DNA/RNA Extraction and Purification Products, by Next-Generation Sequencer Brand (# of Labs)
Exhibit 64: Brand(s) of DNA/RNA Extraction and Purification Products, by Next-Generation Sequencer Brand (% of Labs)
Exhibit 65: Fragmentation Systems/ Products Used for Next-Generation Sequencing
Exhibit 66: Fragmentation Systems/ Products Used for Next-Generation Sequencing, by Brand of Sequencer (# of Labs)
Exhibit 67: Fragmentation Systems/ Products Used for Next-Generation Sequencing, by Brand of Sequencer (% of Labs)
Exhibit 68: Library Preparation Kits/ Products Used for Next-Generation Sequencing, by Brand of Sequencer (# of Labs)
Exhibit 69: Library Preparation Kits/ Products Used for Next-Generation Sequencing, by Brand of Sequencer (% of Labs)
Exhibit 70: Distribution of Targeted Enrichment Systems Used by Labs
Exhibit 71: Distribution of Systems Used to Check Concentration, Size, Quality
Exhibit 72: Brands of Polymerase/ Amplification Products Used in Sequencing Reaction
Exhibit 73: Dye(s) Used in Sequencing Reaction
Exhibit 74: Sequencing Reaction Cleanup Products Used for Capillary/ Gel Sequencing
Exhibit 75: Liquid Handlers/ Robotics Used for Sequencing Applications

CHAPTER FOUR: PREFERENCES AND EVALUATIONS

Exhibit 76: Criteria for Choosing Sample/ Library Preparation Products, Overall
Exhibit 77: Criteria for Choosing Sample/ Library Preparation Products, by Next-Generation vs Capillary (# of Labs)
Exhibit 78: Criteria for Choosing Sample/ Library Preparation Products, by Next-Generation vs Capillary (% of Labs)
Exhibit 79: Criteria for Choosing Sample/ Library Preparation Products, by Next-Generation Sequencer Brand (# of Labs)
Exhibit 80: Criteria for Choosing Sample/ Library Preparation Products, by Next-Generation Sequencer Brand (# of Labs)
Exhibit 81: Labs’ Satisfaction Ratings of System Features by Brand/ Type (1-very dissatisf., 2-somewhat dissatisf., 3-avg. or indifferent, 4-slightly satisf., 5-very satisf.)
Exhibit 82: Satisfaction Ratings of Next-Generation System Features by Brand (1-very dissatisf., 2-somewhat dissatisf., 3-avg. or indifferent, 4-slightly satisf., 5-very satisf.)
Exhibit 83: Feature or Process Most Wanted to Change or Improve, by Brand/ Type (# of Labs)
Exhibit 84: Feature(s) or Process Most Wanted to Change or Improve, by Brand/ Type (% of Labs)
Exhibit 85: Main Bottleneck(s) in Sequencing Process (# of Labs)
Exhibit 86: Main Bottleneck(s) in Sequencing Process (% of Labs)

CHAPTER FIVE: FUTURE PURCHASE PLANS

Exhibit 87: Time Frame for Sequencer Purchase Plan(s)
Exhibit 88: Time Frame(s) for Sequencer Purchase Plan(s) (# and % of Systems)
Exhibit 89: Time Frame(s) for Sequencer Purchase Plan(s), by Brand/ Type Owned (# of Systems)
Exhibit 90: Time Frame(s) for Sequencer Purchase Plan(s), by Brand/ Type Owned (% of Systems)
Exhibit 91: Sequencer Models Likely to Consider for Future Purchase
Exhibit 92: Barriers or Issues Hindering 2nd and 3rd Generation Sequencers (# of Labs)
Exhibit 93: Barriers or Issues Hindering 2nd and 3rd Generation Sequencers (% of Labs)