Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer

// Kajsa Ericson Lindquist 1, * , Anna Karlsson 2, * , Per Levéen 1 , Hans Brunnström 1, 3 , Christel Reuterswärd 2 , Karolina Holm 2 , Mats Jönsson 2 , Karin Annersten 2 , Frida Rosengren 2 , Karin Jirström 1, 3 , Jaroslaw Kosieradzki 4 , Lars Ek 4 , Åke Borg 2, 5 , Maria Planck 2, 6 , Göran Jönsson 2, 5 and Johan Staaf 2, 5 1 Department of Pathology, Regional Laboratories Region Skåne, Lund SE 22185, Sweden 2 Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden 3 Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund SE 22185, Sweden 4 Department of Respiratory Medicine and Allergology, Skane University Hospital, Lund SE22185, Sweden 5 CREATE Health Strategic Center for Translational Cancer Research, Lund University, Medicon Village, Lund SE 22381, Sweden 6 Department of Oncology, Skåne University Hospital, Lund SE 22381, Sweden * These authors have contributed equally to this work Correspondence to: Johan Staaf, email: johan.staaf@med.lu.se Keywords: lung cancer, NGS, gene fusion, mutation, precision medicine Received: November 01, 2016 Accepted: March 01, 2017 Published: March 16, 2017 ABSTRACT Precision medicine requires accurate multi-gene clinical diagnostics. We describe the implementation of an Illumina TruSight Tumor (TST) clinical NGS diagnostic framework and parallel validation of a NanoString RNA-based ALK , RET , and ROS1 gene fusion assay for combined analysis of treatment predictive alterations in non-small cell lung cancer (NSCLC) in a regional healthcare region of Sweden (Scandinavia). The TST panel was clinically validated in 81 tumors (99% hotspot mutation concordance), after which 533 consecutive NSCLCs were collected during one-year of routine clinical analysis in the healthcare region (~90% advanced stage patients). The NanoString assay was evaluated in 169 of 533 cases. In the 533-sample cohort 79% had 1-2 variants, 12% >2 variants and 9% no detected variants. Ten gene fusions (five ALK , three RET , two ROS1 ) were detected in 135 successfully analyzed cases (80% analysis success rate). No ALK or ROS1 FISH fusion positive case was missed by the NanoString assay. Stratification of the 533-sample cohort based on actionable alterations in 11 oncogenes revealed that 66% of adenocarcinomas, 13% of squamous carcinoma (SqCC) and 56% of NSCLC not otherwise specified harbored ≥1 alteration. In adenocarcinoma, 10.6% of patients (50.3% if including KRAS ) could potentially be eligible for emerging therapeutics, in addition to the 15.3% of patients eligible for standard EGFR or ALK inhibitors. For squamous carcinoma corresponding proportions were 4.4% (11.1% with KRAS ) vs 2.2%. In conclusion, multiplexed NGS and gene fusion analyses are feasible in NSCLC for clinical diagnostics, identifying notable proportions of patients potentially eligible for emerging molecular therapeutics.