As next-generation sequencing (NGS) moves into medicine, its widespread adoption means that sequencing machine manufacturers will require FDA approval to use these instruments in the clinical setting, and test manufacturers will need to adapt approved diagnostics to these platforms. Certain performance specifications will thus need to be established and used to ensure reliable test results.
Created in 2010 at the Center for Disease Control, the Laboratory Science, Policy and Practice Program Office (LSPPPO) is intended to “provide leadership, advocacy, and cross-cutting services to continuously strengthen the quality of laboratory science, policy, and practice at CDC, in the United States, and globally.” Part of this mission includes assistance to laboratories when implementing next-gen sequencing into their practice settings.
To facilitate the effective and appropriate use of next-gen technology, CDC convened a national workgroup for the Next-Generation Sequencing Standardization of Clinical Testing (Nex-StoCT) in April, 2011. Its Genetics Team along with the newly-established Nex-StoCT working group is developing a manuscript that, the organization says, will present “evidence- and quality management-based recommendations for attaining an analytically valid test result and meeting regulatory and professional practice standards for NGS.”
In 2010, the EuroGentest Validation Group published its paper outlining the principles of validation and verification in the context of human molecular genetic testing. The paper describes implementation processes, types of tests and their key validation components, and suggests relevant statistical approaches that can be used by individual laboratories to ensure that tests are conducted to defined standards.
As the CDC and the EuroGentest Validation Group continue to develop standards for the new world of gene-based clinical testing, the two major contenders for the clinical market, Life Technologies’ Ion Torrent and Illumina’s MiSeq, are focusing on FDA approval for their devices and the delivery of validated clinical tests adapted to their sequencing platforms.
Commercializing PGM Sequencer
Life Technologies’ Andy Felton told GEN that the company will first see CE-IVD clearance for the Ion PGM™ Sequencer in Europe in 2012 and then will pursue FDA clearance in the U.S. “We believe there is a lot of demand and we wouldn’t take this step unless we thought the market was ready for next-gen sequencing technology,” he said. “We have had a year on the market to stabilize the platform and to make improvements. The platform is ready to be taken forward.”
Since the PGM sequencer was launched in 2010, with a 10 Mb output on the Ion 314 Chip, a 127 Mb dataset has been released on the same chip. This shows, according to the company, greater than 10x scaling over nine months. The company has also released a 1 Gb dataset on the new Ion 318 chip, demonstrating 100x scaling of the platform in under a year.
Felton also said that “there has been incredible interest among players in diagnostics, a ground swell of demand in large and small companies for a regulated version of a next-gen sequencer. What this means for some of these companies is that they would develop a test and put it onto approved next-gen platforms.”
In October, Life Tech announced availability of its new Ion AmpliSeq™ Cancer Panel, the first product utilizing Ion AmpliSeq technology. It covers oncogenes and tumor suppressor genes. Standardization, Felton said, will boost individual technologies because the reagent and test have been through rigorous tests, providing confidence in answers given by a particular platform. “We believe there will be a large number of tests going forward, and we think the Ion PGM Sequencer is particularly suited because of its flexibility and because and you can scale the experiment to the chip.”
Felton expects applications for Ion PGM Sequencers will grow rapidly in areas like somatic mutation detection for cancers, resequencing for inherited diseases, and mendelian disease research. “Microbial applications will likely come a little bit later except in epidemiological use,” Felton added.
Validating TruGene on MiSeq
On November 2, 2011, Siemens Healthcare Diagnostics and Illumina announced that they entered into a partnership aimed at setting new standards in the use of next-generation sequencing for the rapid, accurate identification of patients’ infectious disease states and potential treatment paths.
Siemens and Illumina will initially work on making Siemens’ TruGene® HIV-1 Genotyping Assay, one of the first FDA-approved HIV-1 DNA sequencing-based tests, compatible with Illumina’s MiSeq analyzer.
“We had an FDA-cleared product on the market, TruGene, based on a slab gel sequencing technology, for eight years,” said Trevor Hawkins, Ph.D., head of next-generation diagnostics for Siemens’ Healthcare Diagnostics. “We looked at it and said this is a great starting point for Siemens to begin to understand how these next-generation sequencing devices could be used in real clinical settings. We have a large global TruGene community developing a lot of datasets and understanding of how to use sequencing in the clinic.”
He further explained that Siemens “got into this as we wanted to see what it would take to understand how to standardize methodologies, workflow, and IT/automation and answer all the questions on the table, including those related to chemistries and how data management would be handled.
“The key things we have been doing over the last couple of months include validation of results run on a standard TruGene platform versus those run with the MiSeq system and analyzing any differences in the data.” There is so much data that one of the key questions Dr. Hawkins seeks to answer is at what depth and sensitivity levels do you start to use the data in a clinical setting.
Dr. Hawkins also noted that Siemens has “been looking at cloud-based IT solutions; all these devices are cloud-enabled, so what will the impact be of cloud-based systems in the next 10 years? How will the TruGene community use cloud-based tools?”
Siemens is working on analyzing HIV sequences from the traditional platform for its HIV tests and analyzing output for known drug resistance. “The way in which next-gen systems work is inherently different from Sanger-based sequencing,” Dr. Hawkins pointed out. “The issues at hand are ones of using new chemistries and then validating that you are getting the same quality of results over large datasets.
“That is the work that has to go on: sequencing the same sample multiple times using the old technology and the new technology to ensure you are arriving at the same end-point answer at the same or better qualities with the new approaches.”
Siemens plans to go to the FDA this year with its next-gen sequencer-based tests. “Our programs in HIV are going as expected, and we are now looking at what potential assays could be our next challenge in taking next-gen sequencing to the clinic,” Dr. Hawkins stated. He anticipates that the FDA will be a partner in understanding how the devices will be used.
“Next-gen sequencers will change the way in which we interact with healthcare,” he asserted. “Everything we have seen before is going to change over the next five years because of these devices. We formed the partnership because Siemens wanted to be at the table talking to the customers, the community, and the FDA to see a real-world example of a widely used test.”
Investigators studying the use of next-gen sequencing in identifying patients, for example, at risk for breast cancer say that the cost savings in applying such technologies will allow the application of genetic testing to a wider range of individuals than is the current standard.
They also say as more next-generation sequencing technologies become available for genetic testing, results on sensitivity and specificity should be made freely accessible to those who order the test. Hopefully, they say, comparisons of various technologies will also become available.