Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci

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dc.citation.articleNumber100590
dc.citation.issueNumber7
dc.citation.journalTitleCell Genomics
dc.citation.volumeNumber4
dc.contributor.authorGrochowski, Christopher M.
dc.contributor.authorBengtsson, Jesse D.
dc.contributor.authorDu, Haowei
dc.contributor.authorGandhi, Mira
dc.contributor.authorLun, Ming Yin
dc.contributor.authorMehaffey, Michele G.
dc.contributor.authorPark, KyungHee
dc.contributor.authorHöps, Wolfram
dc.contributor.authorBenito, Eva
dc.contributor.authorHasenfeld, Patrick
dc.contributor.authorKorbel, Jan O.
dc.contributor.authorMahmoud, Medhat
dc.contributor.authorPaulin, Luis F.
dc.contributor.authorJhangiani, Shalini N.
dc.contributor.authorHwang, James Paul
dc.contributor.authorBhamidipati, Sravya V.
dc.contributor.authorMuzny, Donna M.
dc.contributor.authorFatih, Jawid M.
dc.contributor.authorGibbs, Richard A.
dc.contributor.authorPendleton, Matthew
dc.contributor.authorHarrington, Eoghan
dc.contributor.authorJuul, Sissel
dc.contributor.authorLindstrand, Anna
dc.contributor.authorSedlazeck, Fritz J.
dc.contributor.authorPehlivan, Davut
dc.contributor.authorLupski, James R.
dc.contributor.authorCarvalho, Claudia M. B.
dc.date.accessioned2024-08-09T16:25:25Z
dc.date.available2024-08-09T16:25:25Z
dc.date.issued2024
dc.description.abstractThe duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved. Here, we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping, and single-cell DNA template strand sequencing (strand-seq), the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of ∼2.2–5.5 kb of 100% nucleotide similarity within inverted repeat pairs. These data provide experimental evidence that inverted low-copy repeats act as recombinant substrates. This type of CGR can result in multiple conformers generating diverse SV haplotypes in susceptible dosage-sensitive loci.
dc.identifier.citationGrochowski, C. M., Bengtsson, J. D., Du, H., Gandhi, M., Lun, M. Y., Mehaffey, M. G., Park, K., Höps, W., Benito, E., Hasenfeld, P., Korbel, J. O., Mahmoud, M., Paulin, L. F., Jhangiani, S. N., Hwang, J. P., Bhamidipati, S. V., Muzny, D. M., Fatih, J. M., Gibbs, R. A., … Carvalho, C. M. B. (2024). Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci. Cell Genomics, 4(7). https://doi.org/10.1016/j.xgen.2024.100590
dc.identifier.digitalPIIS2666979X24001745
dc.identifier.doihttps://doi.org/10.1016/j.xgen.2024.100590
dc.identifier.urihttps://hdl.handle.net/1911/117630
dc.language.isoeng
dc.publisherElsevier
dc.rightsExcept where otherwise noted, this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND) license.  Permission to reuse, publish, or reproduce the work beyond the terms of the license or beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.titleInverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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