Next Generation Sequencing Trends (Clinical Applications, Systems Used, Accreditation Status, Regulated Patient Sample Handling and Other Trends)

Jul 1, 2013
159 Pages - Pub ID: KLI5088424
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Next Generation Sequencing Trends (Clinical Applications, Systems Used, Accreditation Status, Regulated Patient Sample Handling and Other Trends)

Next-generation sequencing is discussed frequently as a key to clinical diagnostics in the future. This report looks at the status of NGS today, and seeks to provide insights on the “on-the-ground” status of clinical sequencing. In the course of doing this, the report seeks to answer the following questions: What is the status of clinical applications for Next Gen in laboratories currently? What vendors are winning? What systems are seeing usage and for what applications? How are labs responding to business pressures and regulatory challenges? What disease areas are seeing the most applications? What are labs future purchasing plans and how are clinical applications driving these decisions?

This study, Next Generation Sequencing Trends focuses on an email and telephone consultation of 110 laboratories which was carried out from April to June of 2013, with the majority in the latter portion. The survey effort targeted labs likely to be doing, or likely to be planning, applications of sequencing in either diagnostic or clinical research settings. Due to the increasing importance of 2nd and 3rd-generation systems in the market, the scope leans towards these types of sequencers. There are only 13 laboratories that have exclusively capillary systems, but these systems are still widely used. About 30% of the systems in the respondents’ labs overall are capillary systems. The mix of labs reached in the surveys provides both a range of industry segments as well as groups of labs with both types of systems.

The survey asked labs about the following trends in Next Generation Sequencing and provides insights into the status of sequencing applications, including the following:
  • Number of Sequencers Owned
  • Models Owned
  • Applications Run
  • Number of Samples Run
  • Outsourcing Trends
  • Accreditation Status For Regulated Patient Samples
  • Future Accreditation Plans
  • Sequencers Used for Regulated Patient Samples
  • Volume Change Expected In NGS
  • Use of Capillary Systems and Expectation for Future
  • Bottlenecks in Sequencing Process
  • Future Purchase Plans
  • Data Analysis and Management Challenges
  • Other (non NGS) technologies Used
  • Regional Differences (Europe, US, ROW)
A particular focus of this report is on the clinical future of sequencing. Questions address how labs are dealing with the handling of regulated patient samples and what disease areas are seeing the most applications and sample runs. Labs were queried on which systems were seeing the most clinical applications and the usage. Capillary systems are covered in the survey’s scope, and survey details the extent to which these systems are used vs. NGS and what future purchasing plans are.

The survey was conducted by Justin Saeks the author of Kalorama Information's DNA Sequencing and Equipment Markets, published in several editions. The survey effort targeted any lab that uses a sequencer for any application, but with the goal of achieving as close a representative breadth of labs as possible. Due to the increasing importance of next generation systems in the market, the scope leans towards these types of sequencers. However, the market inevitably includes labs that use capillary systems as well.

Labs were mostly contacted by phone and asked to participate in a phone interview/survey for around 10 to 15 minutes. A small fraction of the labs completed the survey on a website set up with the questions. The survey included both open-ended and multiple-choice type questions. In most cases, 49% of labs, the lab manager was the party interviewed. Research scientists or associates were spoken to in 35% of cases. The remaining respondents were technicians, executives, professors or others.
I: EXECUTIVE SUMMARY
Scope
Methodology
Outline
Main Findings of the Study
II: DEMOGRAPHICS
Regional Distribution of Respondents
Industrial Distribution of Respondents
Laboratory Function of Respondents
Distribution by Number of Sequencers
Total Numbers of Systems in Labs
Numbers of 2nd and 3rd Generation Systems
Numbers of Capillary Systems
Brand(s)/ Types(s) of Sequencers Owned, Overall
Position/ Role of Respondents
III: SYSTEM INSTALLATIONS
Distribution of Sequencer Models
Installed Base by System Owned
Number of Systems Owned Per Lab
Installed Base by Region
USA, Europe, Rest of World
Installed Base, NextGeneration Systems
Installed Base, Capillary Systems
Installed Base by Industry Segment
Overall Brand/ Type
NextGeneration Systems
Capillary Systems
Installed Base by Laboratory Function
Overall Brand/ Type
NextGeneration Systems
Capillary / Gel Systems
Date of Installation
Distribution by NextGeneration vs Capillary
IV: SEQUENCER APPLICATIONS, CLINICAL APPLICATIONS, AND USAGE TRENDS
Sequencer Applications and Usage
Applications Run, Overall and by Brand/ Type
Likely Increases in Applications and Volume
by Brand of NextGeneration System Owned
Growth in Sequencing, NGS vs Capillary Systems
Capacity Usage of Systems
Outsourcing
Clinical Applications
Sequencing of CLIA Regulated Patient Samples
Verbatim Comments: Approaching Clinical Applications
Certification for Regulated Samples
Plans, Expectations for Certification & Usage
Time frame
Type of Accreditation Planned/ Considered
Change in Regulated Samples vs. NonRegulated Samples
Certified Labs
NonCertified Labs
Sequencers Used or Planned for Patient/ Human Samples
Regulated Patient/ Human Samples
Nonregulated Patient/ Human Samples
Disease/ Therapeutic Areas Where Sequencing Applied
Regulated Patient/ Human Samples
NonRegulated Patient/ Human Samples
Disease Areas Expected to Grow Fastest
Other Technologies Used for Patient/ Human Samples
Challenges for Growth of Clinical Sequencing
V: IMPROVEMENTS AND FUTURE PURCHASE PLANS
Changes or Improvements, NextGeneration Systems
Difficulty of Data Analysis & Data Management
Data Analysis Difficulty
Data Management Difficulty
TimeFrame of Purchase Plans
Overall
by Brand/ Type Owned
by Laboratory Function
by Region
Systems Likely to Consider for Purchase
Overall
by Brand/ Type Owned
by NextGeneration Systems vs Capillary Systems Owned
by Industry/ Segment
by Laboratory Function
by Region
LIST OF EXHIBITS
II: DEMOGRAPHICS
Table 2-1: Regional Distribution of Respondent Labs
Figure 2-1: Regional Distribution of Respondent Labs
Table 2-2: Primary Industry/ Segment Labs Belong To
Figure 2-2: Primary Industry/ Segment Labs Belong To
Table 2-3: Industry/ Segment(s) Labs Belong To, by Region
Table 2-4: Industry/ Segment(s) Labs Belong To, by Region
Figure 2-3: Industry/ Segment(s) Labs Belong To, by Region
Table 2-5: Major Function(s) of Respondent Labs
Figure 2-4: Major Function(s) of Respondent Labs
Table 2-6: Major Function(s) of Labs, by Region
Table 2-7: Major Function(s) of Labs, by Region
Figure 2-5: Major Function(s) of Labs, by Region
Table 2-8: Distribution of Total Sequencers in Labs
Figure 26: Distribution of Total Sequencers in Labs
Table 2-9: Number of NextGeneration Sequencers in Labs
Figure 2-7: Number of NextGeneration Sequencers in Labs
Table 2-10: Number of Capillary Sequencers in Labs
Figure 2-8: Number of Capillary Sequencers in Labs
Table 2-11: Brand(s)/ Type(s) of Sequencers Owned by Labs
Table 2-12: Number of a Given Brand / Type in Labs Owning That Type
Figure 2-9: Avg. Number of a Given Sequencer in Labs Owning That Type
Table 2-13: Position/ Role of Respondent
Figure 2-10: Position/ Role of Respondent
III: SYSTEM INSTALLATIONS
Table 3-1: Sequencer Models in Respondents’ Labs
Figure 3-1: Sequencer Models in Respondents’ Labs
Table 3-2: Installed Base of Labs, by System(s) Owned (# of Systems)
Table 3-3: Installed Base of Labs, by System(s) Owned (% of Systems)
Figure 3-2: Installed Base of Labs, by System(s) Owned (% of Systems)
Table 3-4: Installed Base of Labs, by System(s) Owned (% of Systems)
Table 3-5: Distribution of NGS vs. Capillary Systems (No. of Labs)
Figure 3-3: Distribution of NGS vs. Capillary Systems (No. of Labs)
Table 3-6: No. of NGS Systems by No. of Capillary Systems (% of Labs)
Figure 3-4: No. of NGS Systems by No. of Capillary Systems (% of Labs)
Table 3-7: No. of Capillary Systems by No. of NGS Systems (% of Labs)
Figure 3-5: No. of Capillary Systems by No. of NGS Systems (% of Labs)
Table 3-8: Number of Systems Installed in Labs, by Region
Table 3-9: Sequencer Models in Respondents’ Labs, by Region (No. of Systems)
Table 3-10: Sequencer Models in Respondents’ Labs, by Region (% of Systems)
Figure 3-6: Sequencer Models in Respondents’ Labs, by Region (% of Systems)
Table 3-11: NGS Models in Respondents' Labs, by Region (No. of Systems)
Table 3-12: NGS Models in Respondents' Labs, by Region (% of Systems)
Figure 3-7: NGS Models in Respondents' Labs, by Region (% of Systems)
Table 3-13: Capillary Models in Respondents' Labs, by Region (# of Systems)
Table 3-14: Capillary Models in Respondents' Labs, by Region (% of Systems)
Figure 38: Capillary Models in Respondents' Labs, by Region (% of Systems)
Table 3-15: Number of Systems Installed, by Industry/ Segment(s)
Table 3-16: Brand / Type of Sequencer Systems Installed, by Industry/ Segment (# of Systems)
Table 3-17: Brand / Type of Sequencer Systems Installed, by Industry/ Segment (% of Systems)
Figure 3-9: Brand / Type of Sequencer Systems Installed, by Industry/ Segment (% of Systems)
Table 3-18: Brand / Type of Sequencer Systems Installed, by Industry/ Segment (% of Systems)
Figure 3-10: Brand / Type of Sequencer Systems Installed, by Industry/ Segment (% of Systems)
Table 3-19: Number of NGS Systems Installed, by Industry/ Segment
Table 3-20: NextGeneration Models in Respondents' Labs, by Industry/ Segment (# of Systems)
Table 3-21: NextGeneration Models in Respondents' Labs, by Industry/ Segment (% of Systems)
Figure 3-11: NextGeneration Models in Respondents' Labs, by Industry/ Segment (% of Systems)
Table 3-22: NextGeneration Models in Respondents' Labs, by Industry/ Segment (% of Systems)
Figure 3-12: NextGeneration Models in Respondents' Labs, by Industry/ Segment (% of Systems)
Table 3-23: Number of Capillary Systems Installed in Labs Owning, by Industry/ Segment
Table 3-24: Number of Systems Installed by Laboratory Function
Table 3-25: Brand / Type of Sequencer System Installed, by Lab Function (# of Systems)
Table 3-26: Brand / Type of Sequencer System Installed, by Lab Function(% of Systems)
Figure 3-13: Brand / Type of Sequencer System Installed, by Lab Function (% of Systems)
Table 3-27: Brand / Type of Sequencer System Installed, by Lab Function(% of Systems)
Table 3-14: Brand / Type of Sequencer System Installed, by Lab Function(% of Systems)
Table 3-28: Number of NGS Installed in Labs Owning, by Lab Function
Table 3-29: NGS Models in Respondents' Labs, by Lab Function (# of Systems)
Table 3-30: NGS Models in Respondents' Labs, by Lab Function (% of Systems)
Figure 3-15: NGS Models in Respondents' Labs, by Lab Function (% of Systems)
Table 3-31: NGS Models in Respondents' Labs, by Lab Function (% of Systems)
Figure 3-16: NGS Models in Respondents' Labs, by Lab Function (% of Systems)
Table 3-32: Number of Capillary Systems Installed in Labs Owning,by Lab Function
Table 3-33: Recent Systems Installed, 2001 Q2 2013 (# of Systems)
Figure 3-17: Date of Recent System Installation, 20012013
Table 3-34: Recent NGS Systems Installed, 2007 – Q2 2013 (# of Systems)
Figure 3-18: Date of Recent NGS Installation (# of Systems)
IV: SEQUENCER APPLICATIONS, CLINICAL APPLICATIONS, AND USAGE TRENDS
Table 4-1: NGS Application Volume by Model (% of Sequencing)
Figure 4-1: NGS Application Volume by Model (% of Sequencing)
Table 4-2: Applications Expected to Increase the Most
Figure 4-2: Applications Expected to Increase the Most Overall
Table 4-3: Applications Expected to Increase, by NGS Brand Owned (# of Labs)
Table 4-4: Applications Expected to Increase, by NGS Brand Owned (% of Labs)
Figure 4-3: Applications Expected to Increase, by NGS Brand Owned (% of Labs)
Table 4-5: Expected Growth in Sequencing Volume (# of Labs)
Table 4-6: Expected Growth in Sequencing Volume (% of Labs)
Figure 4-4: Expected Growth in Sequencing Volume (% of Labs)
Table 4-7: Avg. Percentage of Systems’ Capacity Used, by Brand
Figure 4-5: Percentage of Systems’ Capacity Used, by Brand
Table 4-8: Percentage of Sequencing Volume Outsourced
Figure 4-6: Percentage of Sequencing Volume Outsourced
Table 4-9: Percentage of Sequencing Volume Outsourced, by Region
Table 4-10: Percentage of Sequencing Volume Outsourced, by Region
Table 4-11: Reasons for Outsourcing
Figure 4-7: Reasons for Outsourcing
Table 4-12: How Labs Address Sequencing of Regulated Patient Samples(# of Labs)
Table 4-13: How Labs Address Sequencing of Regulated Patient Samples(% of Labs)
Figure 4-8: How Labs Address Sequencing of Regulated Patient Samples(% of Labs)
Figure 4-14: Labs’ Certification for Regulated Patient Samples
Figure 4-9: Labs’ Certification for Regulated Patient Samples
Table 4-15: Plans for New or Additional Certification
Table 4-16: Plans for New or Additional Certification
Figure 4-10: Plans for New or Additional Certification
Table 4-17: Type of Accreditation Planned/ Considered (# of Labs)
Table 4-18: Type of Accreditation Planned/ Considered (% of Labs)
Figure 4-11: Type of Accreditation Planned/ Considered (% of Labs)
Table 4-19: Distribution of Samples, Est. 2013 (# of Labs)
Table 4-20: Distribution of Samples, Est. 2013 (% of Labs)
Figure 4-12: Distribution of Samples, Est. 2013 (% of Labs)
Table 4-21: Distribution of Samples, Expected 2014 (# of Labs)
Table 4-22: Distribution of Samples, Expected 2014 (% of Labs)
Figure 4-13: Distribution of Samples, Expected 2014 (% of Labs)
Table 4-23: Volume of Regulated vs. NonRegulated Samples (% of Sequencing)
Figure 4-14: Volume of Regulated vs. NonRegulated Samples, Est. 2013 (% of Sequencing)
Figure 4-15: Volume of Regulated vs. NonRegulated Samples, Expected 2014(% of Sequencing)
Table 4-24: Distribution of Samples, Est. 2013 (# of Labs)
Table 4-25: Distribution of Samples, Est. 2013 (% of Labs)
Figure 4-16: Distribution of Samples, Est. 2013 (% of Labs)
Table 4-26: Distribution of Samples, Expected 2014 (# of Labs)
Table 4-27: Distribution of Samples, Expected 2014 (% of Labs)
Figure 4-17: Distribution of Samples, Expected 2014 (% of Labs)
Table 4-28: Volume of Regulated vs. NonRegulated Samples, Est. 2013(% of Sequencing)
Figure 4-18: Volume of Regulated vs. NonRegulated Samples, Est. 2013(% of Sequencing)
Figure 4-19: Volume of Regulated vs. NonRegulated Samples, Expected 2014(% of Sequencing)
Table 4-29: Distribution of Samples, Est. 2013 (# of Labs)
Table 4-30: Distribution of Samples, Est. 2013 (% of Labs)
Figure 4-20: Distribution of Samples, Est. 2013 (% of Labs)
Table 4-31: Distribution of Samples, Expected 2014 (# of Labs)
Table 4-32: Distribution of Samples, Expected 2014 (% of Labs)
Figure 4-21: Distribution of Samples, Expected 2014 (% of Labs)
Table 4-33: Sequencers Used for Regulated Patient Samples
Figure 4-22: Sequencers Used for Regulated Patient Samples (% of Systems)
Table 4-34: Sequencers Likely to be Used for Regulated Patient Samples (% of Labs)
Figure 4-23: Sequencers Likely to be Used for Regulated Patient Samples (% of Labs)
Table 4-35: Sequencers Used for NonRegulated Patient/Human Samples
Figure3-24: Sequencers Used for NonRegulated Patient/Human Samples (% of Systems)
Table 4-36: Disease Areas Where Sequencing Applied, by NGS vs Capillary (Percentage and Number of Systems)
Figure 4-25: Disease Areas Where Sequencing Applied, by NGS vs Capillary
Table 4-37: Disease Areas Where Sequencing Applied, by NGS vs Capillary(% of Volume)
Figure 4-26: Disease Areas Where Sequencing Applied, by NGS vs Capillary (% of Volume)
Table 4-38: Regulated Sequencing Expected to Grow Fastest
Figure 4-27: Regulated Sequencing Expected to Grow Fastest (% of Labs)
Table 4-39: NonRegulated Patient/ Human Sequencing Expected to Grow Fastest
Figure 4-28: NonRegulated Patient/ Human Sequencing Expected to Grow Fastest
Table 4-40: Other Technologies Used in Lab
Figure 4-29: Other Technologies Used in Lab (% of Labs)
Table 4-41: Challenges for Growth of Clinical Sequencing
V: IMPROVEMENTS AND FUTURE PURCHASE PLANS
Table 5-1: Major Changes or Improvements Wanted by EndUsers
Figure 5-1: Major Changes or Improvements Wanted by EndUsers
Table 5-2: Bottleneck in Sequencing Process
Figure 5-2: Bottleneck in Sequencing Process
Table 5-3: Difficulty Level of Data Analysis
Figure 5-3: Difficulty Level of Data Analysis
Table 5-4: Difficulty Level of Data Management
Figure 5-4: Difficulty Level of Data Management
Table 5-5: Time Frame for Future Purchase
Figure 5-5: Time Frame for Future Purchase
Table 5-6: Time Frame for Future Purchase, by Brand Owned (# of Labs)
Table 5-7: Time Frame for Future Purchase, by Brand Owned (% of Labs)
Table 5-8: Time Frame for Future Purchase, by Lab Function (# of Labs)
Table 5-9: Time Frame for Future Purchase, by Lab Function (% of Labs)
Table 5-10: Time Frame for Future Purchase, by Region (# of Labs)
Table 5-11: Time Frame for Future Purchase, by Region (% of Labs)
Figure 5-6: Time Frame for Future Purchase, by Region (% of Labs)
Table 5-12: Sequencer Models Likely to Consider
Figure 5-7: Sequencer Models Likely to Consider (% of Labs)
Table 5-13: Sequencer Models Likely to Consider, by Brand/ Type Owned (# of Labs)
Table 5-14: Sequencer Models Likely to Consider, by Brand/ Type Owned (% of Labs)
Figure 5-8: Sequencer Models Likely to Consider, by Brand/ Type Owned (% of Labs)
Table 5-15: Sequencer Models Likely to Consider, by Industry/ Segment Owned (# of Labs)
Table 5-16: Sequencer Models Likely to Consider, by Industry/ Segment Owned (# of Labs)
Table 5-17: Sequencer Models Likely to Consider, by Lab Function (# of Labs)
Table 5-18: Sequencer Models Likely to Consider, by Lab Function (% of Labs)
Table 5-19: Sequencer Models Likely to Consider, by Region (# of Labs)
Table 5-20: Sequencer Models Likely to Consider, by Region (% of Labs)
Figure 5-9: Sequencer Models Likely to Consider, by Region (% of Labs)

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