Breakpoint mapping of Hs578T cell line.

Two groups of primers: F_A (F_A1-F_A4) and R_X (R_X1-R_X5) were used for PAMP based on our previous mapping. The product was labeled for array hybridization (A). Only single peak is evident from the plot. It indicates the location of the other breakpoint is not covered by this minigenomic array. Two primers (R_X3 and R_X4) located near the genomic location of the probe (human chromosome 9, 21969229 to 21970477, NCBI build 36) that was hybridized and two primers (F_A1 and F_A2) located outside the array coverage were chosen for uniplex PCR. The F_A2-R_X3 pair is expected to have the shortest distance when a deletion occurs. A band of about 2 kb on agarose gel was excised from the gel, purified and sequenced (B). The breakpoint and location is indicated (from #21955827 to #21968338 according to NCBI human genome sequence build 36).