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DEEPGENTM: a novel variant calling assay for low frequency variants

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...

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Main Authors: Hermann, Bernd Timo (Author) , Pfeil, Sebastian (Author) , Groenke, Nicole (Author) , Schaible, Samuel (Author) , Kunze, Robert (Author) , Ris, Frédéric (Author) , Hagen, Monika Elisabeth (Author) , Bhakdi, Johannes (Author)
Format: Article (Journal)
Language:English
Published: 30 March 2021
In: Genes
Year: 2021, Volume: 12, Issue: 4, Pages: 1-11
ISSN:2073-4425
DOI:10.3390/genes12040507
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.3390/genes12040507
Verlag, lizenzpflichtig, Volltext: https://www.mdpi.com/2073-4425/12/4/507
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Author Notes:Bernd Timo Hermann, Sebastian Pfeil, Nicole Groenke, Samuel Schaible, Robert Kunze, Frédéric Ris, Monika Elisabeth Hagen and Johannes Bhakdi
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Summary: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.
Item Description:Im Titel ist "TM" hochgestellt
Gesehen am 15.06.2021
Physical Description:Online Resource
ISSN:2073-4425
DOI:10.3390/genes12040507

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