Awareness of mutational artefacts in suboptimal DNA samples: possible risk for therapeutic choices

ABSTRACT

Background: Technical biases due to PCR artefacts could represent an insidious obstacle for mutational analysis and precision medicine.

Methods: The authors report a retrospective analysis by fast COLD-PCR and sequencing of 31 suboptimal tumor DNA samples obtained from FFPE tissues and liquid biopsies.

Results: In FFPE tumor tissues and plasma liquid biopsies of patients with lung and colorectal adenocarcinoma, we observed a significant rate of artefactual KRAS mutations, unveiled by repeated analysis following UDG pretreatment as well as by simple repetition without UDG pretreatment step, thus suggesting a DNA damage different from cytosine deamination. UDG pretreatment was not only unnecessary to contrast artefacts occurrence, but also hampered the efficiency of mutational screening, reducing the analytical sensitivity. Taken individually or considered together, the reduced DNA input per reaction and UDG pretreatment limited the detection of ‘real’ mutated alleles, decreasing PCR sensitivity enough to hamper distinction between artefactual and true subclonal mutations of KRAS.

Conclusions: Careful validation of analytical sensitivities should always be carried out through standard controls, and strategies other than UDG pretreatment need to be identified to avoid both amplification of artefactual mutations and failure to identify real subclonal mutations.

KEYWORDS:

• UDG
• mutational artefacts
• PCR
• liquid biopsy
• sequencing
• FFPE

Declaration of interest

The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

This work was supported by the Italian Ministry of University [ex-60% 2016–2017 to S Mariani and ex 60% 2016 and 2015HAJH8E to C Marchiò] and by Rete Oncologica Piemonte e Valle d’Aosta (to P Cassoni).