Genome-wide copy number alterations in all 22 chromosomes. A) Copy number alterations in controls, Ollier enchondromas (ECs) and chondrosarcoma (CS) grade I, II, III. The upper panel shows genome-wide frequency plots of gains and losses in 29 controls and 32 Ollier tumors. Gains are plotted in green above 0% baseline and losses are plotted in red below 0% baseline. The X-axis corresponds to the genomic region from chromosomes 1 to 22 and the Y-axis represents the percentage of gains and losses of all selected samples at the specific location in genome. The lower panel shows frequency plot of 29 controls, 14 ECs, 12 CS I, 4 CS II and 2 CS III. The number and size of genomic alterations increases with increasing tumor grade. Enchondromas and control samples show a comparable number and size of genomic alterations, which can be attributed to common copy number variation. B) An example of copy number alterations in Ollier enchondroma (L206). This figure shows copy number alterations in all 22 chromosomes of enchondroma (L206). The black band indicates the number of copies of the chromosomes. The blue bands show the unpaired LAIR value. The lower band of this contains the originally uninformative homozygous SNPs. The top band indicates heterozygous informative SNPs. With LOH or imbalances between the alleles, the position of this band will decrease. As a loss of chromosome 6 these heterozygous SNPs are becoming homozygous showing the LOH. C) An example of copy number alterations in Ollier chondrosarcoma grade III (L810). Copy number loss with LOH is present at chromosome 4, 5q, 6q, 9p, 12p, 13 and 14q.