AuthorsKim Chang, S
Rothwell, Dominic G
Miller, Crispin J
AffiliationClinical and Experimental Pharmacology Group, University of Manchester, Alderley Park, Manchester, UK
MetadataShow full item record
AbstractMotivation: Circulating-free DNA (cfDNA) profiling by sequencing is an important minimally invasive protocol for monitoring the mutation profile of solid tumours in cancer patients. Since the concentration of available cfDNA is limited, sample library generation relies on multiple rounds of PCR amplification, during which the accumulation of errors results in reduced sensitivity and lower accuracy.Results: We present PCR Error Correction (PEC), an algorithm to identify and correct errors in short read sequencing data. It exploits the redundancy that arises from multiple rounds of PCR amplification. PEC is particularly well suited to applications such as single-cell sequencing and circulating tumour DNA (ctDNA) analysis, in which many cycles of PCR are used to generate sufficient DNA for sequencing from small amounts of starting material. When applied to ctDNA analysis, PEC significantly improves mutation calling accuracy, achieving similar levels of performance to more complex strategies that require additional protocol steps and access to calibration DNA datasets. Availability and implementation: PEC is available under the GPL-v3 Open Source licence, and is freely available from: https://github.com/CRUKMI-ComputationalBiology/PCR_Error_Correction.git. Supplementary information: Supplementary figures are available at Bioinformatics online.
CitationKim CS, Mohan S, Ayub M, Rothwell DG, Dive C, Brady G, et al. In silico error correction improves cfDNA mutation calling. Bioinformatics. 2018 Dec 6.
- SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA.
- Authors: Kockan C, Hach F, Sarrafi I, Bell RH, McConeghy B, Beja K, Haegert A, Wyatt AW, Volik SV, Chi KN, Collins CC, Sahinalp SC
- Issue date: 2017 Jan 1
- ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA.
- Authors: Casiraghi N, Orlando F, Ciani Y, Xiang J, Sboner A, Elemento O, Attard G, Beltran H, Demichelis F, Romanel A
- Issue date: 2020 May 1
- Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA.
- Authors: Gawroński AR, Lin YY, McConeghy B, LeBihan S, Asghari H, Koçkan C, Orabi B, Adra N, Pili R, Collins CC, Sahinalp SC, Hach F
- Issue date: 2019 Apr 23
- TNER: a novel background error suppression method for mutation detection in circulating tumor DNA.
- Authors: Deng S, Lira M, Huang D, Wang K, Valdez C, Kinong J, Rejto PA, Bienkowska J, Hardwick J, Xie T
- Issue date: 2018 Oct 20
- A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA.
- Authors: Wu L, Deng Q, Xu Z, Zhou S, Li C, Li YX
- Issue date: 2020 Apr 3