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Sci Rep. 2017 Sep 5;7(1):10574. doi: 10.1038/s41598-017-10269-2.

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

Author information

1
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
2
Quebec Clinical Research Organization in Cancer (Q-CROC), Exactis Innovation and the Segal Cancer Centre, Montreal, QC, Canada.
3
Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada.
4
Department of Pathology and Laboratory Medicine and Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada.
5
Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada.
6
Division of Oncology, Hematology and Bone Marrow Transplant, British Columbia Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada.
7
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada. rdmorin@sfu.ca.

Abstract

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.

PMID:
28874686
PMCID:
PMC5585219
DOI:
10.1038/s41598-017-10269-2
[Indexed for MEDLINE]
Free PMC Article

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