Delineation of CGRs in PTLS cases. A) CGRs revealed by aCGH. Human chromosome 17p11.2 is illustrated as a horizontal line on the top of the figure with coordinates (Mb) indicated below. Red blocks represent duplicated regions and blue segments indicate triplications. RAI1 is indicated by the vertical gray shadow. Yellow and blue shaded areas represent LCRs; purple arrows indicating the orientation . Vertical black lines define the 7 Mb (14.9-21.9 Mb) targeted by the SMS/PTLS probe set. Individual array results are below the schematics, focused on of copy number alterations. Coordinates coordinates (in Mb) are indicated below arrays. Previously determined junctions are labeled with a “1” so that the rearrangement joins together the two number “1”s, and junctions identified by PacBio-LITS are labeled with a “2”. Data for 2714  and 2695  were published previously. B) Novel breakpoint junction sequences detected with PacBio-LITS. Breakpoint sequences for the three new junctions identified by PacBio-LITS are aligned to the reference sequence. Transitions between the sequences are indicated with different colors, with gray denoting regions of disagreement with the junction sequence. Chromosome 17 coordinates (hg19/GRCh37) are indicated. Red lettering denotes microhomology. The Alu-Alu mediated alignment in BAB2695 has asterisks (*) denoting regions where the two Alu elements do not align. C) Formation of CGRs. Case BAB2714 i) A map of the reference genome. Colored boxes represent sequence blocks. ii) Black arrows indicate the two template switches resulting in the rearrangement. The template switches could also have occurred in the opposite order. iii) The rearranged region, which has an inversion-duplication for the blue sequence block followed by a direct duplication of the red sequence block. Case BAB2695 i) A map of the reference genome. ii) The resultant rearrangement. Both junctions are mediated by Alu elements, and are in a head-to-tail tandem orientation (no inversion).