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In this context, the suggested duplicated regions could have resulted from a complex duplication, loss and rearrangement pattern, and not from "en bloc" duplications [ 18].
The only "complex" duplication was found in patient BR1, and consisted of an inverted duplicated segment.
This revealed the presence of complex duplication junction architectures (Fig. 3A).
The order and orientation of mosaic duplicons within complex duplication blocks was delineated with DupMasker [ 28] with customized Perl scripts.
Complex duplication segments were then clustered into several duplication groups by hierarchical clustering on the basis of the similarity of their phylogenetic profiles.
Judging from the branch lengths of the DgriGr64a1P/2 copies, this gene complex duplication is relatively old and may be present in all Hawaiian Drosophila.
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Breakpoint analysis showed that the predominant mechanism of formation of these complex duplication-associated variants was microhomology-mediated repair.
Collectively, these findings indicate that dupINVdups, as well as other complex duplication-associated rearrangements, represent relatively common sources of genomic variation that is cryptic to population-based microarray and low-depth whole-genome sequencing.
These analyses revealed a diverse landscape of complex duplications in the human genome.
Moreover, we showed that most PRC1 subunits underwent a complex, duplication-rich history that differs significantly between Brassicaceae and other eudicots.
This implies that further NAHR occurred within these CNVs may create different breaking points, leading to a complex duplication-within-duplication structure.
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