Clinical NGS Process Report

Transcription

1 Clinical NGS Process Report Table of Contents January 2018 enlightenbio LLC 650/ enlightenbio.com

2 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

3 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 4 th 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 White 3

4 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 White 4

5 Table and Figures Figure 1: The three high-level categories of the Clinical NGS workflow Figure 2: Clinical data analysis and interpretation Figure 3: The variant calling and classification process steps with examples of public data used for these steps Figure 4: The Clinical NGS workflow with processing steps and primary end-users Figure 5: End-user interviewees mapped to the Clinical NGS Process Figure 6: Clinical end-user unmet needs and gaps Figure 7: Invitae and Foundation Medicine test volumes Figure 8: Patent search results using terms that included sequencing for the years and Figure 9: Patent family search results for large public companies Figure 10: Patent family search results for DNA Sequencer, Instruments, and Reagents/Consumables Providers Figure 11: Patent family search results for NGS Data Management, Analysis, and Process Infrastructure/Platform Providers Figure 12: Patent family search results for NGS Data Interpretation, Decision Making, and Reporting Providers Figure 13: Patent family search results for Clinical-grade genetic/diagnostic testing and services providers Figure 14: The Clinical NGS Ecosystem Figure 15: Funding versus number of employees for the researched startup companies Table and Tables Table 1: Overview of clinical NGS workflow target users successes and challenges Table 2: Genetic Counselor user profile Table 3: Clinical Geneticist user profile Table 4: Physician user profile Table 5: Patient user profile Table 6: Bench Researcher user profile Table 7: Bioinformatician/Computational Scientist user profile Table 8: End-user feedback on clinical testing labs Table 9: Testing lab selection criteria Table 10: Detailed list of challenges that clinical end-users encounter Table 11: Feedback on delivered clinical NGS reports

6 Table 12: Clinical trends driven by NGS Table 13: NGS Adoption Challenges Table 14: Technology trends that will positively influence the adoption and implementation of NGS in the clinic Table 15: Fourth generation sequencing platforms Table 16: NGS clinical applications Table 17: Agilent Mergers & Acquisitions Table 18: Illumina Acquisitions & Mergers Table 19: Roche Acquisitions & Mergers Table 20: Thermo Fisher Scientific Mergers & Acquisitions Table 21: Qiagen Mergers & Acquisitions Table 22: Other Acquisitions Table 23: Number of patent families and top patent assignees for trending NGS domains Table 24: Overview of public and private consortia/initiatives Table 25: 100,000 Genomes Project Table 26: 10K Human Longevity Genomes HLIQ Table 27: Actionable Genome Consortium (ACG) Table 28: All of Us Research Program Table 29: AZ 2 Million Genome Project Table 30: BabySeq Table 31: California Initiative to Advance Precision Medicine (CIAPM) Table 32: UC Cancer Consortium Table 33: China Precision Medicine Initiative Table 34: ClinGen Table 35: Clinical Sequencing Evidence-Generating Research (CSER2) consortium Table 36: ClinVar Table 37: Earth Microbiome Project (EMP) Table 38: ENCODE Project Table 39: France Genome Medicine Plan Table 40: Gant Family Precision Cancer Medicine Consortium Table 41: Genome 10K Table 42: HapMap Table 43: Human Longevity Database White 6

7 Table 44: Human Microbiome Project (HMP) Table 45: Illinois Precision Medicine Table 46: Intl. Cancer Genome Consortium (ICGC) Table 47: Lung-Map Table 48: Matchmaker Exchange (MME) Table 49: MD Anderson Cancer Moon Shots Program Table 50: MedSeq Table 51: MetaSUB (Metagenomics and Metadesign of Subways & Urban Biomes) Table 52: Microbiome Coalition Table 53: Million Veteran Program (MVP) Table 54: National Microbiome Initiative (NMI) Table 55: Precision Health at the University of Michigan Table 56: St. Jude Washington University Pediatric Cancer Genome Project Table 57: The Cancer Genome Atlas (TCGA) Table 58: The Center for Health Information Partnerships (CHiP) Table 59: The ClinSeq Study Table 60: The Epilepsy Study Consortium Table 61: The International Genome Sample Resource (IGSR) Table 62: The NIH Roadmap Epigenomics Mapping Consortium Table 63: Set of data processing/analysis (2 O ) and tertiary interpretation (3 O ) companies analyzed in this report Table 64: Overview of speed, scalability, and configurability for the companies and their offerings analyzed Table 65: Types of pipelines offered by DNA processing companies Table 66: Infrastructure overview for the Infrastructure/Platform/Data Processing companies Table 67: Overview of companies providing direct sequencing machine integration Table 68: Data Interpretation, decision making, AI, ACMG guidelines, and reporting support for companies providing tertiary data interpretation Table 69: Overview of embedded content that enhances data interpretation in tertiary analysis tools Table 70: Overview of commercial analysis and interpretation tool companies partnership Table 71: Data security and compliance support Table 72: Companies in the clinical NGS space Table 73: Company profile 10x Genomics Table 74: Company profile Agilent Technologies White 7

8 Table 75: Company profile Illumina Table 76: Company profile Oxford Nanopore Table 77: Company profile Pacific Biosciences Table 78: Company profile Qiagen Table 79: Company profile Thermo Fisher Scientific Table 80: Company profile Bluebee Table 81: Company profile DNAnexus Table 82: Company profile Edico Genome Table 83: Company profile Genestack Table 84: Company profile Lab7 Systems Table 85: Company profile Seven Bridges Genomics Table 86: Company profile Congenica Table 87: Company profile Fabric Genomics Table 88: Company profile Genoox Table 89: Company Profile Golden Helix Table 90: Company profile PierianDx Table 91: Company profile Sophia Genetics Table 92: Company profile Station X Table 93: Company profile Sunquest Table 94: Company profile Blueprint Genetics Table 95: Company profile Invitae Table 96: Company profile Veritas Genetics Table 97: Company profile WuXi NextCODE Table 98: Abbreviations White 8

9 The Clinical NGS Process Report January 2018 The impact of next-generation sequencing on genomic medicine is tremendous the success of the first era of the human genome revolution created a stable foundation for today s discoveries. Technology development has allowed us to sequence and uncover mutational events at unprecedented scale and facilitates linking genomic data to high quality clinical data and diagnosis. As a result, data management and genomic analysis tools are rapidly developed a critical necessity to manage and make sense of the data to benefit research, the drug discovery process, and, of course, the clinic. Adoption and implementation of NGS and genomics discovery technologies have advanced clinical assessment of genomic alterations associated with oncology, hereditary cancer, cardiology, pediatrics, rare disease, among others. The next logical goals for NGS solutions, besides risk detection and disease identification, are disease prevention and management. The multi-faceted, complex Clinical NGS Workflow demands powerful, yet user-friendly, solutions across the entire process. The complex NGS technology bears many challenges beyond overcoming hurdles such as regulatory oversight, reimbursement challenges, or educating the physician/clinician on the benefits of this powerful enablement. While data production is not a challenge anymore, and targeted panels are well adopted, the expected dramatic rise in whole exome and genome sequencing will result in unforeseeable quantities of data at the clinical level that need to be managed, understood, and communicated. Low-cost sequencing of whole genomes, at population scale is already in existence, but not yet widespread in the clinic, as we are still unable to fully interpret what most of the observed changes at the genome level mean, and how they explain an existing phenotype. Scalable, fully automated analysis and knowledge extraction solutions incorporating rich annotation information are necessary to overcome these challenges. Over time, the clinical variant-to-gene-to-disease knowledge will become available for interpretation, requiring correct, complete, and integrated content for expedited knowledge extraction. With rising, massive quantities of NGS data (linked to different types of data), artificial intelligence and machine learning are hailed as pivotal solutions to address the data interpretation and knowledge extraction challenges and advancing the application of NGS in the clinic. In line with this demand, the sequence data analysis, knowledge extraction, and clinical reporting space is rich with commercial platforms and software solution providers trying to address this need via a multitude of offerings. Some of these commercial solutions support or overlap with clinical NGS workflow components or features, while others differ substantially in their inherent capabilities. This creates a competitive environment, which presents challenges to the end-users and different organizations seeking the appropriate product for their specific clinical NGS workflow needs. While commercial companies struggle with understanding White 9

10 the competitive landscape or how to best partner for a successful product and business strategy, this report clarifies similarly aligned solutions providers and those providers whose technology may fill a current gap in a company s portfolio. Clinical end-user interviews pointed out the challenges associated with received clinical testing results that includes limited annotations, particularly when it comes to VUSs (variants of uncertain significance) and communicating those results to the patient and physician. Our Clinical NGS Workflow Report examines the clinical NGS process and includes a review of the clinical end-users, the current market trends, players across the data analysis and interpretation part of the workflow, their offerings, funding situation, strategic partnerships, mergers and acquisitions, number of patents, and a comparative analysis of a range of capabilities that uniquely address different components across the data analysis and extraction process. This deeper analysis uncovers differences in product characteristics related to data processing, analysis, knowledge extraction and reporting of findings (including type of content integrated for meaningful extraction), and compliance and security mechanisms. Both clinical end-users and commercial companies who require insight into this expanding industry and its providers and products will benefit from our critical, investigative report. A set of commercial companies was analyzed revealing top players across the entire Workflow: Bluebee, DNAnexus, Edico Genome, Illumina (with BaseSpace), Lab7 Systems, and Seven Bridges Genomics are leading the group with different fast and secure data processing platforms and implementations; Agilent (with Alissa Clinical Informatics), Congenica, Fabric Genomics, Golden Helix (with VarSeq), PierianDx, Sophia Genetics, Station X, Sunquest, Qiagen, and WuXi NextCODE are among the top players on the knowledge extraction and clinical reporting side, integrating and providing different types of content for data interpretation; while Ambry Genetics, Blueprint Genetics, Color Genomics, Fulgent Genetics, Foundation Medicine, Myriad Genetics, and Invitae were the primary choices of genetic testing labs as indicated by clinical end-users. While this report does not intend to provide direct recommendations on commercial offerings, the deep-dive analysis is an insightful review to help clinicians, researchers, commercial entities, and investors choose the best partner for success. The 209 page Ecosystem Analysis Report consists of 15 Figures, 98 Tables, and 26 comprehensive Company Profiles which includes company metrics, funding sources, product details, founder/executive and board information, additional notes, and company visions. For more information contact info@enlightenbio.com or visit our website, enlightenbio.com. White 10

11 The Clinical NGS Process Our Clinical NGS Process Report details the observations through the Data/Insights generation process stages, which predominantly address data analysis, data interpretation to extract knowledge from sequence data, and reporting of clinical findings. The report data highlights end-users unmet clinical needs and challenges, market trends, an overview of in the clinical NGS space, and an extensive comparative ecosystem analysis of key solutions providers in the clinical NGS processing, analysis, and interpretation space, including clinical DNA testing service providers. White 11

12 Objectives of this Report Our Clinical NGS Workflow Report details the observations and learnings across the complex, multi-step informatics aspects following clinical NGS sample preparation and sequencing, and which includes data analysis, knowledge extraction, and clinical reporting of actionable findings. Market trends, including listing of major initiatives, merger and acquisitions, and a summary of patents are detailed within the report, while also highlighted are clinical customer/end-users unmet interpretation and knowledge extraction needs and challenges, and genetic testing lab preferences. Finally, an extensive comparison of solution providers in the SaaS and PaaS sector for the analysis and interpretation of clinical NGS data is included. To create our robust comparison, we followed a research path rooted in these questions: who are the clinical end-users and what are their unmet needs and challenges; who are the key commercial solution companies and what products do they offer; who are the genetic testing service providers and what services do they provide? When researching the analysis and interpretation market, what needs do these companies address with what product capabilities, and how do they compare across the ecosystem of solution providers? 1) End-user interviews: Conducted to understand clinical needs, testing lab preferences, and challenges when receiving clinical variant data and communicating findings to the physician and the patient. 2) Meta-Data analysis: Performed a deep-dive interrogation of individual software, platform solutions, and genetic testing providers with publicly available information on the internet. 3) Patents analysis: Studied the last ten years of NGS assignees across all NGS patent families, number of patents of leading commercial companies, and clinical-grade genetic/diagnostic testing providers. Patent analysis contributed by our partner company Pramoedya Biointelligence. 4) Deep ecosystem level analysis: Evaluated key commercial software and platform providers (N=23) that offer a clinical NGS analysis or interpretation solution, to understand their product focus and offered capabilities, their strategy to address end-user needs, and more. 5) Company/product profiles: Reviewed key companies with comprehensive solutions across the entire Clinical NGS Workflow (N=26), including genetic testing/diagnostics service providers their product focus, offered capabilities, and their strategy to address end-user needs, and more. 6) Key representative input: Interviewed company representatives of established commercial software product suppliers to learn about their vision for product solutions in the current and future product solutions space. White 12

13 Eight (8) Clinical End-User Interviews Eight end-users were interviewed. Each organizational logo represents an interviewee. The organizational logos align with the interviewee s focus within the clinical NGS process. Furthermore, the one patient interviewed is an ALL (acute lymphocytic leukemia) patient. White 13

14 The Clinical NGS Solutions Ecosystem A Comparative Analysis The advancements in high-throughput next-generation sequencing demand powerful, secure, accurate, and cost-effective solutions for the clinic to adopt NGS, a driving force to realize the future of precision medicine. The entire workflow includes sequence data generation, data analysis and meaningful knowledge extraction, and reporting of clinical findings for the end-users in the clinic. Current commercial offerings provide various sequencing, analysis, interpretation, and reporting solutions and approaches. The four main stages are: Consumables/Sequencer/ Instruments, Infrastructure/Platform/Data Processing, Data Interpretation/Decision Making/Reporting, and Clinical-Grade DNA Testing & Services. Companies within each of the stages provide varied products that address specific needs, as well as different value propositions (see also chapter Company/Product Profiles ). Within this report, we focus predominantly on the different players and their products within the Infrastructure/Platform/Data Processing, Data Interpretation/Decision Making/Reporting, and Clinical-Grade DNA Testing & Services stages. Numerous companies exist in the secondary and tertiary analysis space. They either provide a solution for secondary data analysis (2 o ), tertiary data interpretation (3 o ), or reporting of the findings. Some of these companies offer a focused capability in one sector, whereas others attempt to address the entire analysis and interpretation section in a true end-to-end solution. Many of these companies are either niche companies, only tangential to the secondary or tertiary analysis space, or do not have the same company momentum as the companies included in this analysis. This comparative analysis focuses on 23 key players/products. The companies selected have high funding power, a well-received customer perception, are strategically well connected with relevant partner companies, or enjoy a general high visibility in the sector. Not included are companies focusing exclusively on information management. Companies/Products included in the analysis: Alissa Clinical Informatics (Agilent), Appistry, BaseSpace Sequence Hub (lllumina), NxClinical (BioDiscovery), Bluebee, Congenica, DNAnexus, DNASTAR, Edico Genome, Fabric Genomics, Genalice, Genestack, Genoox, Golden Helix (VarSeq), IVA and CLC Genomics Workbench (Qiagen), Lab7 Systems, N-of-One, PierianDx, Seven Bridges Genomics, Sophia Genetics, Station X (with GenePool), Sunquest Mitogen, and WuXi NextCODE. White 14

15 A comparative analysis with key players in the secondary and tertiary analysis space provides an understanding of product focus, strategy to address end-user needs, and status of specific providers (funding, strategic investments and partnerships, number of employees, and more). Only a subset of 23 companies shown in this graph is included in this comparative analysis. Input from key representatives of established commercial research product suppliers provide learnings about their vision for product solutions in the current - and future - space. White 15

16 Twenty-Six (26) Company/Product Profiles 10x Genomics - I/C Agilent Technologies (Alissa Clinical Informatics - formerly Cartagenia) - I/C, DA, DI Bluebee - DA Blueprint Genetics - GT Congenica (Sapientia) - DI DNAnexus - DA Edico Genome - DA Fabric Genomic DA, DI Genalice - DA Genestack - DA Genoox DA, DI Golden Helix (VarSeq) DI Illumina (BaseSpace) - I/C, DA, DI Invitae- GT Lab7 Systems DA, DI Oxford Nanopore - I/C Pacific Biosciences - I/C PierianDx DA, DI Qiagen (IVA & CLC Genomics Workbench) - I/C, DA, DI Seven Bridges Genomics - DA Sophia Genetics DA, DI Station X DI Sunquest DA, DI Thermo Fisher Scientific - I/C Veritas Genetics DI, GT WuXi NextCODE DI, GT Company/product profiles of Clinical NGS Process companies, including DNA sequencer, instruments, and reagents/consumables providers (I/C); NGS data management, analysis, and process infrastructure/platform providers (DA); NGS data interpretation, decision making, and reporting providers (DI), Clinical-grader genetics/diagnostics testing and services providers (GT). Company profiles highlight company metrics (funding, number of employees, etc.), product details, data security and privacy guarantees, founder/executive and board information, additional notes, and the respective company vision. White 16

17 Key Data from Secondary Sources Clinical NGS workflow end-user challenges, & unmet needs User interviews Clinical NGS market trends User interviews Company representatives Press releases Public databases World Wide Web Product details Company websites Press releases Public reports User interviews Company representatives Clinical SaaS & PaaS ecosystem analysis Company websites Press releases Public reports User interviews Company representatives Ten years of NGS patents overview Patent classification systems Clinical NGS projects/ initiatives Press releases Public databases World Wide Web Company profiles Company websites Annual reports Press releases Public databases World Wide Web White 17

18 Companies & Products Mentioned in Report 10xGenomics, Agilent Technologies (& Alissa Clinical Informatics), Amazon, Ambry Genetics, Appistry, BGI, Illumina (with BaseSpace), BioDiscovery (NxClinical), Bluebee, Blueprint Genetics, ACLC Bio, Congenica, DNAnexus, DNASTAR, Edico Genome, Fabric Genomics, Foundation Medicine, Fulgent Genetics, Genia (Roche Sequencing System), Genalice, Genestack, Genoox, Golden Helix (VarSeq), Google, Human Longevity, Illumina, IBM, IMS Health, Ingenuity Systems, Invitae, Lab7 Systems, LabCorp, Microsoft, Myriad Genetics, Nanostring, N-of-One, Oxford Nanopore Technologies, Pacific Biosciences, Perking Elmer, PierianDx, Qiagen (with CLC Genomics Workbench and Ingenuity s IVA), Raindance, Seven Bridges Genomics, Sophia Genetics, Station X (with GenePool), Sunquest, Thermo Fisher Scientific, Veritas Genetics, Wuxi AppTec, and WuXi NextCODE. White 18

19 About enlightenbio LLC enlightenbio was founded in 2013 in the San Francisco Bay Area to provide a conduit between research and related technical and analytical resources. Our company consists of PhD level research scientists who bring decades of industry experience and expertise in the biotechnology, molecular diagnostics, pharma, and life science research markets. We are dedicated to communicating in the researcher s language, identifying unmet needs, and understanding product development. Our goals are aligned to researcher s needs to increase experiment productivity and to make sense of the resulting biological data. In addition to our varied industry experiences - Applied Biosystems (now Thermo Fisher Scientific), DNAnexus, Iconix Biosciences, Incyte, Ingenuity Systems (now a Qiagen company), and Pfizer we have built and maintained content curation services, defined product strategy, managed tactical product projects, performed extensive ecosystem analyses, and defined go-to-market plans. Building on our initial success and previous experiences - microarray and next-generation sequence data analysis, toxicogenomics, solutions for sequence data management, analysis, and interpretation, drug discovery, and biochemistry - we continuously monitor worldwide market trends in healthcare information technology, life sciences, genomics, clinical diagnostics, and medical devices space to expand our critical service offerings. Combined with our extensive global network, we can identify target market pain points and unmet needs, preform detailed market and product research, and undertake horizontal and vertical ecosystem or competitive analyses, and more. This background with our future-focus makes us a resourceful and agile alternative to traditional market research companies. Our comprehensive knowledge of the market we live and breathe is invaluable to our partnerships and potential. enlightenbio, along with market research reports is managed by Brigitte Ganter, PhD, Founder & Managing Director of enlightenbio LLC. White 19