Abstract 6687: Prevalence of four major gene mutation classes in a survey of ctDNA recovery from early and advanced stage NSCLC
Authors: Gould Claire , Jackson Leisa , Cochran Colin , Audetat Audrey , D'Alessio Brittany , Weaver Amanda , Riley Janice , Pestano Gary A. 
Published: April 2023

Abstract
Introduction: Circulating tumor DNA (ctDNA) has emerged as a powerful biomarker with many applications in oncology including early and late-stage disease prognosis and in treatment decision making. Liquid biopsies have become critical in non-small cell lung cancer (NSCLC) given the patient risks associated with biopsies. It is well established that circulating nucleic acid levels representative of all solid tumors are increased in advanced stages of the disease. Less well characterized is the status of cfDNA levels in the earliest stages of solid tumor progression. We used validated methods for quantitative fluorometry and a high sensitivity amplicon based NGS method to survey cfDNA recovery and prevalence for the four major mutation classes (copy number amplifications (CNAs), single nucleotide variations (SNVs), fusions, and insertions/deletions (INDELs)) from patients previously diagnosed with NSCLC.
Methods: Cell-free nucleic acid was extracted from 1,139 late-stage and 185 early-stage NSCLC plasma specimens. cfDNA was quantified using fluorometry, and the 52 gene GeneStrat NGS Test was used for the detection of CNAs, SNVs, fusions and INDELs. We evaluated cfDNA concentration (normalized to plasma input volume), quantity in circulation, and the prevalence of the four classes of mutations in early-stage (I-IIIA) versus late-stage (IIIB-IV) NSCLC.
Results: We observed significantly lower average concentrations of cf nucleic acids in plasma recovered from early versus late-stage NSCLC specimens (early-stage: 13.7 ng/mL; range (3.14, 118.65); n = 185; late-stage: 18.3 ng/mL; range (0.67, 187.2); n =1,139; p=0.00176). We also evaluated total cfDNA recovered for the sample set and observed significantly lower average measurements for early-stage specimens versus late-stage (early-stage: 101.4 ng; range (18.38, 652.6); n=185; late-stage: 140.5 ng; range (9.802, 1534); n=1,139; p=0.00692). We do note that there were overlaps at the low end of the ranges. Also significant was the finding that all mutation classes were more prevalent in late versus early-stage NSCLC. Specifically, 56 of 58 CNAs (96.6%); 737 of 805 SNVs (91.6%); 42 of 43 INDELs (97.3%) and 12 fusions (100%) were associated with late-stage specimens.
Conclusion: In this observational study cohort, cfDNA yields were significantly higher in late-stage NSCLC patients compared to early-stage. We also observed significantly more and varied mutations in plasma from late-stage patients. These initial findings need to be extended to additional cancers and refined by stage at diagnosis. We are currently expanding our study to include additional technologies and panels to assess ctDNA mutations especially for the early-stage patients. Quantitative cfDNA data may be of utility in diagnosis, monitoring and recurrence of cancer.
Citation Format: Claire Gould, Leisa Jackson, Colin Cochran, Audrey Audetat, Brittany D'Alessio, Amanda Weaver, Janice Riley, Gary A. Pestano. Prevalence of four major gene mutation classes in a survey of ctDNA recovery from early and advanced stage NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6687.