An in-house, next-generation sequencing assay developed at University Hospitals Cleveland Medical Center, Ohio, was reliable, efficient, and cost-effective for genome sequencing of patients with advanced lung adenocarcinoma, according to a study published in Journal of Clinical Pathology.1
The assay tested variants across 52 genes relevant to solid tumors, and allowed concurrent analysis of RNA and DNA in a single workflow “to detect hot spots, single nucleotide variants, indels, copy number variants, and gene fusions in various types of solid tumors.” The assay can be performed on low-input, low-quality and formalin-fixed paraffin embedded tissue, including fine needle aspirate.
“By conducting a larger panel upfront, we are able to provide clinicians and patients with alteration data for the standard genes included in the FDA [US Food and Drug Administration] and NCCN [The National Comprehensive Cancer Network] guidelines in about the same amount of time and same reliability as a single-gene in-house EGFR assay,” researchers wrote. “Additionally, with the same assay, we are able to provide clinicians with information on a large number of other alterations, including the expanded FDA and NCCN guideline alterations and alterations outside these guidelines.”
To validate the use of this assay, the researchers tested it on cases that had previously been tested by several other FDA-approved assays. The new assay was able to detect all alterations identified by the approved assays.
Next, the assay was implemented on an institution-wide basis for any cases of advanced stage lung adenocarcinoma. With a sample cohort that consisted of biopsies (64%), excisions/recisions (16%), and fine needle aspirations (20%), the assay was reliable 95% of the time.
The assay had an average turnaround time of 4.8 days, half of the guideline-recommended period of 10 days, the researchers pointed out, and the cost of the assay was “competitive with single-gene testing.”
Finally, in 18% of cases, the assay identified FDA-approved or NCCN guideline-recommended targeted therapies for patients. Within this group, 60% of patients went on to receive genomically driven therapies for their disease.
“This information could be used to start patients on newly approved genomically driven therapies, enroll patients in current or future clinical trials, start patients on therapies through off-label use, inform management of immunotherapy, or change overall treatment strategy,” according to the researchers.
- Miller TE, Yang M, Bajor D, et al. Clinical utility of reflex testing using focused next-generation sequencing for management of patients with advanced lung adenocarcinoma [published online September 18, 2018]. J Clin Pathol. doi:10.1136/jclinpath-2018-205396