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Predictive Accuracy of Liquid Biopsy for Comprehensive Genomic Profiling of Solid Tumors

Cancer Genetics and Therapeutics
  • Primary Categories:
    • Cancer
  • Secondary Categories:
    • Cancer
Introduction:
Precision oncology relies on identifying somatic molecular abnormalities through Next-Generation Sequencing (NGS) analysis to identify targetable therapeutic recommendations (Tier 1 variants) and diagnostic/prognostic information. The development of targeted therapies has continued to progress, with numerous agents available for common oncogenic driver mutations in ALK, BRAF, EGFR, ERBB2, ESR1, KRAS, MET, PIK3CA, and ROS1. The gold standard for comprehensive genomic profiling (CGP) to identify somatic molecular abnormalities has traditionally been NGS performed on biopsied FFPE tissue. Recently, the development of liquid biopsy assays (LBx) has helped to identify somatic molecular abnormalities via NGS from circulating tumor DNA (ctDNA) in blood. Others have used LBx as a non-invasive testing option for various applications including early screening and diagnosis, treatment selection, and detection of residual disease and recurrent cancer.

Methods:
Using TruSight Oncology 500 (TSO500) NGS assays, a dataset was generated from patients that had both CGP from FFPE tissue and LBx from blood plasma (both kits are from Illumina Inc.). This dataset is comprised of small nucleotide variants (SNVs), multi nucleotide variants (MNVs), insertions and deletions (indels), and chromosomal rearrangements. Other somatic variables analyzed in this dataset include tumor type, tumor content, tumor mutation burden (TMB), microsatellite instability (MSI), patient age, and patient sex. 

Results:
The predictive accuracy of LBx relative to CGP data was generated from a large cohort of patients. Preliminary results from the paired tests revealed a high predictability. For lung cancer patients (n=41), LBx identified >80% of Tier 1 variants found in the corresponding CGP. For non-lung cancer patients (breast carcinoma (n=6), colorectal adenocarcinoma (n=5), salivary gland carcinoma (n=3), appendiceal carcinoma (n=1), cholangiocarcinoma (n=1), pancreatic adenocarcinoma (n=1)), LBx identified a high percentage (>95%) of Tier 1 variants found in the corresponding CGP.

Conclusion:
Liquid biopsy continues to be explored for its utilities in identifying somatic molecular abnormalities as precision oncology continues to progress. This comparative study demonstrates the predictability of LBx and CGP using the TSO500 platform, with a subset assessment for clinically relevant alterations and therapeutic targets. Somatic molecular abnormalities were also evaluated to determine their impact on identification of NGS results.

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