Figure 2

Outline of our whole-genome plasma analysis strategy. After blood draw, plasma preparation, and DNA-isolation we start our analysis, which is two-fold: first (left side of the panel), an Illumina shotgun library is prepared (time required, approximately 24 h). Single-read whole genome plasma sequencing is performed with a shallow sequencing depth of approximately 0.1x (approximately 12 h). After alignment we calculate several z-scores: a genome-wide z-score, segments with identical log2-ratios required to establish corresponding segmental z-scores, and gene-specific z-scores, for example, for the AR-gene. Each of these z-scores calculations takes approximately 2 h so that these analyses are completed within 48 h and the material costs are only approximately €300. Second (right side of the panel), we prepare a library using the SureSelect Kit (Agilent) and perform sequence enrichment with our GB-panel (approximately 48-72 h), consisting of 55 high-interest genes and 38 introns with frequent fusion breakpoints. The GB-panel is sequenced by paired-end sequencing with an approximately 50x coverage (around 26 h). The evaluation of the sequencing results may take several hours, the confirmation by Sanger sequencing several days. Hence, complete analysis of the entire GB-panel analysis will normally require around 7 days.