Figure 5
Identification of a t(9;22) translocation in the K562 cell line. (a) As only the ABL1 gene was directly targeted, we first identified reads in which one paired read mapped to ABL1 and the other did not using Breakdancer. This produced a table of ∼150 hits (partial list shown), the majority representing matches to repeat regions. Of the 150 hits, 11 (including the actual breakpoint) had maximal scores of 99. (b) Breakdancer coordinates were then passed to SLOPE to perform single end chimeric read verification. Only a single high-scoring hit was identified using this methodology. (c) These findings were subsequently verified by constructing PCR primers flanking the proposed translocation and then Sanger sequencing the products. To demonstrate specificity we attempted to amplify the same translocation from other cell lines as shown.
