Figure 4: Changing proportions of SCNAs associated with increasing NSE. | Nature Communications

Figure 4: Changing proportions of SCNAs associated with increasing NSE.

From: Whole-genome plasma sequencing reveals focal amplifications as a driving force in metastatic prostate cancer

Figure 4

(a) Genome-wide log2-ratio plots of plasma samples P148_1 (upper panel) and P148_3 (centre panel), which was obtained 12 months later. Between these two samples, relative copy-number losses and gains for 42.2% and 23.3%, respectively, of chromosomal regions (overlay plots in bottom panel; black: first analysis (P148_1); blue: third analysis (P148_3) were observed; regions with different log2-ratios >0.2 are marked with blue and red bars below or above the respective regions). (b) Enlarged X-chromosome profiles demonstrating that the AR amplification is only present in sample P148_1. (c) Confirmation of the AR copy-number status by quantitative PCR in duplicates. Y axis represents RQ (relative quantity) compared with a pooled male reference DNA sample; error bars indicate minimum and maximum values. (d) Plots of P170 illustrating changing chromosomal copy-number patterns over a period of 15 weeks (black: first analysis (P170_1); blue: second analysis (P170_2)). Between the two analyses 26.7% of the genome differs in terms of copy-number status (235 and 590 Mb were gained or lost, respectively, in P170_2 compared with P170_1). Log2-ratios of sample P170_1 have been adjusted to correct for different tumour ratios. Estimated tumour DNA content ratio: 1:4.34 (P170_1/P170_4). (e) Comparison between first and last analysed plasma samples from P179 (black: first analysis (P179_1); blue: second analysis (P179_4)). These analyses do not show major changes on the autosomes, but do show loss of the AR amplicon (indicated as blue bar below the X chromosome).

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