Scientific Reports (Feb 2024)

Analytical evaluation of circulating tumor DNA sequencing assays

  • Wenjin Li,
  • Xiayu Huang,
  • Rajesh Patel,
  • Erica Schleifman,
  • Shijing Fu,
  • David S. Shames,
  • Jingyu Zhang

DOI
https://doi.org/10.1038/s41598-024-54361-w
Journal volume & issue
Vol. 14, no. 1
pp. 1 – 12

Abstract

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Abstract In China, circulating tumor DNA analysis is widely used and numerous assays are available. Systematic evaluation to help users make informed selections is needed. Nine circulating tumor DNA assays, including one benchmark assay, were evaluated using 23 contrived reference samples. There were two sample types (cell-free DNA and plasma samples), three circulating tumor DNA inputs (low, 50 ng), two variant allele frequency ranges (low, 0.1–0.5%; intermediate, 0.5–2.5%), and four variant types (single nucleotide, insertion/deletion, structural, and copy number). Sensitivity, specificity, reproducibility, and all processes from cell-free DNA extraction to bioinformatics analysis were assessed. The test assays were generally comparable or superior to the benchmark assay, demonstrating high analytical sensitivity. Variations in circulating tumor DNA extraction and quantification efficiency, sensitivity, and reproducibility were observed, particularly at lower inputs. These findings will guide circulating tumor DNA assay choice for research and clinical studies, allowing consideration of multiple technical parameters.