A small amount of adapter-dimers seen at the pre-capture library preparation QC (as seen in fig.3 Q16 above) should not be carried over to the final library pool. If your libraries show a significant adapter-dimer peak (see fig. 4 below) this may be because you have input less than 50ng of DNA into the initial reaction without diluting the adapters to 1.5 µM (1:10 dilution). Always ensure you have accurately determined the concentration in your samples immediately prior to library preparation (see Q.1). You can attempt to reduce the adapter-dimer peak by performing a 0.9X (bead to sample ratio) clean-up step. However, this will result in sample loss and you will need to perform additional PCR cycles to ensure you have sufficient material to continue.
Figure 4. Library preparation from cfDNA showing significant adapter-dimer peak at 152bp