Nanopore WGS produces support for clinically relevant small-scale structural variants affecting genes associated with ALL and AML, including CRLF2-P2RY8 interstitial deletion (0060, 0136, 0163, 0238), partial or total loss of CDKN2A (0153, 0165), and heterogeneous ERG deletion (0162). Here, CRLF2 is linked to acute lymphoblastic leukemia.