Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits

Ultrasensitive methods for rare allele detection are critical to leverage the full potential offered by liquid biopsies. Here, we describe a novel molecular barcoding method for the precise detection and quantification of circulating tumor DNA (ctDNA). The major benefits of our design include straig...

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Bibliographic Details
Published in:Scientific reports 2017-09, Vol.7 (1), p.10574-10574, Article 10574
Main Authors: Alcaide, Miguel, Yu, Stephen, Davidson, Jordan, Albuquerque, Marco, Bushell, Kevin, Fornika, Daniel, Arthur, Sarah, Grande, Bruno M, McNamara, Suzan, Tertre, Mathilde Couetoux du, Batist, Gerald, Huntsman, David G, Cavallone, Luca, Aguilar, Adriana, Basik, Mark, Johnson, Nathalie A, Deyell, Rebecca J, Rassekh, S Rod, Morin, Ryan D
Format: Article
Language:English
Subjects:
Biopsy
Cancer
Contamination
Deoxyribonucleic acid
DNA
DNA sequencing
Genotyping
Minimal residual disease
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Summary:Ultrasensitive methods for rare allele detection are critical to leverage the full potential offered by liquid biopsies. Here, we describe a novel molecular barcoding method for the precise detection and quantification of circulating tumor DNA (ctDNA). The major benefits of our design include straightforward and cost-effective production of barcoded adapters to tag individual DNA molecules before PCR and sequencing, and better control over cross-contamination between experiments. We validated our approach in a cohort of 24 patients with a broad spectrum of cancer diagnoses by targeting and quantifying single-nucleotide variants (SNVs), indels and genomic rearrangements in plasma samples. By using personalized panels targeting a priori known mutations, we demonstrate comprehensive error-suppression capabilities for SNVs and detection thresholds for ctDNA below 0.1%. We also show that our semi-degenerate barcoded adapters hold promise for noninvasive genotyping in the absence of tumor biopsies and monitoring of minimal residual disease in longitudinal plasma samples. The benefits demonstrated here include broad applicability, flexibility, affordability and reproducibility in the research and clinical settings.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-017-10269-2