130 Chapter 5 fraction with the highest log likelihood was reported. Fragmentation patterns of urine cfDNA for both non-converted and converted samples were analyzed by retrieving the fragment sizes of the trimmed and filtered reads using picard CollectInsertSizeMetrics (v. 2.22.2) with HISTOGRAM_WIDTH=1000 [https://gatk.broadinstitute.org/hc/en-us]. Shallow whole-genome sequencing for the analysis of SCNA in paired FFPE primary tumor tissue was performed as described previously with a few adaptations (8). Sequencing libraries were prepared using the KAPA HyperPlus Kit (Roche, Basel, Switzerland), following manufacturer’s protocol. Libraries were sequenced using a NextSeq2000 (Illumina). Sequence reads were aligned to the GRCh38 human genome assembly using bwa mem (v. 0.7.17). PCR duplicates (marked by Picard v. 2.20.8), as well as low-quality reads (MAPQ < 37), were filtered out using samtools (v. 0.1.1830). Reads passing the filtering step were submitted for SCNA analysis using ichorCNA software as described for urine samples.
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