Clinical NGS Process Report

  • ID: 4448887
  • Report
  • Region: Global
  • 209 Pages
  • EnlightenBio
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FEATURED COMPANIES

  • 10x Genomics
  • Congenica
  • Genestack
  • Invitae
  • PierianDx
  • Station X
  • MORE

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 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.

The 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.

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FEATURED COMPANIES

  • 10x Genomics
  • Congenica
  • Genestack
  • Invitae
  • PierianDx
  • Station X
  • MORE

1. Objectives

2. Learnings

3. The Clinical NGS Workflow

  • Data Analysis and Interpretation in the Clinical NGS Workflow
  • The Clinical NGS Process End-Users
  • Clinical NGS Workflow Personas
  • The Clinical NGS Workflow Users

4. User Type

  • The Genetic Counselor
  • The Clinical Geneticist
  • The Physician
  • The Patient
  • The Bench Researcher/Non-Computational scientist
  • The Bioinformatician/Computational Scientist

5. Clinical End-User Feedback

  • Choice of Clinical Testing Lab
  • Clinical End-User Challenges
  • Feedback on Reported Data
  • The Dutch Model

6. Clinical NGS Market Trends

  • NGS Market Trends
  • NGS adoption in the clinic
  • Single-cell applications
  • Emerging RNA-based applications
  • Clinical cfDNA applications
  • Mendelian genetic testing
  • Point-of-care testing
  • Data decentralization
  • Scaling NGS data analysis
  • Targeted therapies aimed at narrow patient populations
  • Sequencing and diversification into new markets

7. NGS Adoption Challenges

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

8. Other interesting market trends

  • Segmentation by Type
  • The increasing trend of clinical genetic testing
  • Segmentation by Application
  • Mergers and Acquisitions Impacting Clinical NGS

9. Ten Years of NGS Patents

  • International Patent Classification (IPC)

10. Leading Commercial Companies and their Patents

  • Large Public Company Patents

11. Patents of Instruments, Consumables Companies

  • Patents of NGS Data Management, Analysis, & Process Infrastructure/Platform Provid
  • Patents of NGS Data Interpretation, Decision Making, and Reporting Providers
  • Patents of Clinical-Grade Genetic/Diagnostic Testing and Services Providers
  • Top Patent Assignees Across all NGS Patent Families

12. Clinical NGS Projects/Initiatives

13. The Clinical NGS Solutions Ecosystem

  • Data Processing, Knowledge Extraction, and Reporting Companies Side-by-Side
  • Infrastructure, Platform, Data Processing Providers

14. Data processing speed, scalability, and flexibility

  • Data analysis pipelines
  • Infrastructure requirements of data processing/analysis products
  • Sequencing machine integration

15. Data Interpretation/Decision Making/Reporting

  • Tertiary Analysis - Sequence Data Interpretation and Insight Generation
  • Tertiary Analysis - Embedded interpretation content for insight generation
  • Partnerships and collaborations of data analysis and interpretation companies
  • Data Security and Compliance
  • The funding situation

16. Company/Product Profiles

  • DNA sequencer, instruments, and reagents/consumable provider
  • NGS data management, analysis, and processing infrastructure/platform providers
  • NGS data interpretation, decision making, and reporting providers
  • Clinical-grade genetic/diagnostic testing and services providers

List of 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 2007-2011 and 2012-2017
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
 
List of 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
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
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°) and tertiary interpretation (3°) 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
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

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  • 10x Genomics
  • Agilent Technologies
  • Bluebee
  • Blueprint Genetics
  • Congenica
  • DNAnexus
  • Edico Genome
  • Fabric Genomics
  • Genestack
  • Genoox
  • Golden Helix
  • Illumina
  • Invitae
  • Lab7 Systems
  • Oxford Nanopore
  • Pacific Biosciences
  • PierianDx
  • Qiagen
  • Seven Bridges Genomics
  • Sophia Genetics
  • Station X
  • Sunquest
  • Thermo Fisher Scientific
  • Veritas Genetics
  • WuXi NextCODE
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