Shallow whole-genome sequencing (sWGS) of ccfDNA
Libraries were cleaned up a second time to remove adapter dimers using SPRIselect (Beckman Coulter) according to the manufacturer’s recommendations. The libraries were pooled in equimolar amounts and sequenced in multiplexes of 51 sWGS libraries per lane (10 nM multiplex input) using 150 bp paired-end runs on Illumina NovaSeq 6000 S4 v.15 NGS platform (Illumina) at the DKFZ NGS Core Facility according to the manufacturer’s instructions. The quality scores Q30 were between 87.6% and 87.2%, total read count prior deduplication was 38 444 522x mean coverage per library (range: 6480 950x – 90,511 187x). Raw sequencing reads were processed and aligned using the automated pipeline OTP