Clinical NGS Process Report - enlightenbio Blog CLINICAL NGS MARKET TRENDS 33 NGS Market Trends 33...

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Transcript of Clinical NGS Process Report - enlightenbio Blog CLINICAL NGS MARKET TRENDS 33 NGS Market Trends 33...

  • Clinical NGS Process Report

    Table of Contents – January 2018

    enlightenbio™ LLC

    info@enlightenbio.com

    650/ 204.1938

    enlightenbio.com

  • Table of Contents

    CONTENTS 2 OBJECTIVES 3 LEARNINGS 4 TABLE OF CONTENTS 6 THE CLINICAL NGS WORKFLOW 12 Data Analysis and Interpretation in the Clinical NGS Workflow 12 THE CLINICAL NGS PROCESS END-USERS 14 Clinical NGS Workflow Personas 15 The Clinical NGS Workflow Users 17 User Type 17 • The Genetic Counselor 17 • The Clinical Geneticist 17 • The Physician 17 • The Patient 18 • The Bench Researcher / Non-Computational scientist 18 • The Bioinformatician / Computational Scientist 18

    CLINICAL END-USER FEEDBACK 24 Choice of Clinical Testing Lab 25 Clinical End-User Challenges 27 Feedback on Reported Data 30 The Dutch Model 30 CLINICAL NGS MARKET TRENDS 33 NGS Market Trends 33 • NGS adoption in the clinic 34 • Single-cell applications 34 • Emerging RNA-based applications 34 • Clinical cfDNA applications 34 • Mendelian genetic testing 34 • Point-of-care testing 35

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    • Data decentralization 35 • Scaling NGS data analysis 35 • Targeted therapies aimed at narrow patient populations 35 • Sequencing and diversification into new markets 36

    NGS Adoption Challenges 37 Innovations and Technology Trends Impacting Clinical NGS Applications 37 • 4th Generation sequencing technology 38 • Electron Optica 38 • Electronic Biosciences 38 • Genapsys 38 • Genia Technologies 38 • GnuBIO 38 • IBM’s DNA Transistor 38 • LaserGen 38 • Lightspeed Genomics 38 • NABsys 38 • Oxford Nanopore Technologies 38 • Qiagen’s GeneReader 38 • QuantuMDx 39 • Stratos Genomics 39 • Two Pore Guys 39 • ZS Genetics 39 • Artificial intelligence 39 • Cloud computing 40 • Liquid biopsy 40 • Long-read sequencing technology 41 • 10X Genomics 41 • Genia Technologies, 41 • Oxford Nanopore 41 • Pacific Biosciences 41

    Other interesting market trends 42 Segmentation by Type 43 • The increasing trend of clinical genetic testing 43

    Segmentation by Application 44 Mergers and Acquisitions Impacting Clinical NGS 44

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    TEN YEARS OF NGS PATENTS 53 • International Patent Classification (IPC) 53

    Leading Commercial Companies and their Patents 53 • Large Public Company Patents 54

    Patents of Instruments, Consumables Companies 54 • Patents of NGS Data Management, Analysis, & Process Infrastructure/Platform Providers 55 • Patents of NGS Data Interpretation, Decision Making, and Reporting Providers 55 • Patents of Clinical-Grade Genetic/Diagnostic Testing and Services Providers 55

    Top Patent Assignees Across all NGS Patent Families 57 CLINICAL NGS PROJECTS / INITIATIVES 59 THE CLINICAL NGS SOLUTIONS ECOSYSTEM 81 Data Processing, Knowledge Extraction, and Reporting Companies Side-by-Side 81 Infrastructure, Platform, Data Processing Providers 87 Data processing speed, scalability, and flexibility 87 • Data analysis pipelines 89 • Infrastructure requirements of data processing/analysis products 90 • Sequencing machine integration 93

    Data Interpretation/Decision Making/Reporting 93 • Tertiary Analysis – Sequence Data Interpretation and Insight Generation 94 • Tertiary Analysis – Embedded interpretation content for insight generation 97

    Partnerships and collaborations of data analysis and interpretation companies 101 Data Security and Compliance 112 The funding situation 118 COMPANY/PRODUCT PROFILES 120 DNA sequencer, instruments, and reagents / consumable provider 123 NGS data management, analysis, and processing infrastructure / platform providers 150 NGS data interpretation, decision making, and reporting providers 170 Clinical-grade genetic / diagnostic testing and services providers 193 ABBREVIATIONS 207 ABOUT ENLIGHTENBIO LLC 209

  • Table and Figures

    Figure 1: The three high-level categories of the Clinical NGS workflow. ................................................................................................ 12

    Figure 2: Clinical data analysis and interpretation. ................................................................................................................................ 13

    Figure 3: The variant calling and classification process steps with examples of public data used for these steps. ............................... 14

    Figure 4: The Clinical NGS workflow with processing steps and primary end-users. ............................................................................. 15

    Figure 5: End-user interviewees mapped to the Clinical NGS Process. .................................................................................................. 25

    Figure 6: Clinical end-user unmet needs and gaps. ................................................................................................................................ 28

    Figure 7: Invitae and Foundation Medicine test volumes. ..................................................................................................................... 43

    Figure 8: Patent search results using terms that included “sequencing” for the years 2007-2011 and 2012-2017. ............................. 53

    Figure 9: Patent family search results for large public companies. ........................................................................................................ 54

    Figure 10: Patent family search results for DNA Sequencer, Instruments, and Reagents/Consumables Providers. ............................. 55

    Figure 11: Patent family search results for NGS Data Management, Analysis, and Process Infrastructure/Platform Providers. .......... 56

    Figure 12: Patent family search results for NGS Data Interpretation, Decision Making, and Reporting Providers. ............................... 56

    Figure 13: Patent family search results for Clinical-grade genetic/diagnostic testing and services providers. ....................................... 57

    Figure 14: The Clinical NGS Ecosystem. .................................................................................................................................................. 83

    Figure 15: Funding versus number of employees for the researched startup companies. .................................................................. 119

    Table and Tables

    Table 1: Overview of clinical NGS workflow target users’ successes and challenges. ............................................................................ 16

    Table 2: Genetic Counselor user profile. ................................................................................................................................................ 19

    Table 3: Clinical Geneticist user profile. ................................................................................................................................................. 20

    Table 4: Physician user profile. ............................................................................................................................................................... 21

    Table 5: Patient user profile. .................................................................................................................................................................. 22

    Table 6: Bench Researcher user profile. ................................................................................................................................................. 23

    Table 7: Bioinformatician/Computational Scientist user profile. ........................................................................................................... 24

    Table 8: End-user feedback on clinical testing labs. .............................................................................................................................. 26

    Table 9: Testing lab selection criteria. .................................................................................................................................................... 27

    Table 10: Detailed list of challenges that clinical end-users encounter. ................................................................................................ 29

    Table 11: Feedback on delivered clinical NGS reports. .......................................................................................................................... 30

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    Table 12: Clinical trends driven by NGS. ................................................................................................................................................. 33

    Table 13: NGS Adoption Challenges. ...................................................................................................................................................... 37

    Table 14: Technology trends that will positively influence the adoption and implementation of NGS in the clinic. ............................. 38

    Table 15: Fourth generation sequencing platforms. .............................................................................................................................. 39

    Table 16: NGS clinical applications. ........................................................................................................................................................ 44

    Table 17: Agilent Mergers & Acquisit