Prospective Blinded Study of Somatic Mutation Detection in Cell-Free DNA Utilizing a Targeted 54-gene Next Generation Sequencing Panel in Metastatic Solid Tumor Patients

Oncotarget. 2015 Nov 24;6(37):40360-9. doi: 10.18632/oncotarget.5465.

Abstract

Sequencing of the mutant allele fraction of circulating cell-free DNA (cfDNA) derived from tumors is increasingly utilized to detect actionable genomic alterations in cancer. We conducted a prospective blinded study of a comprehensive cfDNA sequencing panel with 54 cancer genes. To evaluate the concordance between cfDNA and tumor DNA (tDNA), sequencing results were compared between cfDNA from plasma and genomic tumor DNA (tDNA). Utilizing next generation digital sequencing technology (DST), we profiled approximately 78,000 bases encoding 512 complete exons in the targeted genes in cfDNA from plasma. Seventy-five patients were prospectively enrolled between February 2013 and March 2014, including 61 metastatic cancer patients and 14 clinical stage II CRC patients with matched plasma and tissue samples. Using the 54-gene panel, we detected at least one somatic mutation in 44 of 61 tDNA (72.1%) and 29 of 44 (65.9%) cfDNA. The overall concordance rate of cfDNA to tDNA was 85.9%, when all detected mutations were considered. We collected serial cfDNAs during cetuximab-based treatment in 2 metastatic KRAS wild-type CRC patients, one with acquired resistance and one with primary resistance. We demonstrate newly emerged KRAS mutation in cfDNA 1.5 months before radiologic progression. Another patient had a newly emerged PIK3CA H1047R mutation on cfDNA analysis at progression during cetuximab/irinotecan chemotherapy with gradual increase in allele frequency from 0.8 to 2.1%. This blinded, prospective study of a cfDNA sequencing showed high concordance to tDNA suggesting that the DST approach may be used as a non-invasive biopsy-free alternative to conventional sequencing using tumor biopsy.

Trial registration: ClinicalTrials.gov NCT02067754.

Keywords: cell-free DNA (cfDNA); digital sequencing; genomic test.

Publication types

  • Clinical Trial
  • Observational Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Antineoplastic Combined Chemotherapy Protocols / therapeutic use
  • Cetuximab / administration & dosage
  • Class I Phosphatidylinositol 3-Kinases
  • Colorectal Neoplasms / blood
  • Colorectal Neoplasms / drug therapy
  • Colorectal Neoplasms / genetics
  • DNA Mutational Analysis / methods*
  • DNA, Neoplasm / blood
  • DNA, Neoplasm / chemistry
  • DNA, Neoplasm / genetics*
  • Female
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Male
  • Middle Aged
  • Mutation*
  • Neoplasm Metastasis
  • Neoplasm Staging
  • Neoplasms / blood
  • Neoplasms / drug therapy
  • Neoplasms / genetics*
  • Phosphatidylinositol 3-Kinases / genetics
  • Prospective Studies
  • Proto-Oncogene Proteins p21(ras) / genetics
  • Reproducibility of Results

Substances

  • DNA, Neoplasm
  • KRAS protein, human
  • Phosphatidylinositol 3-Kinases
  • Class I Phosphatidylinositol 3-Kinases
  • PIK3CA protein, human
  • Proto-Oncogene Proteins p21(ras)
  • Cetuximab

Associated data

  • ClinicalTrials.gov/NCT02067754