2021
DOI: 10.1038/s41587-021-00981-w
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Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA

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Cited by 208 publications
(175 citation statements)
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“…Usually designed for the surveillance in patients whose mutations are known from the tumor, these assays have a limit of detection as low as 0.01% variant allele frequency (VAF) [7][8][9][10][11][12]. Higher sensitivities have been reported with the CAPP-seq technique by the implementation of the integrated digital error suppression (IDES) barcoding strategy, or more recently of a process called PhasED-seq based on the identification of several somatic variants on the same DNA fragment [13,14]. The CAPP-seq technique is described as an ultrasensitive and cost-efficient method for the quantification of ctDNA (Figure 1).…”
Section: Introductionmentioning
confidence: 99%
“…Usually designed for the surveillance in patients whose mutations are known from the tumor, these assays have a limit of detection as low as 0.01% variant allele frequency (VAF) [7][8][9][10][11][12]. Higher sensitivities have been reported with the CAPP-seq technique by the implementation of the integrated digital error suppression (IDES) barcoding strategy, or more recently of a process called PhasED-seq based on the identification of several somatic variants on the same DNA fragment [13,14]. The CAPP-seq technique is described as an ultrasensitive and cost-efficient method for the quantification of ctDNA (Figure 1).…”
Section: Introductionmentioning
confidence: 99%
“…8 In an elegant twist, Kurtz et al reasoned that another avenue to curb the impact of sequencing errors would be to detect SNVs that are located in close proximity in the genome such that they may be identified on the same sequencing read (termed phased variants) (Figure 1). 1 The key guiding intuition is that such occurrences can leverage conditional probabilities, whereby the likelihood of observing a rare event twice is the product of multiplying their separate probabilities. Thus, if the chance of observing a random sequencing error is 1:10 3 , the chance of observing two such events on the same sequencing read will be the product of multiplying the probabilities, or 1:10 6 .…”
mentioning
confidence: 99%
“…Kurtz et al performed an in vitro mixing study to evaluate the lower limit of detection of phasED-seq and compared it to previous assays (CAPP-seq and duplexseq). 1 To demonstrate the strength of their assay, they mixed minute fractions of cell-free DNA from lymphoma patients to cell-free DNA of healthy individuals for estimated tumor fractions ranging from 0.5 to 1000 parts per million (ppm). CAPP-seq allowed detection in ctDNA concentrations as low as 100 ppm, while duplex-seq was accurate down to 10 ppm.…”
mentioning
confidence: 99%
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