Figure 3

Validation of predicted breakpoints in cell lines by PCR and Sanger sequencing. (a) Confirmation of chromosome rearrangements by PCR. A primer pair (K562DF1 and R1) yielded a junctional DNA fragment using genomic DNA from K562 (lane 2) but not from normal lung tissues (lane 4). This primer set failed to amplify a DNA fragment using genomic DNA from KU812. PCR primer sets (KU812DF1, R1 and DF2, R2) amplified junctional DNA fragments using genomic DNA prepared from KU812 (lanes 5 and 7) but not from normal lung tissues (lanes 6 and 8). (b) Each PCR amplified junctional DNA fragment was cloned into a plasmid vector and Sanger sequencing performed. Solid lines enclose the BCR region and broken lines enclose the ABL1 region. In K562, a microhomology (GAGTG) exists on the BCR and ABL1 sides of the breakpoint, so we assume that the ligation point was somewhere in this GAGTG sequence.