The U.S. Food and Drug Administration (FDA) has cleared for clinical lab use a gene sequencing test designed by molecular pathologists at NYU Langone Health and its Laura and Isaac Perlmutter Cancer Center to guide treatment decisions for patients who have received a cancer diagnosis.
Cleared by the agency on July 15, 2021, under its 510(k) designation, the NYU Langone Genome Profiling of Actionable Cancer Targets (PACT) test detects changes in the DNA code of 607 genes linked by past studies to the development of multiple types of cancer.
PACT uses next-generation sequencing (NGS) technology, which can read the order (sequence) of the molecular “letters” making up DNA code within hundreds of genes simultaneously, and covers the most genes of any FDA-cleared NGS test to date. The technology matches the genetics of each patient’s tumor cells with a growing number of approved therapies targeted to address specific sets of cancer-causing DNA changes.
“The FDA decision on PACT reaffirms the goal behind its design, which was to provide our patients with the best understanding of the genetic changes driving their cancers,” says PACT designer Matija Snuderl, MD, director of molecular pathology and diagnostics in the Department of Pathology at NYU Langone. “Knowing the genetics of the tumor can help to determine which therapies will work for a given patient and their eligibility for specific clinical trials.”
As the NYU Genome PACT test generates huge amounts of data, a bioinformatics team led by Aristotelis Tsirigos, PhD, director of NYU Langone’s Applied Bioinformatics Laboratories, built a system that converts thousands of details on DNA code changes into a clear report for each clinician and patient on genes mutated in a given cancer sample and the implications.
The test development effort also featured a collaboration for genomic processing, interpretation, and reporting with the healthcare technology company Philips, which worked with the team to build an interface between the new test and EPIC, NYU Langone Health’s electronic medical records system. The PACT test was designed from the beginning, say the designers, to be integrated into electronic records, such that the tests can be seamlessly ordered, reviewed, and shared by a patient’s care team.
Why Certain Genes Were Included
The FDA clearance relates to deoxyribonucleic acid (DNA), the molecular chain in human cells that contains the blueprint for the body. As cells divide and multiply they must copy their DNA, a process that introduces errors into the code. The result is slight, continual, random changes called genetic mutations, some of which cause disease, including cancer when the affected genes influence tissue growth.
NGS rapidly determines the order of molecular letters (bases) in a DNA sample by breaking it into pieces and reading them in parallel. Along with speed and accuracy, such tests must achieve relevance by including the genes most often changed in disease. The PACT research team selected genes for inclusion in their test because their roles in cancers are established, or because the genes are related to targets of currently approved cancer drugs.
“We also included genes related to compounds currently in clinical trials, or some cases, where the evidence is strongly linked to cancers by basic science studies,” says Dr. Snuderl. “Beyond the genetic changes that are important to the field now, we also wanted PACT to detect the changes anticipated to be important in diagnosis and treatment of cancer over the next 5 to 10 years.”
While it is usually companies, not academic medical centers, that apply to have tests cleared by the FDA, Dr. Snuderl says, the NYU Langone Health team chose to do so to ensure that its test met the most stringent standards as they prepared to apply it to clinical care.
Further, the new test was designed to be part of ongoing efforts by the NYU Langone research community to find previously unknown changes in genes that further improve diagnoses, or yield new pathways to target with drugs. The PACT effort has already revealed genetic alterations (novel variants) that may be important to cancers, with the results validated by NYU Langone’s Genome Technology Center led by Adriana Heguy, PhD, assistant dean for advanced research technologies. Dr. Snuderl, Dr. Heguy, and Dr. Tsirogos are members of Perlmutter Cancer Center. The test is cleared for use by the FDA at this time only for use in patients of NYU Langone Health.
The work was supported by funding from the Department of Pathology at NYU Langone and Perlmutter Cancer Center, as well as by gifts from the Gray Foundation, The Holliday Foundation, Randye and Brian Kwait, Making Headway Foundation, and The Ambrose Monell Foundation.