1783P Multi-parametric T cells profiling in broncho-alveolar lavage fluid (BAL) and blood from advanced lung cancer patients

Abstract

Background: High-throughput sequencing and ctDNA are driving the precision medicine paradigm shift. However, the analysis and the interpretation of the resulting data is an open challenge. By an integrated and multidisciplinary work among wet and dry lab experts, we have explored the feasibility of an automated BAM data solution with built-in variant calling.Methods: A cohort of 49 women with metastatic breast cancer was prospectively enrolled within the CRO-2018-56 clinical trial and characterized for ESR1 and PIK3CA genes by NGS of ctDNA. The resulting BAM files were analyzed using FreeBayes, GATK, Miseq Reporter, LoFreq, Mutect2, SAMtools and SNVer variant callers. Their concordance was evaluated by Cohen's kappa (k) with respect to manual annotation, both before and after filtering for clinical significance, based on the OncoKB database.