Schematic representations of the genomic architecture for 5 exemplary regulatory and <i>FOXL2</i>-encompassing deletion.

<p>For deletions A, 1, 5, 7 and 12, both breakpoint regions joined by the deletion are shown. These deletions were selected as an example for each group (group 1: deletion A, group 2: deletion 7, and group 3: deletions 1, 5 and 12) of most likely molecular mechanism as described in the discussion. A breakpoint region is displayed as the combination of two colored, solid lines together representing a 150 bp DNA sequence. The proximal breakpoint region consists of a non-deleted blue line and a deleted red line while the distal breakpoint region consists of a deleted red line and a non-deleted green line. Each deletion is composed of the two red, solid lines joined by the red dashed line which represents the different size of the deletion for every patient. The actual size of the deletions is indicated above the red, dotted lines. The pink vertical arrows mark the position of the breakpoints displaying the number of base pairs of microhomology between both breakpoint regions and the junction product (see also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003358#pgen-1003358-g004" target="_blank">Figure 4</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003358#pgen.1003358.s003" target="_blank">Figure S3</a>). The presence of repetitive elements is shown as bars of different shades of gray (<i>Alu</i> elements are shown in light grey bars, other repetitive elements are shown in dark grey bars). Sequence motifs are indicated with orange, skewed lines intersecting with the sequence. Direct repeats, oligo(G)_n tracts and Z-DNA are represented by dark purple arrows, dark purple bars and light purple bars respectively. The schematic representations for the other deletions can be found in the online supplement (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003358#pgen.1003358.s002" target="_blank">Figure S2</a>).