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. 2018 May:119:85-90.
doi: 10.1016/j.lungcan.2018.03.003. Epub 2018 Mar 7.

Feasibility of endobronchial ultrasound transbronchial needle aspiration for massively parallel next-generation sequencing in thoracic cancer patients

Simon R Turner  1 , Darren Buonocore  2 , Patrice Desmeules  2 , Natasha Rekhtman  2 , Snjezana Dogan  2 , Oscar Lin  2 , Maria E Arcila  2 , David R Jones  1 , James Huang  3
Affiliations

Feasibility of endobronchial ultrasound transbronchial needle aspiration for massively parallel next-generation sequencing in thoracic cancer patients

Simon R Turner et al. Lung Cancer. 2018 May.

Abstract

Introduction: Next-generation sequencing (NGS) allows for the identification of a growing number of therapeutic and prognostic molecular targets. However, NGS typically requires greater quantities of DNA than traditional molecular testing does. Endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive procedure used to sample central thoracic lesions, but it is not well established whether this technique provides sufficient material for NGS.

Methods: We performed a retrospective review of EBUS-TBNA at our institution (3/1/14-9/28/16). NGS was performed using a comprehensive hybrid-capture based assay (MSK-IMPACT) that detects >340 gene mutations. Samples found to be diagnostic for malignancy and for which MSK-IMPACT had been attempted were identified. Pathologic and clinical data were obtained from the medical record, and the results of MSK-IMPACT were examined.

Results: In total, 784 EBUS-TBNA procedures were performed during the study period. MSK-IMPACT was requested for 115 malignant samples and was successful for 99 (86.1%), identifying an average of 12.7 mutations at a mean coverage depth of 806X. NGS was performed on paraffin-embedded cell blocks in 93 cases (93.9%) and on cell-free DNA in needle rinse fluid in 6 cases. The success rate of the assay improved significantly from the first third of cases (76.3%), to 92.3% for the final one-third of cases (p < 0.05).

Conclusions: EBUS-TBNA reliably provided adequate tissue for hybrid capture NGS, and is a suitable option for comprehensive NGS testing in patients with thoracic malignancies.

Keywords: Endobronchial ultrasound; Lung cancer; MSK-IMPACT; Next-generation sequencing.

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Conflict of interest statement

Competing interest: All authors have no competing interest.

Figures

Figure 1
Figure 1
CONSORT diagram of endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA)procedures performed during the study period. Numbers refer to individual EBUS procedures
Figure 2
Figure 2
Success rate of the MSK-IMPACT assay over time, by third of cases included in the study.
Figure 3
Figure 3
Reasons for unsuccessful MSK-IMPACT assay and alternative molecular assays performed. cfDNA, cell-free DNA.
See this image and copyright information in PMC

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