Whole exome sequencing (WES) and RNA sequencing (RNA-seq) in routine clinical practice for colorectal cancer (CRC) and non-small cell lung cancer (NSCLC) patients (pts)

Abstract

Background: Precision medicine is a promising approach to select effective treatments for cancer pts. Here we report the use of WES and RNA-seq analysis in routine clinical practice, to select targeted therapies (TT) for pretreated metastatic cancer pts. Methods: CRC and NSCLC pts without druggable genetic alterations were selected during a multidisciplinary medical board. Fresh frozen (FF) and/or formalin-fixed paraffin embedded (FFPE) tissue of the primary and/or metastasis tumors were collected. Re-biopsy was performed when possible. Blood was drawn for comparative germline analysis. WES was performed on tumor/germline DNA, and RNA-seq on FF tumor RNA. Pts were systematically referred for genetic counseling and written informed consent was recorded. Results were reviewed during a second medical board, to identify molecular alterations and propose a relevant TT. Results: Between 09/2014 and 4/2016, 35 pts were selected; 1 pt refused WES analysis. 34 pts (13 CRC, 21 NSCLC) had WES and/or RNA-seq of their tumor; 1 pt refused to be informed of incidental germline mutations. The median age was 49 years (27-74). 8 pts had undergone a tumor re-biopsy. 45 tumor tissues (17 primary/28 metastatic) and 30 germline samples were tested. Germline mutations (BRCA2, STK11, MEN1, COL3A1, MYBPC3) were found in 5 pts. An average of 1.3 tumors (1-3) by pt was tested. WES was done on 37 FF and 4 FFPE tissues; 1 analysis failed because of low tumor cellularity. RNA-seq was done on 34 FF tissues. The median analysis turnaround was 21.5 days (8-92). Potential driver alterations were found in 27 pts, most frequently in HER/RAS/MAPK (n = 14), PTEN/PI3K/AKT (n = 6), STK11 (n = 4) pathways. Gene alterations were identified in chromatin organization (ARID1A/ ARID2/EZH2, n = 8), cell cycle checkpoint signaling (ATR/ATRX/ATM, n = 4), and DNA repair (BRCA1/BRCA2, n = 4) pathways. Therapy could be personalized in 13 pts, of whom 7 were included in a clinical trial. Conclusions: These results are encouraging on the feasibility of WES and RNA-seq analysis in routine clinical basis, in order to select dedicated TT in pretreated pts.