Sequencing of SNPs at the duplicated chromosome 6 junction in HCC1806 reveals products of the reciprocal translocation between chromosomes 4 and 6 have the same haplotype. (A) An ideogram of chromosome 6 is shown, with abnormal chromosome 6 segments in HCC1806 indicated with black lines, labeled with their short chromosome names, chromosome B, etc. They are the der(4)t(1;6;4) (Chr B), the der(6)t(4;6) (Chr N), the der(4)t(4;6) (Chr E), and the del(6) (Chr j) (Howarth et al. 2008). Balanced breaks are indicated by *. The 46-kb region of chromosome 6 common to all chromosomes is highlighted with a gray box and shown expanded to the right. The approximate location of PCR primer pairs 1 and 2 is shown (giving PCR products of 250 bp and 350 bp, respectively; not to scale). (B) Examples of sequences from primer pairs 1 and 2 from the different flow-sorted chromosomes. SNPs are highlighted with gray boxes.