Background: Systematic genomic testing to identify potential predictive biomarkers to select targeted therapy is emerging for NSCLC. DFCI introduced systematic testing for mutations in BRAF, HER2, PIK3CA and EML4-ALK translocations in addition to routine characterization of EGFR and KRAS in July 2009 as part of a prospective study. One and a half years have passed, thus we report our initial experience. Methods: Providers consented patients with advanced non-squamous NSCLC. Pathology specimens were dissected and analyzed by PCR-Sanger sequencing for mutations in selected exons of EGFR, KRAS, BRAF, PIK3CA and HER2. ALK rearrangements were detected with fluorescence in-situ hybridization. Results: Between 7/1/2009 and 4/12/2010, 226 consecutive patients were tested. The median age was 62 years. 134 (59%) were female, 195 (86%) had adenocarcinoma, 174 (77%) were former/current smokers and 182 (81%) had stage IIIB/IV disease. Five patients had two different specimens tested; three of these had repeat analyses due to test failure, one patient had two sites tested and another had two synchronous tumors tested. Of the 231 specimens, 25 (11%) either failed analysis or were inconclusive. The most frequent reason for inconclusive results was less than 50% tumor in the specimen (15/25). Of the remaining 206 specimens (204 pts), all underwent mutation testing for BRAF, HER2 and PIK3CA; 197/204 for EGFR, 187/204 for KRAS and 116/204 for ALK rearrangements. Mutations were identified in 110/204 (54%) patients (EGFR: 30; KRAS: 52; BRAF: 9; HER2: 9; ALK: 8; PIK3CA: 5) of whom three had concurrent mutations, all involving PIK3CA. The median time to complete testing for this initial phase was 30 days. From 7/1/2009 to 6/15/2010, 31 of 61 (51%) patients with EGFR, HER2, BRAF or EML4-ALK alterations were treated with molecularly targeted therapy based on their genetic alteration. Compared to 67% of patients with EGFR mutations, 9.6% patients with KRAS mutations received erlotinib. Conclusions: Large scale testing for alterations in EGFR, KRAS, BRAF, PIK3CA, HER2 and EML4-ALK is feasible and has an impact on treatment at our center. Updated results will be presented in June 2011.