After a switch in reference laboratories for next-generation sequencing (NGS) of lung specimens at the University of Oklahoma College of Medicine, there was a drop in NGS adequacy rates which may be explained by a difference in specimen requirements.

These data were first presented by Omar Anani, MD, University of Oklahoma College of Medicine, at the American Society for Clinical Pathology (ASCP) 2025 Annual Meeting in Orlando, Florida.

In March of 2023, the reference laboratory used by the department of pathology at University of Oklahoma College of Medicine for NGS testing of lung specimens changed. This changed from pathologist-ordered NGS to clinician ordered NGS. In addition, submission of aspirate smears were no longer allowed by the new laboratory. 

This study included records for 275 lung cytology specimens from 3 months prior to the change in reference laboratory (pre-transition, n = 156) and 3 months after the change (post-transition, n = 119. For each procedure, the specimen adequacy, diagnosis, molecular testing results, pathologist, and clinician were recorded. Study authors noted that there were no changes in pathologist or pulmonologist staffing performing these procedures, nor were there any changes in collection methods or needle size or caliber. 

Among the pre-transition cases, 15(33%) were adequate for NGS testing. Of all, 98 were malignant, of which 46 were diagnosed as primary lung adenocarcinoma or non-small cell lung cancer (NSCLC). Among the post-transition cases, 6 (18%) were adequate for NGS testing. Of all, 79 were malignant, of which 32 were diagnosed as primary lung adenocarcinoma/NSCLC. The study authors explained that a potential contributing factor to the decrease in adequacy rates may be the change “from evaluating quantity of tumor present on a smear slide to identifying the presence of malignancy and saving additional passes for cell block."

Dr Anani et al concluded that there was “a drop in NGS adequacy rates after changing reference labs” and hypothesize this drop can at least in part be explained by “the disallowance of aspirate smears as a specimen type” which in turn forced “a change in the process for determining adequacy” at rapid on-site evaluation. 

The study authors added that the acceptance of aspirate smears for NGS testing could result in “more cost-effective patient care by reducing the need for repeated procedures.”

Source:

Anani O, Hamilton C, Adhikari L, and Peterson JEG. Lung adequacy assessment is dependent on specimen requirements for next-generation sequencing testing: A pilot study on changing reference laboratories. Presented at ASCP 2025 Annual Meeting. November 17-20, 2025; Orlando, Florida.