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

Abstract

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.

Table of Contents

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, Next-Generation Systems
  • Installed Base, Capillary Systems
  • Installed Base by Industry Segment
  • Overall Brand/ Type
    • Next-Generation Systems
    • Capillary Systems
  • Installed Base by Laboratory Function
  • Overall Brand/ Type
    • Next-Generation Systems
  • Capillary / Gel Systems
  • Date of Installation
    • Distribution by Next-Generation 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 Next-Generation 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. Non-Regulated Samples
    • Certified Labs
    • Non-Certified Labs
    • Sequencers Used or Planned for Patient/ Human Samples
    • Regulated Patient/ Human Samples
    • Non-regulated Patient/ Human Samples
  • Disease/ Therapeutic Areas Where Sequencing Applied
  • Regulated Patient/ Human Samples
  • Non-Regulated 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, Next-Generation Systems
  • Difficulty of Data Analysis & Data Management
  • Data Analysis Difficulty
  • Data Management Difficulty
  • Time-Frame 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 Next-Generation Systems vs Capillary Systems Owned
    • by Industry/ Segment
    • by Laboratory Function
    • by Region

LIST OF EXHIBTS

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 2-6: Distribution of Total Sequencers in Labs
  • Table 2-9: Number of Next-Generation Sequencers in Labs
  • Figure 2-7: Number of Next-Generation 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 3-8: 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: Next-Generation Models in Respondents' Labs, by Industry/ Segment (# of Systems)
  • Table 3-21: Next-Generation Models in Respondents' Labs, by Industry/ Segment (% of Systems)
  • Figure 3-11: Next-Generation Models in Respondents' Labs, by Industry/ Segment (% of Systems)
  • Table 3-22: Next-Generation Models in Respondents' Labs, by Industry/ Segment (% of Systems)
  • Figure 3-12: Next-Generation 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, 2001-2013
  • 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. Non-Regulated Samples (% of Sequencing)
  • Figure 4-14: Volume of Regulated vs. Non-Regulated Samples, Est. 2013 (% of Sequencing)
  • Figure 4-15: Volume of Regulated vs. Non-Regulated 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. Non-Regulated Samples, Est. 2013 (% of Sequencing)
  • Figure 4-18: Volume of Regulated vs. Non-Regulated Samples, Est. 2013 (% of Sequencing)
  • Figure 4-19: Volume of Regulated vs. Non-Regulated 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 Non-Regulated Patient/Human Samples
  • Figure3-24: Sequencers Used for Non-Regulated 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: Non-Regulated Patient/ Human Sequencing Expected to Grow Fastest
  • Figure 4-28: Non-Regulated 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 End-Users
  • Figure 5-1: Major Changes or Improvements Wanted by End-Users
  • 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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