Endobronchial Ultrasound Guided Transbronchial Needle Aspiration and Next Generation Sequencing Yields

Abstract

Purpose: The use of endobronchial ultrasound (EBUS) is standard practice for lung cancer diagnosis and staging. Next generation sequencing (NGS) for detection of genetic alterations is recommended in advanced, non-squamous, non-small-cell lung cancer (NSCLC). Existing protocols for NGS testing are minimal and reported yields vary. This study aimed to determine the yield of EBUS samples obtained for NGS using a sampling protocol at our institution and assess predictive factors to form collection protocols.

Methods: We reviewed EBUS bronchoscopies from 2016 to 2021 with non-squamous NSCLC diagnoses. For target lesions suspected to be malignant, the sampling protocol was: (a) two slides for on-site evaluation, (b) three to five fine needle aspirations rinsed into saline for immunohistochemical staining and in-house molecular markers, and (c) additional three to five rinses for NGS. Sufficiency for NGS processing was determined by the pathology department.

Results: Two hundred and seventy-eight non-squamous NSCLC samples were obtained by EBUS (205 adenocarcinoma; 73 not otherwise specified). EBUS was performed under general anesthesia in 75.5% of cases. The overall sample adequacy for NGS testing was 57.5%. Higher adequacy rates were observed when protocol was adhered to 66.0% versus 37.2% (p < 0.001). There was no statistically significant difference based on the size of the lesion or location of the sample.

Conclusion: When a protocol of three to five dedicated needle rinses for NGS was followed, we nearly doubled our sample adequacy rate for NSG as compared to standard care. Studies are needed to determine the ideal collection and processing modality to preserve tissue samples for genetic sequencing.

Keywords: Bronchoscopy; EBUS-TBNA; Lung cancer; Molecular markers; Next generation sequencing.

Fig. 1

Consort diagram. EBUS endobronchial ultrasound; NSCLC non-small cell lung cancer; NOS not otherwise specified

Fig. 2

Sufficiency of samples for EGFR, ALK, ros-1, and NGS. Samples that were tested for EGFR, ALK, and ros-1 mutations as well as NSG, were evaluated by pathology to determine sufficiency of the sample to run molecular testing. 72.1% of samples were sufficient for EGFR, 73.6% for ALK, 73.3% for ros-1, and 57.5% for NGS

Fig. 3

Molecular genetic sufficiency stratified by number of aspirations of target lesion. Tissue samples sufficient for molecular testing (EGFR, ALK, and ros-1) were stratified by the number of aspirations obtained from the target lesion with the highest yields obtained with 5–10 aspirations

Fig. 4

Molecular genetic sufficiency stratified by size of target lesion. Tissue samples sufficient for molecular testing (EGFR, ALK, and ros-1) were stratified by the size of the target lesion and showed a general trend toward increased sufficiency with larger lesions

Fig. 5

Next generation sequencing yields based on protocol adherence (≥ 3 aspirations). Samples tested for next generation sequencing were stratified by number of aspirations taken from the target lesion. Yields were higher when three or more aspirations were obtained compared to less than three aspirations (66% vs 37.2%)