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Ha Young Park



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    MA25 - Precision Medicine in Advanced NSCLC (ID 352)

    • Event: WCLC 2019
    • Type: Mini Oral Session
    • Track: Advanced NSCLC
    • Presentations: 1
    • Now Available
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      MA25.07 - Genomic Profiling of Lung Adenocarcinoma by Targeted NGS Using Extracellular Vesicle-Derived DNA in Bronchoalveolar Lavage Fluid (Now Available) (ID 1532)

      14:30 - 16:00  |  Author(s): Ha Young Park

      • Abstract
      • Presentation
      • Slides

      Background

      Extracellular vesicles (EV) are membrane-bound and nanometer-sized particles shed from most types of cells in our body and found in circulation, containing double-stranded genomic DNA reflecting mutational status of the parental tumor cells. Recently, we demonstrated that EVs successfully isolated from bronchoalveolar lavage fluid (BALF) in non-small cell lung cancer (NSCLC) patients. Several studies also have shown that EV-derived DNA is superior to cfDNA in plasma for detection of mutations in NSCLC and pancreatic cancer. We identified that liquid biopsy for EGFR genotyping using EV-derived DNA in BALF showed almost 100% sensitivity with tissue typing in advanced NSCLC patients. Therefore, we hypothesized that targeted next–generation sequencing (NGS) using EV-derived DNA in BALF may correlate with results using tissue in patients with EGFR-mutated lung adenocarcinoma.

      Method

      To address this hypothesis, we compared with the targeted NGS profile using between BALF EV-derived DNA and tissue DNA in 20 patients with EGFR-mutated lung adenocarcinoma. Four types of somatic variants (SNVs, small indels, CNVs and gene fusions) of BALF-EV or FFPE tissue samples were analyzed by CancerSCANTM, a capture-based targeted sequencing platform, which targets 375 genes covering about 2.5-megabase genomic regions including full CDSs of 374 genes, selected intronic regions of 23 genes for fusion detection, and 1kb TERT promoter region.

      Result

      Targeted sequencing resulted in over 99% of the target regions covered at a mean depth of 190-750× except one sample. DNA yields were higher in tissue DNA than EV-derived DNA (827.02ng vs 89.10ng). Depth of coverage (753x vs 379x) and estimated tumor purity (53% vs 23%) were also higher in tissue DNA than EV-derived DNA. However, estimated library size was not significantly different between tissue DNA and EV-derived DNA (50G vs 47G) and fragment size of DNA were longer in EV-derived DNA than tissue DNA (175.5bp vs 169.5bp). These findings support that EV-derived DNA has sufficient quality and quantity for NGS. By using mutations detected in tissue DNA as a reference, we achieved 83% sensitivity for somatic and clinically significant variants in EV-derived DNA. Clinically significant mutations in EGFR, TP53, PTEN, APC, JAK3 and PIK3CA were identified with an overall concordance of 81% in matched tissue DNA and EV-derived DNA. Variants in EGFR and TP53 were most common, with concordance of 80% and 100%, respectively. Variant allele frequencies of EGFR and TP53 were most abundant in range of 10-25% in tissue DNA, while much lower (<5%) in EV-derived DNA. Tumor mutation burdens (TMB) of EV-derived DNA showed correlation with tissue DNA (R2=0.21).

      Conclusion

      To our knowledge, this is the first of study of comprehensive clinical NGS panel using EV-derived DNA of BALF and matched tumor tissue biopsies in patients with lung adenocarcinoma. Although EV-derived DNA demonstrated comparable results to tissue DNA, it is needed much higher sequencing coverage and optimization of NGS-pipeline to detect low-allele frequency variants of EV-derived DNA. This study demonstrates the feasibility and clinical utility of BALF EV-derived DNA for patients with lung adenocarcinoma.

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