Yield independent genome-wide kit evaluation using Infinium HumanMethylation27 BeadChip data for external validation.

<p>Fractions of mapped MBD-seq fragments corresponding with specific Infinium methylation degrees (binned per 5%) for two cell lines (A, DU145; B, PC3) and all kits (violet, MethylMagnet; yellow, MethylCollector; blue, MethylCollector Ultra (MC Ultra); red, MethylCap; green, MethylMiner) with indication of the background profile (black, fractions of all Infinium methylation values measured for specific cell line). Additionally, the same fractions after division by the corresponding background profile fractions are plotted (C, DU145; D, PC3).</p

Yield independent genome-wide kit evaluation using RRBS data for external validation.

<p>Fractions of mapped MBD-seq fragments corresponding with specific RRBS methylation degrees (binned per 2%) for the different cell lines (A, HCT15; B, DU145; C, PC3) and kits (violet, MethylMagnet; yellow, MethylCollector; blue, MethylCollector Ultra (MC Ultra); red, MethylCap; green, MethylMiner) with indication of the background profile (black, fractions of all RRBS values measured for specific cell line). Additionally, the same fractions after division by the corresponding background profile fractions are plotted (D, HCT15; E, DU145; F, PC3).</p

Exploratory comparison of MBD-seq and RRBS data.

<p>Visual comparison of MBD-seq results for MethylMagnet (MMag), MethylCollector (MCol), MethylCollector Ultra (MCU), MethylCap (MCap) and MethylMiner (MMin) with RRBS data for the promoter regions of four selected loci, i.e. <i>Igfbp3</i> (panel A, chromosome 7, depicted from position 45959883 to 45962146), <i>Tert</i> (panel B, chromosome 5, 1293850 to 1296219), <i>Epb41l3</i> (panel C, chromosome 8, 5628365 to 5630973) and <i>Socs3</i> (panel D, chromosome 17, 76354158 to 76357420). CpGs assessed by RRBS are indicated as vertical red (fraction methylated)/grey (fraction unmethylated) bars. Note that RRBS only assesses the methylation status of a (sometimes variable) subfraction of CpGs.</p

Fragment CpG-plots.

<p>Fractions of mapped MBD-seq fragments with different CpG-counts for cell lines HCT15 (A), DU145 (B) and PC3 (C) for the different kits: MethylMagnet (violet), MethylCollector (yellow), MethylCollector Ultra (MC Ultra, blue), MethylCap (red) and MethylMiner (green).</p

Frequency of DNA copy number alterations of all 93 samples for the whole genome.

<p>Gains are represented in blue, losses in red.</p

Gain of 16p13.3 is linked with a worse prognosis.

<p>(A) The relation of alteration of the 16p13.3 locus and the number of CNA in the corresponding patient for all tumour stages, R = -0,430 and ***P<0,001. (B) Kaplan Meier survival curve showing a worse prognosis for patients with a gain of the 16p13.3 locus over all tumour stages, **P = 0,010. Gains are represented in green, losses in blue and patients without an alteration are represented in red.</p

Kaplan Meier survival curves showing the number of CNAs and the overall survival.

<p>(A) For all stages, **P = 0,004; (B) for stage IV, *P = 0,015; (C) for stage I, *P = 0,019 and (D) for stage II, *P = 0,019. In the survival curve three groups can be distinguished; the group with less than twelve alterations (blue), the group with twelve untill twenty alterations (green) and the group with more than twenty alterations (red).</p

Kaplan Meier survival curves represented a worse prognosis for patients with loss of chromosome 4.

<p>Loss of chromosome 4 is linked with a shorter RFS, ***P<0,001 (A) and a smaller 2-year OS, **P = 0,002 (B). Patients without an alteration of chromosome 4 are presented in green, those with loss of chromosome 4 in blue.</p