High-Density Sequencing Chips Will Soon Be Able To Sequence Five Million SNPs
Rapid gene sequencing is catching the interest of progressive anatomic pathologists. These medical laboratory professionals are interested in using rapid gene sequencing technology to allow them to study tens and hundreds of genes on a patient specimen.
The technologies used in rapid gene sequencing are being developed and improved by a handful of biotech companies who are racing each other be first to deliver systems to the marketplace that can sequence whole human genomes at a cost of $1,000 or less. Some innovative medical laboratories are beginning to acquire these sequencing systems and explore how they might be used for clinical pathology laboratory testing.
At a recent meeting in Washington, D.C., researchers involved in whole human genome sequencing reported on the latest breakthroughs. However, there was sober recognition of how much work remains to be done before doctors will be able to use multi-gene analysis to diagnose disease.
The meeting of the American Society for Human Genetics (ASHG) included a session titled, “Genomic Medicine: Current Status, Evidence Dilemmas, and Translation into Clinical Practice.” According to a Genetic Engineering & Biotechnology News article, attendees discussed “a real-world view of the opportunities and obstacles in acquiring and applying the data from whole-genome sequencing (WGS) and genome-wide analysis (WGA) studies.”
The article goes on to note that “although the technology is available to sequence an individual’s genome, it is still a relatively costly endeavor, and how best to analyze and interpret the clinical significance of the results is not yet clear.”
Bridging the Practicality Gap in Genetic Testing
At the conference, excitement ran high over new instruments and algorithms that promise to speed genome sequencing ten-fold. High-density chips containing 1 million variant markers will soon be replaced by arrays capable of identifying up to five million single nucleotide polymorphisms (SNP)—variations in DNA occurring in at least 1% of the population that scientist believe might cause predisposition to certain diseases.
Kelly Ormond, Associate Professor and Director of the Master’s program in human genetics and genetic counseling at Stanford University, and the session’s moderator, noted that there are “competing forces” at work driving the industry’s advancements—those who seek early adoption of the technology in clinical settings, and those who advise caution and continued research.
Euan Ashley, D.Phil., an Assistant Professor of Medicine and Director of the Center for Inherited Cardiovascular Disease at Stanford University, noted that current genomic databases need to be “reconfigured in a way that would make them easier to interpret and use in a clinical setting.” Ashley also noted that there are gaps in the data, and that the “regulatory and non-coding genome has been neglected.” Also noted was the need for a method of explaining genomic data to patients.
High Throughput, Lower Cost Technologies Would Help Medical Labs
In her presentation, Debbie Nickerson, Ph.D., Professor of Genomic Sciences at the University of Washington “emphasized the impact that next-generation sequencing (NGS) and emerging third-generation single-molecule sequencing technology will have on advancing knowledge about human genome variation, along with the ability to link genetic and phenotypic variation.” She described the next generation of sequencing technology as “disruptive” and “game-changing.”
Examples of companies developing such technologies include:
- 454 Life Sciences (a Roche company)
- Illumina’s HiSeq sequencing by synthesis technology
- Applied Biosystems/Life Technologies SOLiD system
- Complete Genomics CGA platform
- Pacific Biosciences’ Single Molecule Real-Time (SMRT) sequencing technology
- “The Chip is the Machine” semiconductor chip-based system from Ion Torrent (recently acquired by Life Technologies)
- Oxford NanoPore Technologies’ nanopore-based sequencing strategy.
Opportunities for Clinical Pathology Laboratories
Cecelia Bellcross, Ph.D., and a fellow with the Office of Public Health Genomics of the Center for Disease Control and Prevention, discussed the lack of funding available to “support the back-end of the genomic medicine pathway—comprised of clinical testing, data interpretation and application, and outcomes—compared to the funds available for generating genomic data.”
According to Genetic Engineering & Biotechnology News, Bellcross called for “funders, patients, clinicians, academician researchers, and lawyers to work together and close the gap between evidence and clinical applicability.”
Clinical laboratory administrators and pathologists will want to take note of the comments at this conference that coming soon will be high-density chips that will allow researches and laboratories to sequence five million single nucleotide polymorphisms (SNP) at a time. Not only does this indicate the pace of innovation in the gene sequencing field, but it is a reminder that clinical laboratories and anatomic pathology groups will need a robust informatics solution so that they can handle all this raw data.