Background: Significant progress has been made in improving progression-free survival in lung cancer through the combination of molecular biomarker testing and personalized therapeutics. Broadening access to national guideline recommended comprehensive molecular testing requires overcoming challenges of inadequate tissue biopsies, which can lead to the need for additional procedures and ultimately, delays in obtaining molecular testing. Additionally, there is growing evidence for the use of targeted therapies to treat early stage lung cancer and therefore a need for molecular testing across all stages of lung cancer. We show Percepta Genomic Atlas can identify key molecular alterations in early stage and advanced lung cancers and that it can successfully detect these alterations in surgical lung biopsy (SLB) specimens, transbronchial needle aspirates (TBNA) and bronchial brush specimens obtained during the initial bronchoscopy at the time of diagnosis. 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 orthogonal assays. 92 fresh-frozen SLB samples were purchased from BioIVT and biopsies from 25 patients undergoing a diagnostic bronchoscopy during an IRB approved clinical study were collected into RNAprotect (Qiagen). DNA and RNA were extracted from both sample sets with the AllPrep Micro kit (Qiagen) and analyzed by Percepta Genomic Atlas and orthogonal assays. Results: The Percepta Genomic Atlas assay was used to profile small amounts of RNA and DNA from lung cancer SLB tissues, of which 60% were Stage I, 24% Stage II and 16% Stage III. Genomic alterations were observed in 65% of Stage I, 64% of Stage II and 73% of Stage III samples including single nucleotide variants (SNV) in KRAS, EGFR, and PIK3CA, indels in HER2 exon 20, multiple copy number variants, and RET and MET exon 14 skip rearrangements. Percepta Genomic Atlas was used to successfully profile TBNA and bronchial brush specimens providing molecular data from all 25 patients and identifying multiple alterations including KRAS, EGFR and PIK3CA SNVs. Conclusions: Percepta Genomic Atlas detects clinically actionable alterations in both SLB of early stage lung cancer tumors and in specimens collected at the time of diagnostic bronchoscopy or needle aspiration prior to surgery. The early detection of actionable alterations at the time of initial tissue acquisition could minimize need for additional diagnostic procedures and inform earlier treatment decisions with the expanding field of targeted adjuvant therapy.