Abstract

Liquid Biopsy: Screening for Single Nucleotide Variants and Indels From Cell-Free Tumoral DNA

Yves Rozenholc, Professor, University of Paris Descartes

Analyzing circulating free DNA from blood sample of patient known to have a cancer may help to build a precise picture of the tumoral mutations driving the carcinogenesis process, which can be used as input of a personalized treatment and offers the opportunity to realize a precise follow-up of patient under treatment. However, detecting single-nucleotide variations and insertions/deletions in circulating tumor DNA is challenging because of their low allele frequency. Based on quantification of error rate at each base position [position error rate (PER)], I will present a screening tool called PlasmaMutationDetector, which allows to identify mutations as the result of a statistical test comparing minor-allele frequency to measured PER at each base position. The method is based on a non-optimized commercial kit and allows actually the screening of about 20000 mutations (SNV and INDEL) potentially occurring along several oncogenes. It shows excellent sensibility and specificity and allows detection when minimal mutated allele frequencies is as low as 0.3% for single-nucleotide variations and 0.1% for insertions/deletions. During this presentation, to help adaptation of this method to other oncogenes and/or other NGS techniques, I will present the main technical steps, which allow to deal with multiplicity, hotspot and PER estimation.