The U.S. Food and Drug Administration allowed marketing of four diagnostic devices that can be used for high throughput gene sequencing, often referred to as “next generation sequencing” (NGS). These instruments, reagents and test systems allow labs to sequence a patient’s DNA.
The new technology also gives physicians the ability to take a broader look at their patients’ genetic makeup and can help in diagnosing disease or identifying the cause of symptoms.
“NGS is changing the way we look at genomics,” said Alberto Gutierrez, director of the Office of In Vitro Diagnostics and Radiological Health in FDA’s Center for Devices and Radiological Health. “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.”
Two of the newly cleared devices are used to detect DNA changes in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which can result in cystic fibrosis (CF), an inherited chronic disease that affects the lungs, pancreas, liver, intestines, and other organs of those who inherit a faulty CFTR gene from both parents.
More than 10 million Americans are CF carriers and approximately 30,000 children and adults in the U.S. are affected with CF. Most children with CF are diagnosed by age 2 and the average life span for people with CF who live to adulthood is approximately 37 years.
The cleared devices include:
- The Illumina MiSeqDx Cystic Fibrosis 139-Variant Assay, which checks specific points in the patient’s CFTR gene sequence to detect known variants in the gene. Information about which DNA changes are associated with symptoms of cystic fibrosis is found in the Clinical and Functional TRanslation of CFTR database (CFTR2).
- The Illumina MiSeqDx Cystic Fibrosis Clinical Sequencing Assay, which sequences a large portion of the CFTR gene to detect any difference in the CFTR gene compared to a reference CFTR gene.
Data submitted by Illumina for their cystic fibrosis tests included comparisons of the sequence results to Human Genome Build 19, a reference representation of the human genome. In addition, Illumina evaluated the performance of its instrument and reagent systems against a publically available quality-weighted human reference genome that was created through collaboration between the FDA and the National Institutes of Standards and Technology (NIST).
FDA-authorized sequencing devices provide labs with quality and performance information
The FDA also granted de novo petitions for the Illumina MiSeqDx instrument platform and the Illumina Universal Kit reagents, two devices that 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 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 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,” said Gutierrez. “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.
For the de novo petitions, the FDA based its decision on the demonstrated performance of the MiSeqDx instrument and Universal Kit reagent systems across numerous genomic segments spanning 19 human chromosomes.
Illumina MiSeqDx instrument platform, Universal Kit reagents, MiSeqDx Cystic Fibrosis 139-Variant Assay, and MiSeqDx Cystic Fibrosis Clinical Sequencing Assay are manufactured by Illumina Inc. in San Diego, Calif.