DEEPGEN TM-A Novel Variant Calling Assay for Low Frequency Variants

Genes (Basel). 2021 Mar 30;12(4):507. doi: 10.3390/genes12040507.


Detection of genetic variants in clinically relevant genomic hot-spot regions has become a promising application of next-generation sequencing technology in precision oncology. Effective personalized diagnostics requires the detection of variants with often very low frequencies. This can be achieved by targeted, short-read sequencing that provides high sequencing depths. However, rare genetic variants can contain crucial information for early cancer detection and subsequent treatment success, an inevitable level of background noise usually limits the accuracy of low frequency variant calling assays. To address this challenge, we developed DEEPGENTM, a variant calling assay intended for the detection of low frequency variants within liquid biopsy samples. We processed reference samples with validated mutations of known frequencies (0%-0.5%) to determine DEEPGENTM's performance and minimal input requirements. Our findings confirm DEEPGENTM's effectiveness in discriminating between signal and noise down to 0.09% variant allele frequency and an LOD(90) at 0.18%. A superior sensitivity was also confirmed by orthogonal comparison to a commercially available liquid biopsy-based assay for cancer detection.

Keywords: NGS; early cancer detection; liquid biopsy; performance validation; precision medicine; variant calling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomarkers, Tumor / genetics
  • Computational Biology / methods*
  • Early Detection of Cancer
  • Gene Frequency
  • Genetic Predisposition to Disease
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Liquid Biopsy
  • Mutation*
  • Neoplasms / diagnosis*
  • Neoplasms / genetics
  • Precision Medicine


  • Biomarkers, Tumor