Summary of overlap and loss at balanced breakpoints in breast cancer cell lines HCC1187, HCC1806, and DU4475
[i] All positions are Build36/hg18. Additional balanced breakpoints that were not studied at high resolution are given in Supplemental Table 1.
[ii] aBreakpoint position: The breakpoint interval from array painting is shown in megabases (Mb). Breakpoint by cloning was from sequencing of the cloned junction and is given in base pairs (bp); values in italics are from Howarth et al. (2008).
[iii] bBalanced for Chr 7 only. The der(20) includes 7pter to 7p15, i.e., 0 to 27.75 Mb; the der(7) includes 7p15, i.e., 27.67 Mb, to 7qtel.
[iv] cBased on snp6 data only. Confirmed by PCR on sorted chromosomes.
[v] dCentromere break.
[vi] eBy Chr 6 tiling path and BAC FISH. Could be up to 1.5 Mb but segmental duplications are present.
[vii] fFISH with 2 non-overlapping fosmid clones (fF) or BACs (BF). PCR on sorted chromosomes within overlapping region with flanking control primers. Notes in italics are from Howarth et al. (2008).
[viii] gGenomic shards at the junction—part of an intron of ETV6/BCL2L14 from Chr 12p: 12118416–12118222 and 135-bp unidentified sequence.
[ix] h1.38-kb fragment of chromosome 11 inserted at this junction (Chr 11: 10519531–10520918) typical of “genomic shards.”
[x] iValues are from the paired-end read data of Stephens et al. (2009). Breakpoints agree but have not been validated independently.