{"entity": "researcher", "timestamp": "2026-08-15T07:30:36.680Z", "family": "Sedlazeck", "given": "Fritz J", "initials": "FJ", "orcid": "0000-0001-6040-2691", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/28f940f4fb8b47ec8acb7ba04ca3890b.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/28f940f4fb8b47ec8acb7ba04ca3890b"}}, "publications": [{"entity": "publication", "iuid": "61f674feb9bb47cc945261f439654003", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61f674feb9bb47cc945261f439654003.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61f674feb9bb47cc945261f439654003"}}, "title": "Single cell long read whole genome sequencing reveals somatic transposon activity in human brain.", "authors": [{"family": "Izydorczyk", "given": "Michal B", "initials": "MB"}, {"family": "Kalef-Ezra", "given": "Ester", "initials": "E", "orcid": "0000-0002-1297-3315", "researcher": {"href": "https://publications.scilifelab.se/researcher/7872b77059a7463a9d70214941f2da4e.json"}}, {"family": "Horner", "given": "Dominic W", "initials": "DW", "orcid": "0009-0002-1988-3838", "researcher": {"href": "https://publications.scilifelab.se/researcher/44931007770f44ce8e7f4d71ee2e0f53.json"}}, {"family": "Zheng", "given": "Xinchang", "initials": "X"}, {"family": "Holmes", "given": "Nadine", "initials": "N"}, {"family": "Toffoli", "given": "Marco", "initials": "M", "orcid": "0000-0002-3255-9648", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a1af99369b43d39dd36408491f25c2.json"}}, {"family": "Sahin", "given": "Zeliha", "initials": "Z"}, {"family": "Han", "given": "Yi", "initials": "Y", "orcid": "0000-0001-7605-8979", "researcher": {"href": "https://publications.scilifelab.se/researcher/2773c1d2c94f468fa78eed048bd13d3a.json"}}, {"family": "Mehta", "given": "Heer H", "initials": "HH"}, {"family": "Scholz", "given": "Sonja W", "initials": "SW", "orcid": "0000-0002-6623-0429", "researcher": {"href": "https://publications.scilifelab.se/researcher/7600f820a52a4e99b9b01480e8848669.json"}}, {"family": "Dalgard", "given": "Clifton L", "initials": "CL", "orcid": "0000-0003-2025-8239", "researcher": {"href": "https://publications.scilifelab.se/researcher/5476c12921064b89bd069f7942c40b71.json"}}, {"family": "Muzny", "given": "Donna M", "initials": "DM"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Sedlazeck", "given": "Fritz J", "initials": "FJ", "orcid": "0000-0001-6040-2691", "researcher": {"href": "https://publications.scilifelab.se/researcher/28f940f4fb8b47ec8acb7ba04ca3890b.json"}}, {"family": "Proukakis", "given": "Christos", "initials": "C", "orcid": "0000-0001-6423-6539", "researcher": {"href": "https://publications.scilifelab.se/researcher/c159214a80944c8fa64910a0023d8c42.json"}}], "type": "journal article", "published": "2025-11-20", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "1627", "issn-l": "2399-3642"}, "abstract": "The advent of single cell DNA sequencing revealed astonishing dynamics of genomic variability, but failed at characterizing smaller to mid size variants that on the germline level have a profound impact. In this work we discover previously uncharacterized genomic dynamics in 18 cells from three human brains utilizing single cell long-read whole genome sequencing. This provides key insights into the dynamic of the genomes of individual cells and further highlights brain specific activity of transposable elements, but requires validation in larger studies.", "doi": "10.1038/s42003-025-08805-2", "pmid": "41266782", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Long read": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-025-08805-2"}], "notes": [], "created": "2025-11-21T06:20:40.789Z", "modified": "2025-11-21T06:20:42.030Z"}, {"entity": "publication", "iuid": "a7701b730ae64100a1a1c05e7d0ac0ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7701b730ae64100a1a1c05e7d0ac0ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7701b730ae64100a1a1c05e7d0ac0ac"}}, "title": "Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci.", "authors": [{"family": "Grochowski", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-3884-7720", "researcher": {"href": "https://publications.scilifelab.se/researcher/c94bd6d4a43e41f2990ae8b9426c0312.json"}}, {"family": "Bengtsson", "given": "Jesse D", "initials": "JD"}, {"family": "Du", "given": "Haowei", "initials": "H", "orcid": "0000-0001-9052-1587", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c66b32c1f0f497c8652ac2ec9a9cbe8.json"}}, {"family": "Gandhi", "given": "Mira", "initials": "M"}, {"family": "Lun", "given": "Ming Yin", "initials": "MY"}, {"family": "Mehaffey", "given": "Michele G", "initials": "MG"}, {"family": "Park", "given": "KyungHee", "initials": "K"}, {"family": "H\u00f6ps", "given": "Wolfram", "initials": "W"}, {"family": "Benito", "given": "Eva", "initials": "E"}, {"family": "Hasenfeld", "given": "Patrick", "initials": "P"}, {"family": "Korbel", "given": "Jan O", "initials": "JO"}, {"family": "Mahmoud", "given": "Medhat", "initials": "M", "orcid": "0000-0002-2553-4231", "researcher": {"href": "https://publications.scilifelab.se/researcher/e05f2f3025d34f1e940334615a912e1e.json"}}, {"family": "Paulin", "given": "Luis F", "initials": "LF", "orcid": "0000-0003-2567-3773", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e25b0a91ea84c54af6407fead39e2e7.json"}}, {"family": "Jhangiani", "given": "Shalini N", "initials": "SN"}, {"family": "Hwang", "given": "James Paul", "initials": "JP"}, {"family": "Bhamidipati", "given": "Sravya V", "initials": "SV"}, {"family": "Muzny", "given": "Donna M", "initials": "DM"}, {"family": "Fatih", "given": "Jawid M", "initials": "JM"}, {"family": "Gibbs", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-1356-5698", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82176147e434163a72c946839708743.json"}}, {"family": "Pendleton", "given": "Matthew", "initials": "M", "orcid": "0000-0002-7465-4459", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaf7bfd1f8b6492396f3354447413ea3.json"}}, {"family": "Harrington", "given": "Eoghan", "initials": "E"}, {"family": "Juul", "given": "Sissel", "initials": "S"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Sedlazeck", "given": "Fritz J", "initials": "FJ", "orcid": "0000-0001-6040-2691", "researcher": {"href": "https://publications.scilifelab.se/researcher/28f940f4fb8b47ec8acb7ba04ca3890b.json"}}, {"family": "Pehlivan", "given": "Davut", "initials": "D", "orcid": "0000-0001-5788-0270", "researcher": {"href": "https://publications.scilifelab.se/researcher/161dfab97b5b4438a16506714d94e751.json"}}, {"family": "Lupski", "given": "James R", "initials": "JR", "orcid": "0000-0001-9907-9246", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dd1dee9767489aaf25865670feb7b7.json"}}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1a6b6936aa442384c5aef0eff0715a.json"}}], "type": "journal article", "published": "2024-07-10", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "volume": "4", "issue": "7", "pages": "100590", "issn-l": null}, "abstract": "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 \u223c2.2-5.5 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.", "doi": "10.1016/j.xgen.2024.100590", "pmid": "38908378", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11293582"}, {"db": "pii", "key": "S2666-979X(24)00174-5"}], "notes": [], "created": "2024-08-15T12:10:53.870Z", "modified": "2024-11-27T09:00:48.437Z"}]}