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Next-Generation Sequencing Trends: Kalorama Survey of Laboratories

Next-Generation Sequencing Trends: Kalorama Survey of Laboratories

Next-Generation Sequencing Trends: Kalorama Survey of Laboratories identifies 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 surveys the following aspects of NGS systems: system installations; sequencer applications, clinical applications, and usage trends; preferences and evaluations; and future purchase plans.

This survey – of 78 laboratories, carried out from August to October of 2017 – reached a mix of labs, providing both a range of industry segments as well as groups of labs with both next-generation and capillary systems.

The survey presents results in terms of the types of systems installed by model, by region, by industry, and by lab function.

Responses related to labs’ usage of sequencers in terms of the applications and sample types for which they are run are also provided. Other areas covered include outsourcing and future expectations. The survey also provides segmentation of the applications expected to increase, by brand of next-generation system owned.

The survey gives 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.

Finally, the survey provides responses related to labs’ plans to for future purchase of sequencers.


  • Executive Summary
    • Scope
    • Methodology
    • Outline
  • Survey Demographics
    • Regional Distribution of Respondents' Labs
      • Table Survey Respondents by Region (USA, ROW, Europe, Total)
      • Table Survey Respondents by Region
      • Table World Distribution of Survey Respondents
    • Industrial Distribution of Respondents' Labs
      • Table Primary Industry/ Segment Labs Belong To
    • Laboratory Function of Respondents' Labs
      • Table Respondents by Function (Research, Service provider (external), Core lab / shared facility,
    • Distribution by Number of Sequencers
      • Total Numbers of Systems in Labs
        • Table Distribution by Sequencers in Lab
      • Numbers of 2nd- and 3rd Generation Systems
        • Table Number of Next-Generation Sequencers in Labs
      • Remaining Non-NGS / Capillary Systems
        • Table Number of Non-NGS / Capillary Sequencers in Labs
    • Brand(s) / Types(s) of Sequencers Owned
      • Table Brands / Types of Sequencers Owned by All Respondents
      • Table Number of a Given Brand / Type in Labs Owning Type, 2017
      • Average Number of a Given Sequencer in Labs
        • Table Average Number of a Given Sequencer in Labs Owning Type, 2013
    • Position/ Role of Respondents
      • Table 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)
  • System Installations
    • Distribution of Sequencer Models
      • Overall Totals
        • 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 Cross-Ownership of Sequencing Systems Trend
        • Table Installed Base of Labs, by System(s) Owned (% of Systems)
    • Distribution of Number of Sequencers
      • Table 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 Distribution of Systems by Region (USA, Europe, ROW, Overall)
        • Table Sequencer Models in Respondents' Labs, by Region (% of Systems; USA, Europe, ROW, Overall)
    • Next-Generation Systems
      • Table NGS Models in Respondents' Labs, by Region by Percent of Systems (USA, Europe, ROW, Total)
    • Non-NGS / Capillary Systems
      • Table Non-NGS / Capillary Systems Models by Region (USA, Europe, ROW, Overall)
    • Installed Base by Industry Segment
      • Overall Brand/ Type
        • Table Number of Systems Installed, by Industry / Segment(s)
      • Brand / Type of Sequencer Systems Installed, by Industry/ Segment, 2017
        • Table Brand / Type of Sequencer Systems Installed, by Industry/ Segment, 2017 (% of Systems)
      • Comparison to 2013
        • Table Brand / Type of Sequencer Systems Installed, by Industry/ Segment, 2013 (% of Systems)
    • Installed Base of Next-Generation Systems
      • Table 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 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 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 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
        • Table 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 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 NGS Models in Respondents' Labs, by Lab Function (% of All Respondent Systems) (Research, Service provider (external), Core lab/ shared facility, Diagnostic services/ products, Overall)
      • Table Sequencers per Lab, Average, by Lab Function (Overall; Diagnostic services/ products; Core lab/ shared facility; Service provider (external); Research)
  • 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)
        • Table Applications by Sequencer Model
    • Likely Increases in Applications and Volume
      • Overall
        • Table 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)
        • Table 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 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 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 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 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 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 Expected Growth in Sequencing Volume (% of Labs)
    • Capacity Usage of Systems
      • Table Avg. Percentage of Systems' Capacity Used, by Brand
      • Percentage of Systems' Capacity Used, by Brand
    • Outsourcing
      • Table Percentage of Sequencing Volume Outsourced
      • Percentage of Sequencing Volume Outsourced
        • Table Percentage of Sequencing Volume Outsourced, by Region (N. America, Europe, ROW, Overall)
        • Table Reason for Outsourcing
    • Clinical Applications
      • Sequencing of CLIA Regulated Patient Samples
        • Table How Labs Address Sequencing of Regulated Patient Samples (# of Labs)
    • How Labs Address Sequencing of Regulated Patient Samples
      • Certification for Regulated Samples
        • Table Labs' Certification for Regulated Patient Samples
      • Change in Regulated Samples vs. Non-Regulated Samples
        • Table Distribution of Samples, Est. 2017 (% of Labs)
        • Table Distribution of Samples, Expected 2018 (% of Labs)
      • Certified Labs
        • Table 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 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 Distribution of Samples, Est. 2017 (% of Labs) (Non patient/ human samples; Non CLIA patient/ human samples; CLIA patient samples)
        • Table 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 Sequencers Most Likely to Be Used for Regulated Patient Samples
        • Table Sequencers Used for Regulated Patient Samples (% of Systems)
      • Sequencers Used for Regulated Patient Samples
        • Table Sequencers Likely to Be Used for Regulated Patient Samples (% of Labs)
        • Table Sequencers Likely to Be Used for Regulated Patient Samples (% of Labs)
    • Disease/ Therapeutic Areas Where Sequencing Applied
      • Regulated Patient/ Human Samples
        • Table Regulated Patient/ Human Samples (Rare inherited/ genetic, Cancer, Prenatal, Infectious, Pharmacogenetic, Hematological, Healthy ind'ls)
        • Table Remaining Capillary Systems, How Used (Rare inherited/ genetic, Cancer, Prenatal, Infectious, Pharmacogenetic, Hematological, Healthy individuals)
      • Non-Regulated Patient/ Human Samples
        • Table 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 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 Regulated Sequencing Expected to Grow Fastest (% of Labs) (Rare genetic/ inherited diseases, Cancer, Pharmacogenetics, Infectious, Prenatal)
        • Table 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 Challenges for Growth of Clinical Sequencing
  • Preferences and Evaluations
    • Key Criteria for Choosing Sequencers
      • Overall
        • Table 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 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 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 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 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 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
      • llumina -Comments
      • Oxford Nanopore -Comments
      • Pacific Biosciences -Comments
    • Changes or Improvements
      • Table 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 custome support, Shorter run time, More flexible/ adaptable software)
    • Bottlenecks in Process
      • Table Bottlenecks (Data analysis/ interpretation, Sequencer run time, Library preparation, Reporting, Waiting to fill flow cells)
  • Future Purchase Plans
    • Time Frame of Purchase Plans
      • Overall
        • Table Time Frame for Future Purchase (0-6 months, 7-12 months, 1-2 years, Planned but uncertain time frame, No plan)
        • Table 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 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 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 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 Sequencer Models Likely to Be Considered
      • Sequencer Models Likely to Be Considered
      • Purchase Decision Preference by Brand/ Type Owned
        • Table Sequencer Models Likely to Be Considered, by Brand/Type Owned (% of Labs)
      • By Industry / Segment
        • Table Sequencer Models Likely to Be Considered, by Industry/Segment Owned (% of Labs)
      • By Laboratory Function
        • Table Sequencer Models Likely to Be Considered, by Lab Function (% of Labs) (Research, Service provider (ext), Core lab, Diagnostics/ clinical, Overall)
      • By Region
        • Table Sequencer Models Likely to Be Considered, by Region (% of Labs) (USA, Europe, ROW, Overall)

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