1. Market Research
  2. > Biotechnology
  3. > Genomics Market Trends
  4. > Advances in Clinical Genome Sequencing and Diagnostics - Overview

This report explores the recent surge in clinical genome sequencing, from the point of view of the sequencing providers, the medical organizations delivering these services, and the start-ups offering a variety of interpretation services, platforms, and business models.

Aspects discussed and presented include:

• Progress in clinical genome sequencing
• Organizations leading the way in generating clinical data and its interpretation.
• Determining the causality of documented variants in genetic disease.
• Clinical genome sequencing in oncology.
• Academic and commercial clinical genomics providers.
• The next-gen sequencing landscape.
• Companies providing genome interpretation software.
• Initiatives in setting sequencing standards.
• Interviews with six industry experts, conducted exclusively for this report.
• Results of a custom survey on clinical genome sequencing.
• A list of print and online resources for further investigation into this area.

For many years now, next-generation sequencing (NGS) has been used in clinical research, building on the success of being able to sequence personal genomes affordably, and turning that technology into defining the mutation profile of rare Mendelian diseases and cancer. With the first report of successful exome sequencing in a patient with a mystery illness, the clinical community has embraced NGS—performed in CLIA- and CAP-certified laboratories—for diagnostic testing.

Nevertheless, at the $1,000–5,000 price point, medical practitioners face a dilemma: It is possible to offer to sequence the exome or complete genome of a patient for roughly the same price as a traditional patented genetic diagnostic test or gene panel. Economics alone would appear to dictate that the practice of medical genetics and clinical diagnostics must evolve radically in the face of the remarkable advances in NGS. That sentiment has been bolstered in recent years with more and more anecdotal stories of the identification of mutations in patients suffering mysterious/undiagnosed (presumably) genetic disorders. Emboldened by these success stories, medical centers, sequencing platform providers, and diagnostics companies are rethinking their strategies for delivering exome and/or whole-genome sequencing services.

In a further irony, the cost of sequencing has fallen so fast that it is now a relatively trivial component of the full array of services required to deliver clinical genome information—what some have (literally or tongue-in-cheek) called the $100,000 or $1 million interpretation. Leaving aside the apples-and-oranges debate of the precise cost of genome interpretation, there is no doubt that 2012 proved to be a stunning year for the maturation of clinical genome testing. Several prominent, public stories relating to the successful end of diagnostic odysseys provide gratifying examples of the potential of this technology. Cases of families receiving a confirmed diagnosis after years of false hope and hundreds of thousands of dollars in medical costs show the benefit of this approach, and beg the question of how long the molecular diagnostics industry will continue in its single-gene/multigene panel approach. (After all, the exome is essentially just one giant gene panel with 22,000 genes.)

Exciting, remarkable progress in clinical genome sequencing is being fueled by steady advances in existing platforms, the arrival of new diagnostic platforms, and improvements in genome analysis software. That said, the adoption of clinical NGS is not trivial, and many questions still remain about setting standards, ensuring analytic and clinical validity of the tests, and reimbursement.

About the Author

Kevin Davies, PhD, is the founding editor of Bio-IT World and the journal Nature Genetics. He is the author of three books that explore the impact of technology and genomics in medicine, most recently “The $1,000 Genome” (Free Press, 2010). Kevin also serves as an advisor to Cambridge Healthtech Associates and blogs at NGS Leaders.

Table Of Contents

Advances in Clinical Genome Sequencing and Diagnostics - Overview
Table of Contents

Introduction

Chapter 1 - PROGRESS IN CLINICAL GENOME SEQUENCING
1.1. Proof of Concept
1.2. From Known to Unknown
1.3. Ending Diagnostic Odysseys
1.4. Search Strategy
1.5. Causal Variants and Databases
1.6. Cancer Genomics
1.7. Conclusions

Chapter 2 - CLINICAL GENOMICS PIONEERS AND PROVIDERS
2.1. Academic Medical Centers
Medical College of Wisconsin
Baylor Whole Genome Laboratory
UCLA Medical Genetics Clinic
Children's Hospital of Philadelphia (CHOP)
Emory Genetics Laboratory
Genomics and Pathology Services, Washington University in St. Louis (GPS@WUSTL)
Fox Chase Cancer Center, Philadelphia
2.2. Commercial Sector
Ambry Genetics
GeneDx
EdgeBio
Foundation Medicine
Courtagen Life Sciences
GeneInsight-Illumina Network

Chapter 3 - CLINICAL-GRADE SEQUENCING
3.1. The Next-Gen Sequencing Landscape
Illumina HiSeq/MiSeq
Ion Torrent
Complete Genomics
Pacific Biosciences (PacBio)
Qiagen/IBS
Nanopore Sequencing: Oxford Nanopore, Genia Technologies, and More
Oxford Nanopore
Genia Technologies
Other Technologies
3.2. Genome Interpretation Software
Ingenuity Systems
Omicia
SV Bio
Cypher Genomics
Personalis
Knome
InVitae Corporation
Genomatix
Station X
3.3. Genome Standards
The CLARITY Challenge
Sequencing Standards
Genome in a Bottle
The Archon Genomics X PRIZE

Chapter 4 - INSIGHT PHARMA REPORTS' CLINICAL GENOMICS SURVEY
Survey Questions:What Type of Lab Do You Work In?
Is Your Facility CLIA-Certified?
Is Your Facility CAP-Certified?
Where Is Your Facility Located?
Which Sequencing Instruments Do You Use and How Many of Each Do You Have?
Have You Outsourced To Any Sequencing Provider?
Which Sequencing Providers Have You Used?
What Is the Primary Sequencing Work Done In Your Lab?
Are You Considering Purchasing Any New Sequencing Equipment In the Next 12 Months?
Which Sequencing Platforms Are You Considering Purchasing and How Many?
What Type of Commercial Mapping/Assembly/Variant Caller Platform Do You Mostly Use?
What Other NGS Software/Platforms Do You Principally Use?
What Software Do You Use for Medical Genome Interpretation?
What Would You Estimate the Cost of Delivering a Medical-Grade Genome to Be?
What Do You Consider the Biggest Challenge In Integrating Whole-Genome Sequencing Into The Clinic?
Do You Have Any Experience Storing or Analyzing NGS Data In the Cloud?
Would You Put Clinical Data In the Cloud?

Chapter 5 - THOUGHT LEADER INTERVIEWS
5.1. Nazneen Aziz, PhD
Director of Molecular Medicine, Transformation Program Office, College of American Pathologists (CAP)
5.2. Elizabeth Worthey, PhD
Assistant Professor, Medical College of Wisconsin
5.3. Ashley Van Zeeland, PhD
CEO, Cypher Genomics, San Diego, CA
5.4. Ron Ranauro
Founder/Managing Partner, Incite Advisors
5.5. Karen Seibert, PhD
Professor, Department of Genetics, Washington University in St. Louis
Director, Genetics and Pathology Services (GPS@WUSTL), Washington University School of Medicine
5.6. Catherine Brownstein, MPH, PhD
Project Manager, The Gene Partnership's Research Sequencing Division, Boston Children's Hospital

References

Appendix

FURTHER INFORMATION/RESOURCES
Company Index



FIGURES

Figure 1.1. Filtration Decision Tree for Genomic Variants
Figure 2.1. GeneDx Letter for Pre-Authorization (Edited)
Figure 3.1. The Rapidly Falling Cost of Genome Sequencing

SURVEY FIGURES
Figure 4.1. What Type of Lab Do You Work In?
Figure 4.2. Is Your Facility CLIA-Certified?
Figure 4.3. Is Your Facility CAP-Certified?
Figure 4.4. Where Is Your Facility Located?
Figure 4.5. Which Sequencing Instruments Do You Use and How Many of Each Do You Have?
Figure 4.6. Have You Outsourced To Any Sequencing Provider?
Figure 4.7. Which Sequencing Providers Have You Used?
Figure 4.8. What Is the Primary Sequencing Work Done In Your Lab?
Figure 4.9. Are You Considering Purchasing Any New Sequencing Equipment In the Next 12 Months?
Figure 4.10. Which Sequencing Platforms Are You Considering Purchasing and How Many?
Figure 4.11. What Type of Commercial Mapping/Assembly/Variant Caller Platform Do You Mostly Use?
Figure 4.12. What Other NGS Software/Platforms Do You Principally Use?
Figure 4.13. What Software Do You Use for Medical Genome Interpretation?
Figure 4.14. What Would You Estimate the Cost of Delivering a Medical-Grade Genome to Be?
Figure 4.15. What Do You Consider the Biggest Challenge In Integrating Whole-Genome Sequencing Into The Clinic?
Figure 4.16. Do You Have Any Experience Storing or Analyzing NGS Data In the Cloud?
Figure 4.17. Would You Put Clinical Data In the Cloud?



TABLES

Table 1.1. Proof-of-Concept Identification of Mutation in Freeman-Sheldon Syndrome Exomes
Table 1.2. Companies Applying NGS Toward Cancer Diagnostics and Treatment
Table 3.1. Projected Sequence Throughput for Ion Proton Chips
Table 3.2. Potential Advantages of Nanopore Sequencing
Table 3.3. Comparison of HugeSeq to Other Genome Analysis Platforms
Table 3.4. Categorization of Clinical Variants by InVitae
Table 3.5. The CLARITY Challenge Contestants and Finalists

View This Report »

Get Industry Insights. Simply.

  • Latest reports & slideshows with insights from top research analysts
  • 24 Million searchable statistics with tables, figures & datasets
  • More than 10,000 trusted sources
24/7 Customer Support

Talk to Veronica

+1 718 514 2762

Purchase Reports From Reputable Market Research Publishers
The Chinese Market for DNA Sequencing

The Chinese Market for DNA Sequencing

  • $ 6650
  • Industry report
  • September 2016
  • by BCC Research

Use this report to: - Learn about recent advances and trends in the Chinese sequencing industry and market. - Analyze the Chinese sequencing market by workflow, including sample preparation products, ...

Agrigenomics Market by Application, Sequencer Type, Objective, and Region - Global Forecast to 2021

Agrigenomics Market by Application, Sequencer Type, Objective, and Region - Global Forecast to 2021

  • $ 5650
  • Industry report
  • September 2016
  • by MarketsandMarkets

“The agrigenomics market is projected to grow at a CAGR of 7.8%, in terms of value” The agrigenomics market is projected to reach USD 13.56 billion by 2021. Rising funds toward agrigenomics research ...

US Next-generation Sequencing Services Market

US Next-generation Sequencing Services Market

  • $ 4950
  • Industry report
  • September 2016
  • by Frost & Sullivan

$1,000 Genome Pricing and Throughput to Drive More and Larger Sequencing Projects The next-generation sequencing (NGS) services market includes all sequencing services conducted with next-generation o ...


Download Unlimited Documents from Trusted Public Sources

Genetic Industry in Denmark and Brazil

  • November 2016
    9 pages
  • Genetic  

  • Denmark  

    Brazil  

View report >

Global Nanomedicine Industry - Forecast

  • November 2016
    23 pages
  • Nanomedicine  

    Personal Genomi...  

    Gene Therapy  

  • United States  

    World  

    Japan  

View report >

Genome Sequencing Industry in the UK

  • November 2016
    29 pages
  • Genome Sequenci...  

    Infectious Dise...  

  • United Kingdom  

    United States  

View report >

Related Market Segments :

Genome Sequencing

ref:plp2013

Reportlinker.com © Copyright 2016. All rights reserved.

ReportLinker simplifies how Analysts and Decision Makers get industry data for their business.