2015
DOI: 10.1093/dnares/dsv010
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High-fidelity target sequencing of individual molecules identified using barcode sequences:de novodetection and absolute quantitation of mutations in plasma cell-free DNA from cancer patients

Abstract: Circulating tumour DNA (ctDNA) is an emerging field of cancer research. However, current ctDNA analysis is usually restricted to one or a few mutation sites due to technical limitations. In the case of massively parallel DNA sequencers, the number of false positives caused by a high read error rate is a major problem. In addition, the final sequence reads do not represent the original DNA population due to the global amplification step during the template preparation. We established a high-fidelity target sequ… Show more

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Cited by 76 publications
(84 citation statements)
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“…Because insertion/deletion errors are dominant in the Ion Torrent sequencers, errors in the barcode tags can be monitored by the size of the tags. As revealed in the previous experiment , the erroneous barcode tags were accumulated in the fraction of low numbers of reads. Thus, the fraction whose error‐free tags occupied <90% was removed (Fig.…”
Section: Resultsmentioning
confidence: 83%
“…Because insertion/deletion errors are dominant in the Ion Torrent sequencers, errors in the barcode tags can be monitored by the size of the tags. As revealed in the previous experiment , the erroneous barcode tags were accumulated in the fraction of low numbers of reads. Thus, the fraction whose error‐free tags occupied <90% was removed (Fig.…”
Section: Resultsmentioning
confidence: 83%
“…One cannot simply remove EA-derived variants based on VAF, as there exist clinically actionable variants at VAFs comparable to the frequency of EAs. UMI consensus calling can help resolve down to 0.01 VAF with confidence by polishing out sequencing error, 20 but EAs originate from a physical molecule prior to the ligation of UMIs and thus this strategy is also unhelpful in the elimination of EAs. INDEL-aware variant calls may produce extraneous variant calls by considering the soft-clipped sequences as true INDEL variants.…”
Section: Discussionmentioning
confidence: 99%
“…Deep sequencing with molecular barcodes was performed using the non-overlapping integrated read sequencing system26.…”
Section: Methodsmentioning
confidence: 99%