RNA was extracted from 48 pairs of intratumoral and peritumoral formalin-fixed, paraffin-embedded (FFPE) tissue from hepatocellular carcinoma (HCC) patients with and without bone metastases (BM). The Human Cancer Panel DASL Assay containing 502 cancer-related genes was used to identify novel BM-associated genes. A cDNA-mediated annealing, selection, extension, and ligation assay was performed with an array of 502 known cancer-related genes to identify differentially expressed genes in 96 RNA samples. Overall design: Total RNA was purified from the tissue specimens using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. DASL experiments were performed to identify genes that were differentially expressed between the BM and NBM groups of matched intratumoral and peritumoral tissues by using A cDNA-mediated annealing, selection, extension, and ligation assay.