Author: Ken Rubenstein, PhD
Next-generation sequencing (NGS) has taken the worldwide biomedical research community by storm. Funding is relatively abundant for the moment, collaborative programs and consortia abound, and early results in many cases appear to justify all the activity. Many observers sense imminent new revelations and even paradigm shifts offering significant improvements in the understanding and treatment of disease. Discussed in this report:
Evolution of NGS technologies and applications
Applications of NGS in basic and applied research
Issues related to the popularity, viability, and cost of NGS applications
Key market-related issues in the field
Survey results and views among current and prospective NGS users
Interview transcripts with industry experts
Following an overview of the evolution of NGS, Next-Generation Sequencing Technologies: Applications and Markets turns to an examination of NGS applications in basic and applied research. A great deal of NGS effort today centers on cancer, but other basic research areas stand to benefit as well (e.g., immunogenetic studies, neurological and psychiatric diseases, infectious diseases, metagenomics, evolution). NGS has empowered the growth of epigenomics; several approaches exist, but bisulfite-enabled Methyl-seq currently dominates the scene.
NGS is also becoming increasingly popular for applications once dominated by microarrays. ChIP-seq’s improved data quality compared to microarrays permits greater accuracy in identifying protein-binding DNA targets. RNA-seq provides an alternative to microarrays in assessing cell transcriptomes and is well on its way to becoming the dominant mode in transcriptomics.
Although much of the benefit to date from NGS-based investigation falls in the basic research realm, a number of applied research areas are starting to show progress as well. Essentially all NGS manufacturers have intense interest in diagnostic applications, often both as supplier and participant. Collaborative programs aimed at such applications are now in progress. Several companies have focused on epigenetic assays in cancer resulting in some early commercial activity, but products have generally been slow to emerge.
Personal genomics has also been slow to develop as a business area. The field remains rather controversial, with proponents looking to its brilliant possibilities and opponents emphasizing the limited value of current offerings. However, the rapid pace of NGS basic research is likely to add significant value to personal genome sequencing in the next several years. Nearer-term NGS applications with established value include aneuploidy detection, carrier screening tests for multiple Mendelian diseases, mitochondrial DNA sequencing for a number of diseases, and others.
Next-Generation Sequencing Technologies: Applications and Markets includes observations from a survey we conducted among current and prospective NGS users regarding their practices and views on NGS adoption and applications. Tabulated results from the survey, along with clarifications and discussion, are provided. Also, although this report is focused on NGS applications, we provide some context with a brief look at what is known about the size and nature of the market for next-gen sequencing instruments and reagents. Also examined are trends within particular application areas.
Finally, we provide conclusions and prognosticate on possible future trends in the field. Included are full transcripts of interviews we conducted with researchers and managers knowledgeable in various aspects of NGS applications.
About the AuthorKen Rubenstein, PhD, a biochemist and molecular biologist, received his PhD at the University of Wisconsin and postdoctoral training at the University of Pennsylvania School of Medicine. He was a key innovator and research manager for Syva Company, the diagnostics branch of Syntex Corporation. During his 13 years with Syva, Dr. Rubenstein became Vice President, Scientific Affairs, a function that included strategic planning. Since 1983, he has served as a technology and marketing consultant to biomedical companies and an industry analyst, with more than 40 published studies to his credit.