Figure 6.

Permutation analysis to identify the top library replicate strategies. Artefacts were bioinformatically filtered by their presence in library replicates of untreated and repaired FFPE-DNA. The choice of library combination in a multi-library approach can lead to a different number of remaining artefacts. Here, all possible permutations of libraries were bioinformatically tested. The top permutations for artefact removal are depicted in the graph and the tables for FFPE-DNA replicates processed in two sequencing centres. In addition, all permutations of untreated libraries are included. Untreated FFPE-DNA (U, grey), NEBrepaired FFPE-DNA (N, green), and IQBErepaired FFPE-DNA (Q, magenta) libraries were used. For this combined analysis a 1% VAF detection threshold was applied and artefacts that did not pass this VAF filter in all libraries of the doublets or triplets, respectively, were removed.