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Further studies using FISH or high-resolution CGH will be needed to map the breakpoints precisely.
To investigate the hypothesis of recombination and map the breakpoints, we adapted the bootscanning method (27 ) as follows.
We identified several fusion spanning reads in each of the aforementioned patients (see Additional file 1, Table S4), which enabled us to map the breakpoints with bp resolution.
We used the CREST method (Wang et al., 2011) to detect and map the breakpoints of the somatic rearrangements among the 14 HPR patients.
We collected single dlg5 D48 embryos to map the breakpoints of the deletion created by the P-element excision by PCR (Supporting Information, Figure S1).
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We used PCR to fine-map the breakpoints and amplify a junction fragment of 630 bp.
We therefore mapped the breakpoints of the deficiencies more precisely both genetically by complementation analysis and molecularly by single embryo PCR.
Since the P-element insertion was not the likely cause of the failure of Df 2R 03072 to complement xen72−3, we mapped the breakpoints of the deficiency region using lethal complementation tests between Df 2R 03072 and genes in the Lobe chromosomal region.
Scanning the EST14 intron and ETV1 flanking region by long-range PCR and sequencing mapped the breakpoints in G270 ∼1.9 Kbp upstream of ETV1 exon 1 and ∼5 Kbp downstream of EST14 exon 1.
We have recently mapped the breakpoints of a t(1 2)(q41;p25.3) associated with isolated bilateral renal agenesis.
The in silico CNV detection algorithms used in the present study showed ambiguity in mapping the breakpoints.
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