Molecular profiling in a Peruvian population with advanced non-small cell lung cancer assessed by NGS.

Abstract

e20612 Background: The use of next generation sequencing (NGS) both at diagnosis and disease progression has allowed us to detect changes in the genetic profile of patients that are potentially targetable. In this study we will describe the genetic profile of patients both at diagnosis and disease progression using NGS in tissue sample (TS) and liquid biopsy (LB). Methods: We evaluated 403 patients diagnosed with non-small cell lung cancer (NSCLC) referred to ONCOGENOMICS laboratory from 2016 to 2022 to somatic mutation testing. NGS was performed using the Ampliseq for Illumina FOCUS panel and run on the Illumina MiSeq. The panel targets single nucleotide variants (SNVs) and insertion/deletions (indels), copy number variation (CNVs), and gene fusions in 52 genes associate to solid tumors. Raw data were processed automatically on the BaseSpace Sequence Hub (Illumina) and aligned to the hg19 reference genome The default limit of detection (LOD) was set at 5% allelic frequency (VAF) in tissue samples and 0.5% VAF in ccfDNA samples. The Human Genome Variation Society (HGVS) nomenclature guidelines (http://varnomen.hgvs.org/) were used to annotate identified variants and the ClinVar database (www.ncbi.nlm.nih.gov/clinvar/) was used to determine the biological significance of all reported variants. Results: Of the 403 patients, 351 patients had NGS at diagnosis and 52 patients in disease progression. Regarding the genetic profile at diagnosis, we analyzed 328 tissue samples and 23 liquid biopsies, the most frequent alteration was the EGFR mutation, detected in 116 (33.1%) patients (detection rate TS 32.6% and LB 39.1%), followed by KRAS (15.4%), ALK (2.6%), BRAF (1.9%), and others (4.8%). In the disease progression setting, we analyzed 34 tissue samples and 18 liquid biopsies, the most frequent alteration was the EGFR mutation, detected in 28 (53.8%) patients (TS detection rate 29.4% and LB 44.4%), followed by KRAS (15.4%), ALK (3.9%), and others (3.9%). Conclusions: Peruvian patients are a population with a high mutation rate, in this cohort almost 50% of them had a target mutation, especially the EGFR mutation. Likewise, it was found that the detection rate of the EGFR mutation was higher with NGS in liquid biopsy than in tissue samples, both in the diagnostic and in the disease progression samples. On the other hand, it is important to mention that the frequency of KRAS mutations found is higher than previous Peruvian reports.