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Article

DEEPGENTM—A Novel Variant Calling Assay for Low Frequency Variants

1
Department of Research & Development, Quantgene Inc. 2940 Nebraska Ave, Santa Monica, CA 90404, USA
2
Department of General, Visceral and Accident Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany
3
Department of Surgery, University Hospital Geneva, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva, Switzerland
*
Author to whom correspondence should be addressed.
Genes 2021, 12(4), 507; https://doi.org/10.3390/genes12040507
Received: 25 February 2021 / Revised: 25 March 2021 / Accepted: 29 March 2021 / Published: 30 March 2021
(This article belongs to the Section Technologies and Resources for Genetics)
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. View Full-Text
Keywords: variant calling; performance validation; liquid biopsy; NGS; precision medicine; early cancer detection variant calling; performance validation; liquid biopsy; NGS; precision medicine; early cancer detection
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MDPI and ACS Style

Hermann, B.T.; Pfeil, S.; Groenke, N.; Schaible, S.; Kunze, R.; Ris, F.; Hagen, M.E.; Bhakdi, J. DEEPGENTM—A Novel Variant Calling Assay for Low Frequency Variants. Genes 2021, 12, 507. https://doi.org/10.3390/genes12040507

AMA Style

Hermann BT, Pfeil S, Groenke N, Schaible S, Kunze R, Ris F, Hagen ME, Bhakdi J. DEEPGENTM—A Novel Variant Calling Assay for Low Frequency Variants. Genes. 2021; 12(4):507. https://doi.org/10.3390/genes12040507

Chicago/Turabian Style

Hermann, Bernd T., Sebastian Pfeil, Nicole Groenke, Samuel Schaible, Robert Kunze, Frédéric Ris, Monika E. Hagen, and Johannes Bhakdi. 2021. "DEEPGENTM—A Novel Variant Calling Assay for Low Frequency Variants" Genes 12, no. 4: 507. https://doi.org/10.3390/genes12040507

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