FDA Authorised First Next-Generation Sequencer

Generation of genomic information will ultimately improve patient care

In 2013, the year that marks 60 years since James Watson and Francis Crick described the structure of DNA and 10 years since the complete sequencing of the human genome, the USA Food and Drug Administration (FDA) has granted marketing authorisation for the first high-throughput (next-generation) genomic sequencer.

Sequencing technologies have advanced dramatically, and today a human genome can be sequenced in about 24 hours for less than 5,000 USD. This is a rare example of technology development in which faster, cheaper, and better have coincided. With a platform that took nearly a decade to develop, clinicians can selectively look for an almost unlimited number of genetic changes.

Comprehensive analysis of the genome sequence of individual cancers has helped uncover the specific mutations that contribute to the malignant phenotype, identify new targets for therapy, and increase the opportunities for choosing the optimal treatment for each patient. Recent work from the Cancer Genome Atlas demonstrates that the tissue of origin of a particular cancer may be much less relevant to prognosis and response to therapy than the array of causative mutations. As a result, patients diagnosed with a cancer for which there are few therapeutic options may increasingly benefit from drug therapies originally aimed at other cancers that share common driver mutations.

A major area of opportunity that has yet to be fully exploited is pharmacogenomics. More than 120 FDA-approved drugs have pharmacogenomics information in their labeling, providing important details about differences in response to the drug and, in some cases, recommending genetic testing before prescribing. But the full potential of pharmacogenomics is largely unrealised, because of the logistic challenges in obtaining suitable genomic information in a timely enough fashion to guide prescribing. Placing genomic information in the electronic medical record would facilitate this kind of personalised medicine.

The FDA based its decision to grant marketing authorisation for the Illumina's MiSeqDx platform and reagents on their demonstrated accuracy across numerous genomic segments, spanning 19 human chromosomes. Precision and reproducibility across instruments, users, days, and reagent lots were also demonstrated.

Along with authorising the Illumina technology for marketing, the FDA recognized the need for reference materials and methods that would permit performance assessment. As a result, the FDA collaborated with the USA National Institute for Standards and Technology to develop reference materials consisting of whole human genome DNA, together with the best possible sequence interpretation of such genomes. The first human genome reference materials are expected to be available for public use in the next 12 months.

There are many challenges ahead before personalised medicine can be considered truly embedded in health care. Drs Francis Collins and Margaret Hamburg wrote in the perspective article published in the New England Journal of Medicine that researchers need to continue to uncover variants within the genome that can be used to predict disease onset, affect progression, and modulate drug response. New genomic findings need to be validated before they can be integrated into medical decision making. Doctors and other health care professionals will need support in interpreting genomic data and their meaning for individual patients. Patients will want to be able to talk about their genetic information with their doctor. Reimbursement issues need to be resolved to assure that patients have access to the best tests and that manufacturers have incentives to develop them.

Reference

Collins FS, Hamburg MA. First FDA Authorization for Next-Generation Sequencer. N Engl J Med 2013; 369:2369-2371.