Molecular profiling of dedicated lung cancer biopsy tissue sample collected at time of diagnostic bronchoscopy.
Authors: Bellinger Christina , Bernstein Michael , Lee Hans , Wahidi Momen M. , Mahajan Amit , Chen Alexander , Shu Catherine A. , Hao Yangyang , Cao Manqiu , Griscom Bailey , Huang Jing , Walsh P. Sean , Lofaro Lori , Wilde Jonathan , Bulman William , Kennedy Giulia 
Published: June 2022

e20587

Background: The combined use of molecular biomarker testing and targeted precision therapeutics has led to improved survival in lung cancer. Broadening access to national guideline recommended comprehensive molecular testing requires overcoming the challenges of inadequate tissue biopsies, which can lead to the need for additional procedures and ultimately, delays in initiation of care. We show Percepta Genomic Atlas identifies key molecular alterations in transbronchial needle aspirate (TBNA) and transbronchial biopsy (TBB) samples of lung or lymph node collected during the initial diagnostic bronchoscopy. Methods: Percepta Genomic Atlas combines the whole exome TruSeq RNA Exome and targeted AmpliSeq Focus DNA assays (Illumina) for a comprehensive gene panel including ALK, RET, ROS1, NTRK1/3, MET, EGFR, BRAF, KRAS and HER2. TruSight Oncology 500 DNA and AmpliSeq Focus RNA assays (Illumina) were used as reference assays. DNA and RNA were extracted from samples with the AllPrep Micro kit (Qiagen) and analyzed by Percepta Genomic Atlas and reference assays. 94 biopsy samples (73 TBNA and 21 TBB from 71 patients undergoing a diagnostic bronchoscopy for suspected lung cancer were collected into RNAprotect (Qiagen) under an IRB approved protocol. Local molecular testing results from FFPE biopsy samples taken during the same bronchoscopy procedure were collected. Results: RNA and DNA in sufficient amounts to run the Percepta Genomic Atlas and reference assays was obtained from 85 of 94 lung biopsies from 63 of 71 patients. Percepta Genomic Atlas identified pathogenic variants in 29 bronchoscopy biopsy samples from 23 patients including single nucleotide variants in EGFR, KRAS, BRAF and PIK3CA, an EGFR exon 19 deletion/insertion and copy number amplications in AR, EGFR, CDK4, CCND1, MYC, MYCN and PIK3CA. No fusions were identified. This results in a 100% sensitivity for detecting pathogenic alterations when compared to reference assay results. When comparing Percepta Genomic Atlas results to local molecular testing of bronchoscopy samples performed as part of routine clinical care, we found 100% concordance with 7 of 7 alterations detected in 7 patients, including mutations in EGFR, KRAS and BRAF. In a further 4 patients, Percepta Genomic Atlas and local multi-gene NGS testing results agreed, with neither assay identifying guideline recommended alterations. Conclusions: Using a combination of whole exome RNA and targeted DNA sequencing, Percepta Genomic Atlas detects the clinically actionable mutations in patients with non-small cell lung cancer using fresh tissue specimens collected during bronchoscopic tissue sampling, with high concordance to standard of care testing. By initiating broad molecular testing at the time of the bronchoscopy, Percepta Genomic Atlas may provide timelier results for patients with lung cancer.