SDPS-44 RAPID DETECTION OF MUTATIONS IN CSF-CFTNA WITH THE GENEXUS INTEGRATED SEQUENCER

Abstract

Abstract Brain metastases commonly arise in patients with lung and breast carcinomas and pose distinctive clinical challenges. Genomic alterations are fundamental for diagnosis and therapy selection in cancer patients. However, the turn-around-time (TAT) of standard next generation sequencing (NGS) assays is a limiting factor in the timely delivery of genomic information for clinical decision making. The GenexusTM Sequencer automates the NGS workflow delivering results in less than 24hrs. The Oncomine Precision Assay (OPA) evaluates somatic mutations, copy number variations and fusions in hot-spot regions of 50 cancer-related genes. In this study, we evaluated genomic alterations in 46 cerebrospinal fluid (CSF) samples from 33 patients with metastatic lung cancer (mLC) (N=32) and metastatic breast cancer (mBC) (N=14) to the brain. Cell-free total nucleic acids, (cfTNA) were extracted using QIAamp Circulating Nucleic Acid kit with cfDNA concentrations ranging from 0.1-11.2(ng/ul) and 0.5-6.6 (ng/ul) for mLC and mBC samples, respectively. Median base coverage was 37,913X and 33,576.5X for mLC and mBC samples, respectively, with cfDNA input ranging from 2-20ng. Mutations were detected in 15/32 (46.8%) mLC and 8/14 (57.1%) mBC CSF samples. Among the samples with no mutations detected, 18/23 (78.2%) had suboptimal DNA input (<20ng). The EGFR exon 19 deletion was detected in 4 samples from one patient, with increasing mutant allele fraction in CSF over time, highlighting the potential of CSF-cfTNA analysis for monitoring patients. Moreover, the EGFR T790M mutation was detected in a patient with prior EGFR inhibitor treatment. In addition, ESR1 D538G and ESR1::CCDC170 alterations, associated with endocrine therapy resistance, were detected in 2 mBC patients. The average TAT from cfTNA-to-results was ~16hrs. In summary, our results indicate that CSF-cfTNA analysis with the OPA in the Genexus instrument can provide clinically relevant information in patients with brain metastases with a short TAT.