Exploring the limits of Bionano optical genome mapping to characterize linked interspersed chromosomal duplications

The true structure of linked interspersed duplications and similar complex rearrangements can only be formally established using technologies able to span the entire duplicated segment(s). We assessed whether bionano optical genome mapping (OGM), complemented by orthogonal technologies, could determine the structures of three large interspersed duplications/triplications. Additionally we used the deepC algorithm to predict how different structures might impact local topologically-associating domains (TADs), to assist functional interpretation. The first patient harbored paired interspersed duplications (244 kb and 323 kb) on chromosome 13. By analyzing multiple molecules >300 kb completely spanning the smaller duplication, we unambiguously determined the correct structure, which potentially altered the TAD containing FGF9, a candidate gene. In the second case, involving a child who presented additionally with hypertrichosis and gingival hyperplasia (HGH), duplications on chromosomes 16 (2.01 Mb) and 17 (565 kb) were linked on short-read sequencing. By obtaining three OGM reads spanning the 565 kb segment, we deduced that a t(16;17) translocation was present, with important implications for clinical risk and mechanistic interpretation of the HGH phenotype. The third case involved a local chromoanasynthesis event on chromosome 20. OGM readily resolved all but two of 12 alternative structures; however full resolution required reads to span a 626 kb duplication, which we could not achieve consistently. In summary, OGM represents a powerful tool for disambiguating complex structural variants, but requires multiple individual reads to completely span the duplicated segment. Deducing the correct configuration is critical both for mechanistic understanding of pathogenesis and for accurate recurrence risk counselling.