Tech Intelligence
by Mike May AL
AL but analysis and reimbursement remain challenging
After the completion of the Human Genome Project, it was expected that medicine would change, indeed, our lives would change. By knowing the human genetic code, it would be possible to battle disease by having better- characterized targets and medicines as accu- rate as smart bombs. While medical practice has not been completely transformed, big changes are underway in genome sequencing in clinical situations. “There’ve been huge in- novations and improvements in the past three to four years, in particular,” says Wendy Chung, a pediatrician at Columbia University (New York, N.Y.) and an expert in the applications of clinical sequencing. “You can look at a single gene or the entire whole genome sequence.”
George Asimenos, director of strategic proj- ects at DNAnexus (Mountain View, Calif.), says, “From our perspective, clinical sequencing is increasingly applied in oncology to advance personalized treatment of cancer, identifica- tion and treatment of Mendelian diseases, and in prenatal genetic testing.”
Despite the growing list of clinical applications of sequencing, Jonathan Arnold, senior director of marketing for next-generation sequencing (NGS) at QIAGEN (Hilden, Germany), says, “We’re still in the early days.” For oncology, he notes, “NGS…[allows] clinicians to make a much more comprehensive evaluation of cancer samples.”
Clinical sequencing is being used increasingly, partially because of its decreasing price. In 2001, it cost nearly $10,000 to sequence a mil- lion bases of DNA, and now it’s about a penny, according to U.S. National Institutes of Health’s National Human Genome Research Institute. With sequencing so inexpensive, analysis
creates the real cost now. As Chung says, “The challenge now is more the data interpretation.”
With all of the hubbub surrounding next- generation sequencing, which is basically just faster and more complete than previous meth- ods like Sanger sequencing, scientists might think that only NGS is being used in clinical sequencing, but it’s not. In targeted applica- tions, where a clinician knows just what to look for, Sanger sequencing is still used. “If you had to say what technology is used most, measured as the number of base pairs produced by the industry,” Chung explains, “more than 99.9% is from NGS because you get so much more from one run.”
Whole or part? Some clinical situations call for a whole-
genome screen, while others can be done with screening for limited panels. Panels are fine for some forms of inherited cancer; in other cases, the targets are not clear enough to make an effective panel. “For childhood intellectual disabilities,” Chung says, “no panels give a high enough clinical yield, so you have to sequence the exome”—the entire protein-coding part of the genome.
Clinicians need platforms made specifically for NGS. “Illumina’s MiSeqDx is the world’s first FDA-cleared NGS instrument,” says Raj Kapadia, director of clinical marketing at Illumina (San Diego, Calif.). “It was designed with clinical lab- oratories in mind.” This platform can be used for the growing list of FDA-cleared assays and research-use-only (RUO) applications avail- able for Illumina’s MiSeq sequencer. “This ‘dual mode’ capability gives clinicians the ability to
AMERICAN LABORATORY 26 APRIL 2016
by author
Clinical Sequencing The decreasing cost of data collection increases medical use,
Illumina’s MiSeqDx is cleared for clinical use by the FDA and can also run a variety of research applications. (Image courtesy of Illumina.)
develop diagnostics, and provides researchers with the flexibility to pursue RUO experiments on the same instrument,” Kapadia says.
To make more sequencing tests available clini- cally, they need to be validated, verified and approved. “Illumina is working on developing clinical products, inclusive of informatics solu- tions, in the areas of reproductive and genetic health and oncology,” Kapadia says. “We also look for opportunities to partner with regula- tory agencies, associations and other industry players to set standards.”
QIAGEN’s GeneReader NGS is RUO; Arnold points out that having a complete solu- tion—sample preparation, sequencing and data analysis—in one platform makes it easier for clinical researchers to move to NGS. “This system goes from nucleic-acid extraction to data analysis and interpretation and solves the NGS adoption hurdles that laboratorians have struggled to overcome,” he says.
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