Robust bioinformatic method for estimating tumor content in cfDNAusing denoised target sequencing
Copy number amplifications are the hardest alteration class to call from cell-free DNA, usually demanding high circulating tumor DNA and broad genomic coverage. Pillar built oncoCNA, a Bayesian non-parametric caller inside PiVAT®, and tested it on Seraseq® ctDNA reference material across allele frequencies from 0.25% to 5% at 10, 20 and 30 ng input on the 104-gene oncoReveal® Core LBx panel. Performance was comparable at 10 ng and 30 ng, and the choice of negative control mattered more than input amount — clinical normal samples gave 100% negative percent agreement where synthetic normals did not.
