Frequency of homozygous deletion at chr9.p21, among UMU samples.

<p>The samples are split into two groups, based on their genotype at the EGFR variant rs1015793. HD frequency among samples homozygous for the major allele is plotted on the upper half of the upper panel (grey bars), and the HD frequency among samples homozygous for the rare allele plus heterozygous samples is plotted on the lower half of the upper panel (grey bars). The frequency difference between the groups is illustrated with overlaying red and green bars. The event frequency cutoff is illustrated by the horizontal red lines. The dark grey, vertical lines represent CDKN2A and CDKN2B. The lower panel illustrates the p-values (−log10 transformed) at each genomic site, with the horizontal red line illustrating the permutation derived p-value cutoff (0.0085).</p

Frequency of genomic events among UMU samples.

<p>Frequency (%) is represented on the y-axis and genomic position on the x-axis. The permutation derived event frequency cutoff (used to establish regions with significantly recurring events among the UMU samples) is illustrated by the red line.</p

Genes of interest.

<p>Genes of interest.</p

Significant correlations between germline gene variants and somatic aberrations.

<p><i>n</i> number, <i>major</i> samples homozygous for the major allele, <i>rare+hz</i> samples homozygous for the rare allele plus heterozygous samples, <i>event</i> samples positive for given event, <i>GOI</i> genes of interest.</p>a<p>total number of samples (glioblastoma samples/non-glioblastoma samples).</p

UMU sample set characteristics.

<p>UMU sample set characteristics.</p

Description of genomic events.

a<p>nTot = nA + nB, where nA and nB represent calculated copy numbers for the separate alleles at a given probe.</p

Risk gene variants.

<p><i>LD(r∧2)</i> HapMap linkage disequilibrium (r2) data between used surrogate marker and original risk variant, <i>n</i> number, <i>major</i> samples homozygous for the major allele, <i>rare+hz</i> samples homozygous for the rare allele plus heterozygous samples.</p

ASCAT-profiles.

<p>Whole genome ASCAT-profiles from two samples in the UMU dataset; one diploid (<b>a</b>) and one tetraploid (<b>b</b>). Green represents the allele with the lower copy number, and red represents the allele with the higher copy number (the colors are slightly offsetted to avoid overlap, red downwards and green upwards).</p

Tumor_LogR.GCadjusted_qnorm_117

Adjusted Log R Ratio values for the 117 tumour samples studied, after the application of the GC correction method and quantile normalization