CNV detection from circulating tumor DNA in late stage non-small cell lung cancer patients

We present a method enabling CNV detection from a 150-gene panel using a very low amount of circulating tumor DNA (ctDNA). A read depth-based CNV estimation method without a paired blood sample was developed and cell free DNA sequencing data from healthy people were used to build a panel of normal (PoN) model. In silico and in vitro simulations were performed to define the limit of detection (LOD) for EGFR, ERBB2, and MET from cell line HCC1954 and NCI-H1573.