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


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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.


  • Executive Summary
    • SCOPE
    • METHODOLOGY
    • OUTLINE
    • MAIN FINDINGS OF THE STUDY
  • Demographics
    • REGIONAL DISTRIBUTION OF RESPONDENTS
      • Table Distribution of Respondent Labs
    • INDUSTRIAL DISTRIBUTION OF RESPONDENTS
      • Table Primary Industry/ Segment Labs Belong To
      • Table Industry/ Segment(s) Labs Belong To, by Region
    • LABORATORY FUNCTION OF RESPONDENTS
      • Table Major Function(s) of Respondent Labs
      • Table Major Function(s) of Labs, by Region
      • Distribution by Number of Sequencers
        • Table Distribution of Total Sequencers in Labs
      • Numbers of 2nd and 3rd Generation Systems
        • Table Number of Next-Generation Sequencers in Labs
      • Numbers of Capillary Systems
        • Table Number of Capillary Sequencers in Labs
    • BRAND(S)/ TYPES(S) OF SEQUENCERS OWNED, OVERALL
      • Table Brand(s)/ Type(s) of Sequencers Owned by Labs
      • Table Number of a Given Brand / Type in Labs Owning That Type
    • POSITION/ ROLE OF RESPONDENTS
      • Table Position/ Role of Respondent
  • System Installations
    • DISTRIBUTION OF SEQUENCER MODELS
      • Table Sequencer Models in Respondents' Labs
    • INSTALLED BASE BY SYSTEM OWNED
      • Table Installed Base of Labs, by System(s) Owned (# of Systems)
      • Table Installed Base of Labs, by System(s) Owned (% of Systems)
      • Table Installed Base of Labs, by System(s) Owned (% of Systems)
    • NUMBER OF SYSTEMS OWNED PER LAB
      • Table Distribution of NGS vs. Capillary Systems (# of Labs)
      • Table # of NGS Systems by # of Capillary Systems (% of Labs)
      • Table # of Capillary Systems by # of NGS Systems (% of Labs)
    • INSTALLED BASE BY REGION
      • USA, Europe, Rest of World
        • Table Number of Systems Installed in Labs, by Region
        • Table Sequencer Models in Respondents' Labs, by Region (# of Systems)
        • Table Sequencer Models in Respondents' Labs, by Region (% of Systems)
    • INSTALLED BASE, NEXT-GENERATION SYSTEMS
      • Table NGS Models in Respondents' Labs, by Region (# of Systems)
      • Table NGS Models in Respondents' Labs, by Region (% of Systems)
    • INSTALLED BASE, CAPILLARY SYSTEMS
      • Table Capillary Models in Respondents' Labs, by Region (# of Systems)
      • Table Capillary Models in Respondents' Labs, by Region (% of Systems)
    • INSTALLED BASE BY INDUSTRY SEGMENT
      • Overall Brand/ Type
        • Table Number of Systems Installed, by Industry/ Segment(s)
        • Table Brand / Type of Sequencer Systems Installed, by Industry/ Segment (# of Systems)
        • Table Brand / Type of Sequencer Systems Installed, by Industry/ Segment (% of Systems)
        • Table Brand / Type of Sequencer Systems Installed, by Industry/ Segment (% of Systems)
        • Table Number of NGS Systems Installed, by Industry/ Segment
        • Table Next-Generation Models in Respondents' Labs, by Industry/ Segment (# of Systems)
        • Table Next-Generation Models in Respondents' Labs, by Industry/ Segment (% of Systems)
        • Table Next-Generation Models in Respondents' Labs, by Industry/ Segment (% of Systems)
        • Table Number of Capillary Systems Installed in Labs Owning, by Industry/ Segment
    • INSTALLED BASE BY LABORATORY FUNCTION
      • Overall Brand/ Type
        • Table Number of Systems Installed by Laboratory Function
        • Table Brand / Type of Sequencer System Installed, by Lab Function (# of Systems)
        • Table Brand / Type of Sequencer System Installed, by Lab Function (% of Systems)
        • Table Brand / Type of Sequencer System Installed, by Lab Function (% of Systems)
        • Table Brand / Type of Sequencer System Installed, by Lab Function (% of Systems)
        • Table Number of NGS Installed in Labs Owning, by Lab Function
        • Table NGS Models in Respondents' Labs, by Lab Function (# of Systems)
        • Table NGS Models in Respondents' Labs, by Lab Function (% of Systems)
        • Table NGS Models in Respondents' Labs, by Lab Function (% of Systems)
    • CAPILLARY / GEL SYSTEMS
      • Table Number of Capillary Systems Installed in Labs Owning, by Lab Function
      • Date of Installation
        • Table Recent Systems Installed, 2001- Q2 2013 (# of Systems)
        • Table Recent NGS Systems Installed, 2007 - Q2 2013 (# of Systems)
  • Sequencer Applications, Clinical Applications, and Usage Trends
    • SEQUENCER APPLICATIONS AND USAGE
      • Applications Run, Overall and by Brand/ Type
        • Table NGS Application Volume by Model (% of Sequencing)
      • Likely Increases in Applications and Volume
        • Table Applications Expected to Increase the Most
        • Table Applications Expected to Increase, by NGS Brand Owned (# of Labs)
        • Table Applications Expected to Increase, by NGS Brand Owned (% of Labs)
      • Growth in Sequencing, NGS vs Capillary Systems
        • Table Expected Growth in Sequencing Volume (# of Labs)
        • Table Expected Growth in Sequencing Volume (% of Labs)
      • Capacity Usage of Systems
        • Table Avg. Percentage of Systems' Capacity Used, by Brand
    • OUTSOURCING
      • Table Percentage of Sequencing Volume Outsourced
      • Table Percentage of Sequencing Volume Outsourced, by Region
      • Table Reasons for Outsourcing
    • CLINICAL APPLICATIONS
      • Sequencing of CLIA Regulated Patient Samples
        • Table How Labs Address Sequencing of Regulated Patient Samples (# of Labs)
        • Table How Labs Address Sequencing of Regulated Patient Samples (% of Labs)
      • Verbatim Comments: Approaching Clinical Applications
      • Certification for Regulated Samples
      • Plans, Expectations for Certification & Usage
        • Table Plans for New or Additional Certification
        • Table Type of Accreditation Planned/ Considered (# of Labs)
        • Table Type of Accreditation Planned/ Considered (% of Labs)
        • Table Distribution of Samples, Est. 2013 (# of Labs)
        • Table Distribution of Samples, Est. 2013 (% of Labs)
        • Table Distribution of Samples, Expected 2014 (# of Labs)
        • Table Distribution of Samples, Expected 2014 (% of Labs)
        • Table Volume of Regulated vs. Non-Regulated Samples (% of Sequencing)
        • Table Distribution of Samples, Est. 2013 (# of Labs)
        • Table Distribution of Samples, Est. 2013 (% of Labs)
        • Table Distribution of Samples, Expected 2014 (# of Labs)
        • Table Distribution of Samples, Expected 2014 (% of Labs)
        • Table Volume of Regulated vs. Non-Regulated Samples, Est. 2013 (% of Sequencing)
        • Table Distribution of Samples, Est. 2013 (# of Labs)
        • Table Distribution of Samples, Est. 2013 (% of Labs)
        • Table Distribution of Samples, Expected 2014 (# of Labs)
        • Table Distribution of Samples, Expected 2014 (% of Labs)
        • Table Sequencers Used for Regulated Patient Samples
        • Table Sequencers Likely to be Used for Regulated Patient Samples (% of Labs)
        • Table Sequencers Used for Non-Regulated Patient/Human Samples
      • Disease/ Therapeutic Areas Where Sequencing Applied
      • Regulated Patient/ Human Samples
        • Table Disease Areas Where Sequencing Applied, by NGS vs Capillary (Percentage and Number of Systems)
      • Non-Regulated Patient/ Human Samples
        • Table Disease Areas Where Sequencing Applied, by NGS vs Capillary (% of Volume)
      • Disease Areas Expected to Grow Fastest
        • Table Regulated Sequencing Expected to Grow Fastest
        • Table Non-Regulated Patient/ Human Sequencing Expected to Grow Fastest
      • Other Technologies Used for Patient/ Human Samples
        • Table Other Technologies Used in Lab
      • Challenges for Growth of Clinical Sequencing
        • Table Challenges for Growth of Clinical Sequencing
  • Improvements and Future Purchase Plans
    • CHANGES OR IMPROVEMENTS, NEXT-GENERATION SYSTEMS
      • Table Major Changes or Improvements Wanted by End-Users
      • Table Bottleneck in Sequencing Process
    • DIFFICULTY OF DATA ANALYSIS&DATA MANAGEMENT
      • Data Analysis Difficulty
        • Table Difficulty Level of Data Analysis
      • Data Management Difficulty
        • Table Difficulty Level of Data Management
    • TIME-FRAME OF PURCHASE PLANS
      • Overall
        • Table Time Frame for Future Purchase
      • by Brand/ Type Owned
        • Table Time Frame for Future Purchase, by Brand Owned (# of Labs)
        • Table Time Frame for Future Purchase, by Brand Owned (% of Labs)
      • by Laboratory Function
        • Table Time Frame for Future Purchase, by Lab Function (# of Labs)
        • Table Time Frame for Future Purchase, by Lab Function (% of Labs)
      • by Region
        • Table Time Frame for Future Purchase, by Region (# of Labs)
        • Table Time Frame for Future Purchase, by Region (% of Labs)
    • SYSTEMS LIKELY TO CONSIDER FOR PURCHASE
      • Overall
        • Table Sequencer Models Likely to Consider
        • Table Sequencer Models Likely to Consider, by Brand/ Type Owned (# of Labs)
        • Table Sequencer Models Likely to Consider, by Brand/ Type Owned (% of Labs)
        • Table Sequencer Models Likely to Consider, by Industry/ Segment Owned (# of Labs)
        • Table Sequencer Models Likely to Consider, by Lab Function (# of Labs)
        • Table Sequencer Models Likely to Consider, by Lab Function (% of Labs)
        • Table Sequencer Models Likely to Consider, by Region (# of Labs)
        • Table Sequencer Models Likely to Consider, by Region (% of Labs)

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