Next-Generation Sequencing Trends: Kalorama Survey of Laboratories

 
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Published Nov 21, 2017 | 100 Pages | Pub ID: KLI15538606

Next-Generation Sequencing Trends: Kalorama Survey of Laboratories

The DNA sequencer market has undergone rapid changes in the last few years, continuing its revolutionary trends that hold the promise of bringing major changes to healthcare in the near future. Next-Generation Sequencing Trends: Kalorama Survey of Laboratories aims to identify some of the key changes taking place with both next-generation sequencing (NGS) systems in relation to their usage in labs and in relation to the sequencing of clinical samples for diagnostic or clinical research purposes. The report includes the following survey results:
  • System installations – presents the results in terms of the types of systems installed, the segments and regions where they are found, and other patterns
  • Sequencer applications, clinical applications, and usage trends – presents the responses related to the labs’ usage of sequencers, in terms of the applications and sample types for which they are run
  • Preferences and evaluations – provides the labs’ feedback with regard to which features they find important, which aspects of the systems or the process they want improved, and their evaluation of their current sequencer systems
  • Future purchase plans – provides the responses related to the labs’ plans to purchase sequencers in the near term, along with their views on barriers or issues affecting that
This survey of 78 laboratories was carried out from August to October of 2017. 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 next-generation systems in the market, the scope leans towards these types of sequencers. The mix of labs reached in the survey provides both a range of industry segments as well as groups of labs with both next-generation and capillary systems.

In terms of system installations, the survey presents results in terms of the types of systems installed by model, by region, by industry, and by lab function, including:
  • Sequencer Models in Respondents’ Labs
  • NGS Models in Respondents' Labs, by Region by Percent of Systems (USA, Europe, ROW, Total)
  • Installed Base of Next-Generation Systems, Segmented by Industry (Academia, University; Hospital, Medical Center; Independent Reference Lab; Contract Research/ Svcs; Independent Rsch/ Nonprofit; Biotech/ Diagnostics/ Vaccines; Government; Overall)
  • NGS Models in Respondents' Labs, by Lab Function (% of Systems) (Research, Service provider (external), Core lab/ shared facility, Diagnostic services/ products)
  • Sequencers per Lab, Average, by Lab Function (Overall; Diagnostic services/ products; Core lab/ shared facility; Service provider (external); Research)
In terms of sequencer applications and usage trends, the survey presents the responses related to the labs’ usage of sequencers, in terms of the applications and sample types for which they are run. Other areas are covered such as outsourcing and future expectations. Survey results include:
  • NGS Application Volume by Sequencer Model (% of Sequencing)
  • Applications Expected to Increase the Most (Resequencing/ amplicon; RNA seq, transcriptomics, gene expr.; Metagenomics; De novo sequencing & whole genome; Exome; Methylation, other epigenetics; ChIP-seq; Small RNA, micro RNA; Expect mostly remain the same)
The survey also provides segmentation of the applications expected to increase, by brand of next-generation system owned:
  • Applications Expected to Increase, All Users (Resequencing/ targeted; mRNA-seq / transcriptome; de novo/ whole genome; Metagenomics; Exome; Methylation, other epigenetics; Small/ micro RNA; ChIP-seq)
  • Applications Expected to Increase, Illumina Owners
  • Applications Expected to Increase, Pac Bio Owners
  • Applications Expected to Increase, Thermo Owners
  • Applications Expected to Increase, Capillary Owners
The survey provides preferences and evaluations, giving the labs’ feedback with regard to the most important criteria for sequencer purchase, including cost of system, cost per sample or run, raw accuracy, ease of use, and other factors. Further, the survey provides this information with respect to the brand or type of sequencer system owned:
  • Most Important Criteria for Purchases, Illumina Owners
  • Most Important Criteria for Purchases, Pac Bio Owners
  • Most Important Criteria for Purchase, Thermo Fisher Owners
  • Most Important Criteria for Purchase, Capillary Owners
The survey finally provides responses related to the labs’ plans to for future purchase of sequencers, including the following information:
  • Time Frame for Future Purchase (0-6 months, 7-12 months, 1-2 years, Planned but uncertain time frame, No plan)
  • Time Frame for Future Purchase, by Brand Owned
  • Time Frame for Future Purchase by Type of Lab (Overall, Research, Service provider (ext), Core lab/ shared, Diagnostic svcs/ prod)
  • Time Frame for Future Purchase, by Region (USA, Europe, ROW)
  • Sequencer Models Likely to Be Considered
  • Sequencer Models Likely to Be Considered, by Brand/Type Owned
  • Sequencer Models Likely to Be Considered, by Industry/Segment Owned
  • Sequencer Models Likely to Be Considered, by Lab Function (Research, Service provider (ext), Core lab, Diagnostics/ clinical, Overall)
  • Sequencer Models Likely to Be Considered, by Region (USA, Europe, ROW, Overall)
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 some open-ended and some multiple-choice type questions.
1: EXECUTIVE SUMMARY
SCOPE

METHODOLOGY

OUTLINE

2: SURVEY DEMOGRAPHICS

REGIONAL DISTRIBUTION OF RESPONDENTS’ LABS

Table 2-1: Survey Respondents by Region (USA, ROW, Europe, Total)

Figure 2-1: Survey Respondents by Region

Figure 2-2: World Distribution of Survey Respondents

INDUSTRIAL DISTRIBUTION OF RESPONDENTS’ LABS

Figure 2-3: Primary Industry/ Segment Labs Belong To

LABORATORY FUNCTION OF RESPONDENTS’ LABS

Figure 2-4: Respondents by Function (Research, Service provider (external), Core lab / shared facility, Diagnostic services / products)

DISTRIBUTION BY NUMBER OF SEQUENCERS

Total Numbers of Systems in Labs

Figure 2-5: Distribution by Sequencers in Lab

Numbers of 2nd- and 3rd Generation Systems

Figure 2-6: Number of Next-Generation Sequencers in Labs

Remaining Non-NGS / Capillary Systems

Figure 2-7: Number of Non-NGS / Capillary Sequencers in Labs

BRAND(S) / TYPES(S) OF SEQUENCERS OWNED

Table 2-2: Brands / Types of Sequencers Owned by All Respondents

Table 2-3: Number of a Given Brand / Type in Labs Owning Type, 2017

Average Number of a Given Sequencer in Labs

Table 2-4: Average Number of a Given Sequencer in Labs Owning Type, 2013

POSITION/ ROLE OF RESPONDENTS

Figure 2-8: Distribution of the Respondents’ Positions in the Labs or Organizations (Lab technician, VP or exec. Management, 
Professor/PI, Genetic counselor, Lab manager/director, Research assoc./scientist)

3: SYSTEM INSTALLATIONS

DISTRIBUTION OF SEQUENCER MODELS
Next-Generation Sequencing Trends: Kalorama Survey of Laboratories

Overall Totals

Table 3-1: Sequencer Models in Respondents’ Labs

Installed Base by System Owned

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)

Table 3-4: Cross-Ownership of Sequencing Systems Trend

Table 3-5: Installed Base of Labs, by System(s) Owned (% of Systems)

DISTRIBUTION OF NUMBER OF SEQUENCERS

Table 3-6: Number of Systems in Labs Segmented across Two Dimensions – Number of Next-Generation Systems and Number of Non-
NGS / Capillary Systems

INSTALLED BASE BY REGION
Overall Brand/ Type
Table 3-7: Distribution of Systems by Region (USA, Europe, ROW, Overall)

Table 3-8: Sequencer Models in Respondents’ Labs, by Region (% of Systems; USA, Europe, ROW, Overall)
NEXT-GENERATION SYSTEMS
Table 3-9: NGS Models in Respondents' Labs, by Region by Percent of Systems (USA, Europe, ROW, Total)
NON-NGS / CAPILLARY SYSTEMS
Table 3-10: Non-NGS / Capillary Systems Models by Region (USA, Europe, ROW, Overall)
INSTALLED BASE BY INDUSTRY SEGMENT
Overall Brand/ Type
Table 3-11: Number of Systems Installed, by Industry / Segment(s)
Brand / Type of Sequencer Systems Installed, by Industry/ Segment, 2017
Table 3-12: Brand / Type of Sequencer Systems Installed, by Industry/ Segment, 2017 (% of Systems)
Comparison to 2013
Table 3-13: Brand / Type of Sequencer Systems Installed, by Industry/ Segment, 2013 (% of Systems)
INSTALLED BASE OF NEXT-GENERATION SYSTEMS
Table 3-14: Installed Base of Next-Generation Systems, Segmented by Industry (Academia, University; Hospital, Medical Center; Independent Reference Lab; Contract Research/ Svcs; Independent Rsch/ Nonprofit; Biotech/ Diagnostics/ Vaccines; Government; Overall)

Table 3-15: Next-Generation Models in Respondents' Labs, by Industry/ Segment (% of Labs Owning Given Systems) (Academia, University; Hospital, Medical Center; Independent Reference Lab; Contract Research/ Svcs; Independent Rsch/ Nonprofit; Biotech/ Diagnostics/ Vaccines; Government)

Table 3-16: Next-Generation Models in Respondents' Labs, by Industry/ Segment (% of Total Respondents’ Systems)
INSTALLED BASE BY LABORATORY FUNCTION
Overall Brand/ Type by Laboratory Function
Table 3-17: NGS Models in Respondents' Labs, by Lab Function (% of Systems) (Research, Service provider (external), Core lab/ shared facility, Diagnostic services/ products)
Brand / Type of Sequencer System Installed, by Lab Function
Next-Generation Sequencing Trends: Kalorama Survey of Laboratories
Table 3-18: Brand / Type of Sequencer System Installed, by Lab Function (% of Systems; Research, Service provider (external), Core lab/ shared facility, Diagnostic services/ products)
NEXT-GENERATION SYSTEMS
Table 3-19: NGS Models in Respondents' Labs, by Lab Function (% of Labs Owning Given NGS System) (Research, Service provider (external), Core lab/ shared facility, Diagnostic services/ products)

Table 3-20: NGS Models in Respondents' Labs, by Lab Function (% of All Respondent Systems) (Research, Service provider (external), Core lab/ shared facility, Diagnostic services/ products, Overall)

Figure 3-1: Sequencers per Lab, Average, by Lab Function (Overall; Diagnostic services/ products; Core lab/ shared facility; Service provider (external); Research)

4: SEQUENCER APPLICATIONS, CLINICAL APPLICATIONS, AND USAGE TRENDS

SEQUENCER APPLICATIONS AND USAGE
Applications Run, Overall and by Brand/ Type
Table 4-1: NGS Application Volume by Model (% of Sequencing)

Figure 4-1: Applications by Sequencer Model
LIKELY INCREASES IN APPLICATIONS AND VOLUME
Overall
Table 4-2: Applications Expected to Increase the Most (Resequencing/ amplicon; RNA seq, transcriptomics, gene expr.; Metagenomics; De novo sequencing & whole genome; Exome; Methylation, other epigenetics; ChIP-seq; Small RNA, micro RNA; Expect mostly remain the same)

Figure 4-2: Applications Expected to Increase the Most (Resequencing/ amplicon; RNA seq, transcriptomics, gene expr.; Metagenomics; De novo sequencing & whole genome; Exome; Methylation, other epigenetics; ChIP-seq; Small RNA, micro RNA; Expect mostly remain the same)
Applications Expected to Increase the Most Overall
BY BRAND OF NEXT-GENERATION SYSTEM OWNED
Table 4-3: Applications Expected to Increase, Illumina Owners (Resequencing/ targeted; mRNA-seq / transcriptome; de novo/ whole genome; Metagenomics; Exome; Methylation, other epigenetics; Small/ micro RNA; ChIP-seq)

Table 4-4: Applications Expected to Increase, Pac Bio Owners (Resequencing/ targeted; mRNA-seq / transcriptome; de novo/ whole genome; Metagenomics; Exome; Methylation, other epigenetics; Small/ micro RNA; ChIP-seq)

Table 4-5: Applications Expected to Increase, Thermo Owners (Resequencing/ targeted; mRNA-seq / transcriptome; de novo/ whole genome; Metagenomics; Exome; Methylation, other epigenetics; Small/ micro RNA; ChIP-seq)

Table 4-6: Applications Expected to Increase, Non-NGS / Capillary Owners (Resequencing/ targeted; mRNA-seq / transcriptome; de novo/ whole genome; Metagenomics; Exome; Methylation, other epigenetics; Small/ micro RNA; ChIP-seq)

Table 4-7: Applications Expected to Increase, All Users (Resequencing/ targeted; mRNA-seq / transcriptome; de novo/ whole genome; Metagenomics; Exome; Methylation, other epigenetics; Small/ micro RNA; ChIP-seq)
APPLICATIONS EXPECTED TO INCREASE, BY NGS BRAND OWNED (% OF LABS)
Growth in Sequencing, NGS vs Non-NGS / Capillary Systems
Table 4-8: Expected Growth in Sequencing Volume (% of Labs)
Next-Generation Sequencing Trends: Kalorama Survey of Laboratories
CAPACITY USAGE OF SYSTEMS
Figure 4-3: Avg. Percentage of Systems’ Capacity Used, by Brand
Percentage of Systems’ Capacity Used, by Brand
OUTSOURCING
Table 4-9: Percentage of Sequencing Volume Outsourced
Percentage of Sequencing Volume Outsourced
Table 4-10: Percentage of Sequencing Volume Outsourced, by Region (N. America, Europe, ROW, Overall)

Table 4-11: Reason for Outsourcing
CLINICAL APPLICATIONS
Sequencing of CLIA Regulated Patient Samples
Table 4-12: How Labs Address Sequencing of Regulated Patient Samples (# of Labs)
HOW LABS ADDRESS SEQUENCING OF REGULATED PATIENT SAMPLES
Certification for Regulated Samples
Table 4-13: Labs’ Certification for Regulated Patient Samples
Change in Regulated Samples vs. Non-Regulated Samples
Table 4-14: Distribution of Samples, Est. 2017 (% of Labs)

Table 4-15: Distribution of Samples, Expected 2018 (% of Labs)
Certified Labs
Table 4-16: Volume of Regulated vs. Non-Regulated Samples at Certified Labs, Est. 2017 and Expected 2018 (% of Sequencing; Sample type: Non patient/ human samples; Non CLIA patient/ human sample; CLIA patient samples)

Table 4-17: Volume of Regulated vs. Non-Regulated Samples at Non-Certified Labs, Est. 2017 and Expected 2018 (% of Sequencing; Sample type: Non patient/ human samples; Non CLIA patient/ human sample; CLIA patient samples)

Table 4-18: Distribution of Samples, Est. 2017 (% of Labs) (Non patient/ human samples; Non CLIA patient/ human samples; CLIA patient samples)

Table 4-19: Distribution of Samples, Expected 2018 (% of Labs) (Non patient/ human samples; Non CLIA patient/ human samples; CLIA patient samples)
SEQUENCERS USED OR PLANNED FOR PATIENT/ HUMAN SAMPLES
Regulated Patient/ Human Samples
Table 4-20: Sequencers Most Likely to Be Used for Regulated Patient Samples

Figure 4-4: Sequencers Used for Regulated Patient Samples (% of Systems)
Sequencers Used for Regulated Patient Samples

Table 4-21: Sequencers Likely to Be Used for Regulated Patient Samples (% of Labs)

Figure 4-5: Sequencers Likely to Be Used for Regulated Patient Samples (% of Labs)
DISEASE/ THERAPEUTIC AREAS WHERE SEQUENCING APPLIED
Regulated Patient/ Human Samples
Table 4-22: Regulated Patient/ Human Samples (Rare inherited/ genetic, Cancer, Prenatal, Infectious, Pharmacogenetic, Hematological, Healthy ind'ls)

Table 4-23: Remaining Capillary Systems, How Used (Rare inherited/ genetic, Cancer, Prenatal, Infectious, Pharmacogenetic, Hematological, Healthy individuals)
Next-Generation Sequencing Trends: Kalorama Survey of Laboratories
Non-Regulated Patient/ Human Samples
Table 4-24: Disease Areas Where Sequencing Applied (% of Volume) (Rare inherited/ genetic; Cancer; Pharmacogenetic; Infectious; Autoimmune/ immunology; Neurology; HLA/ MHC/ transplantation; Healthy individuals; Other; Varies, large range)

Table 4-25: Remaining Capillary Systems, Where Used in Non-Regulated Samples (Rare inherited/ genetic; Cancer; Pharmacogenetic; Infectious; Autoimmune/ immunology; Neurology; HLA/ MHC/ transplantation; Healthy individuals; Other; Varies, large range)
Disease Areas Expected to Grow Fastest
Table 4-26: Regulated Sequencing Expected to Grow Fastest (% of Labs) (Rare genetic/ inherited diseases, Cancer, Pharmacogenetics, Infectious, Prenatal)

Table 4-27: Non-Regulated Patient/ Human Sequencing Expected to Grow Fastest Non-CLIA (Cancer, Inherited diseases, Infec./ immunology/ autoimmune, Neurology, Pharmacogenetics, HLA/ MHC/ transplantation, Cardiovascular)
Challenges for Growth of Clinical Sequencing
Table 4-28: Challenges for Growth of Clinical Sequencing

5: PREFERENCES AND EVALUATIONS

KEY CRITERIA FOR CHOOSING SEQUENCERS

Overall
Table 5-1: Most Important Criteria for Sequencer Purchase (cost of system, cost per sample or run, raw accuracy, ease of use user friendliness, flexibility range of apps, throughput, vendor cust svc, specific apps needs, compatibility precedence, software IT, turnaround run time, read length, other)
MOST IMPORTANT CRITERIA FOR SEQUENCER PURCHASE
By System
Table 5-2: Most Important Criteria for Purchases, Illumina Owners (cost of system, cost per sample or run, raw accuracy, ease of use user friendliness, flexibility range of apps, throughput, vendor cust svc, specific apps needs, compatibility precedence, software it, turnaround run time, read length, Other)

Table 5-3: Most Important Criteria for Purchases, Pac Bio Owners (cost of system, cost per sample or run, raw accuracy, ease of use user friendliness, flexibility range of apps, throughput, vendor cust svc, specific apps needs, compatibility precedence, software it, turnaround run time, read length, Other)

Table 5-4: Most Important Criteria for Purchase, Thermo Fisher Owners (cost of system, cost per sample or run, raw accuracy, ease of use user friendliness, flexibility range of apps, throughput, vendor cust svc, specific apps needs, compatibility precedence, software it, turnaround run time, read length, Other)

Table 5-5: Most Important Criteria for Purchase, Capillary Owners (cost of system, cost per sample or run, raw accuracy, ease of use user friendliness, flexibility range of apps, throughput, vendor cust svc, specific apps needs, compatibility precedence, software it, turnaround run time, read length, Other)

Table 5-6: Most Important Criteria for Purchase, Overall NGS Owners (cost of system, cost per sample or run, raw accuracy, ease of use user friendliness, flexibility range of apps, throughput, vendor cust svc, specific apps needs, compatibility precedence, software it, turnaround run time, read length, Other)
EVALUATIONS OF SEQUENCERS
Illumina -Comments

Oxford Nanopore -Comments

Pacific Biosciences -Comments

Next-Generation Sequencing Trends: Kalorama Survey of Laboratories

CHANGES OR IMPROVEMENTS
Table 5-7: Feature Most Wanted to Change or Improve (Lower sequencing cost, Cheaper libr prep, Automate/ shorten library prep, Longer reads, Robustness/ reliability of systems, Improve/ simplify data analysis, Choice of fewer lanes per run, Enable tracking barcodes etc, Flexibility for diff apps, Better customer support, Shorter run time, More flexible/ adaptable software)
BOTTLENECKS IN PROCESS
Table 5-8: Bottlenecks (Data analysis/ interpretation, Sequencer run time, Library preparation, Reporting, Waiting to fill flow cells)

6: FUTURE PURCHASE PLANS

TIME FRAME OF PURCHASE PLANS
Overall
Table 6-1: Time Frame for Future Purchase (0-6 months, 7-12 months, 1-2 years, Planned but uncertain time frame, No plan)

Figure 6-1: Time Frame of the Purchases Planned (0-6 months, 7-12 months, 1-2 years, Planned but uncertain time frame, No plan)
By Brand/ Type Owned
Table 6-2: Time Frame for Future Purchase, by Brand Owned (# of Labs) (0-6 months, 7-12 months, 1-2 years, Planned but uncertain time frame, No plan)
By Laboratory Function
Table 6-3: Time Frame for Future Purchase by Type of Lab (Overall, Research, Service provider (ext), Core lab/ shared, Diagnostic svcs/ prod) (0-6 months, 7-12 months, 1-2 years, Planned but uncertain time frame, No plan)
Purchase Plan Time Frame by Region
Table 6-4: Time Frame for Future Purchase, by Region (% of Labs) (USA, Europe, ROW) (0-6 months, 7-12 months, 1-2 years, Planned but uncertain time frame, No plan)
SYSTEMS LIKELY TO BE CONSIDERED FOR PURCHASE
Overall
Table 6-5: Sequencer Models Likely to Be Considered
Sequencer Models Likely to Be Considered

Purchase Decision Preference by Brand/ Type Owned
Table 6-6: Sequencer Models Likely to Be Considered, by Brand/Type Owned (% of Labs)
By Industry / Segment
Table 6-7: Sequencer Models Likely to Be Considered, by Industry/Segment Owned (% of Labs)
By Laboratory Function
Table 6-8: Sequencer Models Likely to Be Considered, by Lab Function (% of Labs) (Research, Service provider (ext), Core lab, Diagnostics/ clinical, Overall)
By Region
Table 6-9: Sequencer Models Likely to Be Considered, by Region (% of Labs) (USA, Europe, ROW, Overall)

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