FDA OKs 'Next-Gen' Gene Sequencing Devices for Clinical Use

Megan Brooks

November 20, 2013

The US Food and Drug Administration (FDA) has approved 4 next-generation gene sequencing devices for clinical use, the agency announced Monday.

The new technology will enable physicians to "take a broader look at their patients' genetic makeup and can help in diagnosing disease or identifying the cause of symptoms," the FDA said in a news release.

Next-generation sequencing, or NGS, is "changing the way we look at genomics," Alberto Gutierrez, PhD, director of the Office of In Vitro Diagnostics and Radiological Health in the FDA's Center for Devices and Radiological Health, said in the release.

"Before NGS, sequencing genes associated with a particular disease was a long and costly process. Today, we have the capability to read and interpret large segments of DNA very quickly in a single test, and this information-rich technology is becoming more accessible for use by physicians in the care of their patients," he explained.

In a statement, Francis S. Collins, MD, PhD, director of the National Institutes of Health, called the FDA's clearance of these high-throughput gene sequencing devices for clinical use a "landmark move that will help to realize the promise of personalized medicine."

Improving CF Diagnosis

Two of the devices are used to detect DNA changes in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that can lead to cystic fibrosis (CF).

The Illumina MiSeqDx Cystic Fibrosis 139-Variant Assay checks specific points in the patient's CFTR gene sequence to detect known variants in the gene. The Illumina MiSeqDx Cystic Fibrosis Clinical Sequencing Assay sequences a large portion of the CFTR gene to detect any difference in the CFTR gene compared with a reference CFTR gene, the FDA explains.

Data submitted by Illumina for their CF tests included comparisons of the sequence results to Human Genome Build 19, a reference representation of the human genome. Illumina also evaluated the performance of its instrument and reagent systems against a publically available quality-weighted human reference genome, according to the FDA.

The FDA also cleared the Illumina MiSeqDx instrument platform and the Illumina Universal Kit reagents.

These devices "make up the first FDA-regulated test system that allows laboratories to develop and validate sequencing of any part of a patient's genome," the agency explains.

"The Universal Kit reagents isolate and create copies of genes of interest obtained from patient blood samples, and the MiSeqDx platform analyzes the genes. The software compares the patient's genomic sequence to a reference sequence and reports back any differences between the patient and the reference," the agency notes.

"Immediate Impact"

"The FDA's review of the MiSeqDx and sequencer and Universal Kit reagents provides clinical laboratories with information about the expected performance of the device and the quality of the results," Dr. Gutierrez commented. "This information was not previously available for next-generation sequencers, and, with this platform, labs can develop tests for clinical use with greater confidence because they use FDA-authorized devices."

"The FDA reviewed the Illumina MiSeqDx instrument platform and the Illumina Universal Kit reagents through its de novo classification process, a regulatory pathway for some novel low- to moderate-risk medical devices that are not substantially equivalent to an already legally marketed device," the agency said.

Dr. Collins praised the FDA "not only for the immediate impact of its decision but for the pathway it has created for the clearance of future devices that may incorporate further improvements in sequencing technology and cost effectiveness."

"The availability of high-throughput DNA sequencers will enable physicians to take a comprehensive look at a patient's genetic blueprint, or genome, to search for a wide range of variations or changes that increase risk of disease, drive the disease process, and/or affect response to medications and other treatments. Such information has the potential to benefit patients in many ways. For example, an oncologist might use results of a sequencing scan to choose the chemotherapy drug that is most likely to work," Dr. Collins explained.

He cautioned, though, that this is "just the beginning."

"We still need to establish the clinical validity of new genomic findings before they are used to make medical decisions. We also need to work hard to ensure that physicians and other healthcare professionals have the tools they need to use genomic information well. So, while we may have taken one important stride today down the path towards personalized medicine, we must take many more if we are to achieve its full potential for improving human health," Dr. Colllins said.


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