Fig. 2

Molecular alterations within DLGNT case 1. a Schematic of the BCOR gene demonstrating protein domains and the location of the E519* variant. Synonymous mutations have been excluded and data from PeCan incorporated. b CIRCOS plot illustrating the somatic alterations in the tumour and labelling of common tumour suppressor genes (brown) and oncogenes (black) in the MAPK pathway. The CIRCOS plot can be interpreted as follows: The outer first circle demonstrates the 22 autosomal chromosomes and the sex chromosomes. The dark band within the chromosome represents the centrosomes with the p arm to the left of the band and the q arm to the right. The dark bands can also be representative of heterochromatin or missing p arms. The following circle (light purple) illustrates the somatic single nucleotide variants with each dot representing a missense change (C > A blue, C > G black, C > T red, T > A grey, T > A grey, T > C green, T > G pink) and the location of the dot within the circle is associated with its corrected allele frequency (0% at the bottom edge of the ring to 100% at the top edge of the ring). The next ring consists of short insertions and deletions (yellow and red, respectively). The third circle consisting of red and green shading shows the copy number alterations in the tumour with red indicating loss and green indicating gains/amplifications (with the scale ranging from a complete loss of 0 up to gains and above of 6). The fourth circle (orange and blue shading) demonstrates the ‘minor allele copy numbers’ ranging from 0 to 3. Loss of heterozygosity is indicated in orange and is for values below 1, whereas amplification of both alleles is shown in blue and it will be any value above 1. The innermost circle represents different types of structural variants in the tumour (translocations (blue), deletions (red), insertions (yellow), tandem duplications (green) and inversions (black). c LINX plot demonstrating the KIAA1549-BRAF dup in this case. The outer edge shows the chromosomes affected by structural variants (SVs) in the tumour and the position of their breakends. The KIAA1549 and BRAF genes are shown in blue and brown, respectively with their exons numbered. The internal circle shows the derivative chromosome segments with breakends shown as shaded circles and the same event united with the same coloured line. The inner green and pink circles show copy number gain or loss, respectively and the inner blue and orange circles show the minor allele ploidy. The innermost circle demonstrates the break junctions of the SVs