Date published 
March 2013

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Advances in Clinical Genome Sequencing and Diagnostics - 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