Browsing by Author "Bengtsson, Jesse D."

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    Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci
    (Elsevier, 2024) Grochowski, Christopher M.; Bengtsson, Jesse D.; Du, Haowei; Gandhi, Mira; Lun, Ming Yin; Mehaffey, Michele G.; Park, KyungHee; Höps, Wolfram; Benito, Eva; Hasenfeld, Patrick; Korbel, Jan O.; Mahmoud, Medhat; Paulin, Luis F.; Jhangiani, Shalini N.; Hwang, James Paul; Bhamidipati, Sravya V.; Muzny, Donna M.; Fatih, Jawid M.; Gibbs, Richard A.; Pendleton, Matthew; Harrington, Eoghan; Juul, Sissel; Lindstrand, Anna; Sedlazeck, Fritz J.; Pehlivan, Davut; Lupski, James R.; Carvalho, Claudia M. B.
    The 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.
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    Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
    (Cold Spring Harbor Laboratory Press, 2024) Saether, Kristine Bilgrav; Eisfeldt, Jesper; Bengtsson, Jesse D.; Lun, Ming Yin; Grochowski, Christopher M.; Mahmoud, Medhat; Chao, Hsiao-Tuan; Rosenfeld, Jill A.; Liu, Pengfei; Ek, Marlene; Schuy, Jakob; Ameur, Adam; Dai, Hongzheng; Network, Undiagnosed Diseases; Hwang, James Paul; Sedlazeck, Fritz J.; Bi, Weimin; Marom, Ronit; Wincent, Josephine; Nordgren, Ann; Carvalho, Claudia M. B.; Lindstrand, Anna
    Chromosomal inversions (INVs) are particularly challenging to detect due to their copy-number neutral state and association with repetitive regions. Inversions represent about 1/20 of all balanced structural chromosome aberrations and can lead to disease by gene disruption or altering regulatory regions of dosage-sensitive genes in cis. Short-read genome sequencing (srGS) can only resolve ∼70% of cytogenetically visible inversions referred to clinical diagnostic laboratories, likely due to breakpoints in repetitive regions. Here, we study 12 inversions by long-read genome sequencing (lrGS) (n = 9) or srGS (n = 3) and resolve nine of them. In four cases, the inversion breakpoint region was missing from at least one of the human reference genomes (GRCh37, GRCh38, T2T-CHM13) and a reference agnostic analysis was needed. One of these cases, an INV9 mappable only in de novo assembled lrGS data using T2T-CHM13 disrupts EHMT1 consistent with a Mendelian diagnosis (Kleefstra syndrome 1; MIM#610253). Next, by pairwise comparison between T2T-CHM13, GRCh37, and GRCh38, as well as the chimpanzee and bonobo, we show that hundreds of megabases of sequence are missing from at least one human reference, highlighting that primate genomes contribute to genomic diversity. Aligning population genomic data to these regions indicated that these regions are variable between individuals. Our analysis emphasizes that T2T-CHM13 is necessary to maximize the value of lrGS for optimal inversion detection in clinical diagnostics. These results highlight the importance of leveraging diverse and comprehensive reference genomes to resolve unsolved molecular cases in rare diseases.