Exact(11)
The LARS/homotopy provides all the breakpoints τ0 > τ1 > ⋯ > τstop ≥ 0 and the associated solutions p τ0), p τ1),..., p(τstop) where a new component enter or leaves the support (the set of active elements) of p. It can be proved that the sum of powers increases monotonically at each iteration of the algorithm.
We have not managed to detect all the breakpoints.
Using EST data, we identified three chimeric genes that have EST sequences covering all the breakpoints and one chimeric gene that has EST sequence covering some breakpoints.
In one of the first large studies related to monosomy 1p36, Heilstedt et al. [ 5] evaluated the deletion sizes in 61 affected subjects from 60 families and noticed that, although the deletion sizes ranged widely, 12.5% of breakpoints clustered 4.0 4.5 Mb from the telomere, and 40% of all the breakpoints occurred 3.0 5.0 Mb from the telomere.
All the breakpoints seem however localized in the same region.
Interestingly, all the breakpoints mapped to date in t(8 21) are clustered in intron 5 of the RUNX1 gene and intron 1 of the ETO gene.
Similar(49)
TE content of all the breakpoint sequences (see Methods) is summarized in Additional file 7. Our analysis of the breakpoints provides significant information on the causes and consequences of the seven chromosome 2 inversions fixed in D. mojavensis (Table 1) that we present in the following sections.
The Abbott dual fusion probe contains fluorescently labelled DNA that covers approximately 180 kb and 335 kb either side of the PML loci on chromosome 15 including all of the known BCR regions of PML and approximately 700 kb of chromosome 17 spanning all the breakpoint region of RARA (http://www.abbottmolecular.com/products/oncology/fish/hematology-probes.html).html
The initial screen used the Exelixis Df collection (459 lines), which was generated in an isogenic background and all of the breakpoints are molecularly defined (Parks et al. 2004).
We searched all the breakpoint regions (2000 bp each side) for interspersed repeats and low complexity DNA sequences.
With the set of unique recombination events identified by these 6 detection methods a breakpoint map containing the positions of all positively identified breakpoints was constructed by moving a 200 nucelotide window and counting all the identified breakpoints falling within each window.
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