Changes that showed the most significant associations with osteosarcoma gene networks included: overexpression and the most significant copy number gain of the chromosome 6p21.1 RUNX2 locus, loss of expression and genomic loss of the DOCK5 and TNFRSF10A loci at chromosome 8p21.1-21.3, and hypomethylation, copy number gain, and overexpression of the HISTH2BE gene at chromosome 1q21. Here, RUNX2 is linked to osteosarcoma.