In vivo clone tracking by conventional PCR. (A) For each individual clone, clone-specific primers (SP1 and SP2) were designed to anneal to genomic sequences 5′ to the LTR insertion, after band isolation and sequencing of LAM-PCR products. Each set of primers was used for nested PCR, in combination with LTR IV and V primers. (B) DNA isolated from granulocytes before (0 week), and 1 and 20 weeks after busulfan treatment of RQ2314 analyzed using clone-specific primers for 7 individual insertions (nos. 1212, 1247, 1318, 1304, 1337, 1315, and 1340). RQ2265 granulocyte DNA was used as negative control; this animal received transduced cells but should not have any insertions identical to animal RQ2314. Cloned plasmid DNA from each insertion was used as a positive control.