title: Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications.
abstract: The need in cancer research or evolutionary biology to detect rare mutations or variants present at very low frequencies (<10-5) poses an increasing demand on lowering the detection limits of available methods. Here we demonstrated that amplifiable DNA lesions introduce important error sources in ultrasensitive technologies such as single molecule PCR (smPCR) applications (e.g. droplet-digital PCR), or next-generation sequencing (NGS) based methods. Using templates with known amplifiable lesions (8-oxoguanine, deaminated 5-methylcytosine, uracil, and DNA heteroduplexes), we assessed with smPCR and duplex sequencing that templates with these lesions were amplified very efficiently by proofreading polymerases (except uracil), leading to G->T, and to a lesser extent, to unreported G->C substitutions at 8-oxoguanine lesions, and C->T transitions in amplified uracil containing templates. Long heat incubations common in many DNA extraction protocols significantly increased the number of G->T substitutions. Moreover, in ∼50-80% smPCR reactions we observed the random amplification preference of only one of both DNA strands explaining the known 'PCR jackpot effect', with the result that a lesion became indistinguishable from a true mutation or variant. Finally, we showed that artifactual mutations derived from uracil and 8-oxoguanine could be significantly reduced by DNA repair enzymes.
authors.affiliation: Institute of Biophysics, Johannes Kepler University, Linz 4020, Austria.|Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Barbara
authors.initials: B
authors.lastname: Arbeithuber
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Kateryna D
authors.initials: KD
authors.lastname: Makova
authors.affiliation: Institute of Biophysics, Johannes Kepler University, Linz 4020, Austria irene.tiemann@jku.at.
authors.forename: Irene
authors.initials: I
authors.lastname: Tiemann-Boege
mesh_terms: D016477:Artifacts; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards; D006801:Humans; D008297:Male; D009154:Mutation; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards
chemical_list: D004247:DNA
keywords: DNA lesions; PCR jackpot; artifactual mutations; sequencing errors; ultrasensitive detection