ALK and hepatocellular carcinoma: To assess the potential tumorigenic consequences of the identified nonreference genome insertions, we selected and validated, by insertion site PCR, 31 L1, Alu, and SVA insertions in genes generally implicated to play a causal role in cancer (Futreal et al., 2004) or specifically in HCC (Guichard et al., 2012), including L1 insertions in the proto-oncogene ALK and the tumor suppressor FHIT (Table S5).