Association of duplications and syntenic breaks: human versus mouse. (a) Top: ideogram of human chromosome 7 showing the positions of breakpoints in mouse-human synteny. We assessed only breakpoints that represented a change in orientation or difference in chromosome compared with the mouse genome (arrowheads). These breakpoints are designated as duplication-positive and duplication-negative (yellow and brown, respectively). Bottom: human chromosome 7 with blocks of conserved synteny with mouse indicated by colored bars. Segmental duplications are indicated by black bars over the sequence. Regions of duplication abutting the centromere and telomeres were excluded (gray shading). Small tick marks under the colored line represent 1-Mb intervals and breakpoints in synteny are numbered as in the chromosome ideogram. Gaps in conserved synteny were excluded. Conserved syntenic regions less than 100 kb or more than 75% duplicated were ignored. This prevented very small duplicated blocks from interrupting orthologous conservation or inappropriately increasing the number of breaks within a duplicated region. Breakpoints were scored as duplication-positive if they contained ≥ 10 kb of duplicated sequence. By these criteria, 13 of the 27 breakpoints on chromosome 7 (yellow boxes/arrows) were associated with duplications. (b) A histogram of the chromosomal distribution of syntenic breakpoints and their duplication status.
Bailey et al. Genome Biology 2004 5:R23