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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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SKU: KLI5088424 Categories: , Pages: 159

Description

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, 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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