{"entity": "researcher", "timestamp": "2026-10-05T21:21:09.776Z", "family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "affiliations": ["Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden. ida.hoijer@igp.uu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e"}}, "publications": [{"entity": "publication", "iuid": "8faf66ff636b48c1b4a89fdeea549158", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8faf66ff636b48c1b4a89fdeea549158.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8faf66ff636b48c1b4a89fdeea549158"}}, "title": "Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads", "authors": [{"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "van Schendel", "given": "Robin", "initials": "R"}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "\u00d6stlund", "given": "Rebecka", "initials": "R"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Tijsterman", "given": "Marcel", "initials": "M"}, {"family": "den Hoed", "given": "Marcel", "initials": "M"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}], "type": "journal-article", "published": "2026-09-15", "journal": {"title": "Genome Med", "issn": "1756-994X", "issn-l": "1756-994X"}, "abstract": null, "doi": "10.1186/s13073-026-01772-1", "pmid": null, "labels": {"NGI Long read": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Technology development", "National Genomics Infrastructure": "Technology development"}, "xrefs": [], "notes": [], "created": "2026-09-17T08:44:46.850Z", "modified": "2026-09-17T08:44:46.862Z"}, {"entity": "publication", "iuid": "08bfcb7e64c34bec98766776e17b70aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08bfcb7e64c34bec98766776e17b70aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08bfcb7e64c34bec98766776e17b70aa"}}, "title": "Toward the clinical application of long-read sequencing in repeat-expansion disorders.", "authors": [{"family": "Benarroch", "given": "Louise", "initials": "L", "orcid": "0000-0003-2805-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b35bf181d649a887c37a4b7ef71cac.json"}}, {"family": "Pe\u0161ovi\u0107", "given": "Jovan", "initials": "J", "orcid": "0000-0002-8304-2067", "researcher": {"href": "https://publications.scilifelab.se/researcher/abe526e0fdae4892a054e0a3aca873a1.json"}}, {"family": "Rossato", "given": "Marzia", "initials": "M", "orcid": "0000-0002-6101-1550", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c291185114349db846e4e8ed012b500.json"}}, {"family": "Chen", "given": "Zhongbo", "initials": "Z", "orcid": "0000-0001-6668-7202", "researcher": {"href": "https://publications.scilifelab.se/researcher/e64e05d1f791410d933bca331a7309a3.json"}}, {"family": "Lucas", "given": "Morghan C", "initials": "MC", "orcid": "0000-0001-7654-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/12e305e7a4a843b0accb63f40d59c72e.json"}}, {"family": "Cogan", "given": "Guillaume", "initials": "G"}, {"family": "Rajan-Babu", "given": "Indhu-Shree", "initials": "IS"}, {"family": "Prokosch", "given": "Vitus", "initials": "V", "orcid": "0009-0008-5791-3536", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee651390fb2242d18419dd1ea5828a49.json"}}, {"family": "Zarouchlioti", "given": "Christina", "initials": "C", "orcid": "0000-0002-5096-177X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac5b43e2e9b24394bb0258835877994f.json"}}, {"family": "Carlomagno", "given": "Marco", "initials": "M", "orcid": "0009-0009-7079-5797", "researcher": {"href": "https://publications.scilifelab.se/researcher/6582154d2b0c49bb856c34eb05c95acc.json"}}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "Sauer", "given": "Mayra", "initials": "M"}, {"family": "Jamail", "given": "Ismail", "initials": "I"}, {"family": "Shibata", "given": "Shota", "initials": "S", "orcid": "0000-0002-9131-5408", "researcher": {"href": "https://publications.scilifelab.se/researcher/e15a351248094f00ac17a4f7fb8bc83c.json"}}, {"family": "Sequiera", "given": "Glen Lester", "initials": "GL"}, {"family": "Kleinstiver", "given": "Benjamin P", "initials": "BP", "orcid": "0000-0002-5469-0655", "researcher": {"href": "https://publications.scilifelab.se/researcher/59ee5fb344754d169bb03638273394f1.json"}}, {"family": "Lameiras", "given": "Sonia", "initials": "S"}, {"family": "Mouro Pinto", "given": "Ricardo", "initials": "R", "orcid": "0000-0001-6744-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccbcca302ed74a7c9cbe7ea92043655b.json"}}, {"family": "Novelli", "given": "Giuseppe", "initials": "G", "orcid": "0000-0002-7781-602X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6a6a7759bc043c399af7995628c531d.json"}}, {"family": "Hensman Moss", "given": "Davina", "initials": "D", "orcid": "0000-0003-2467-0917", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9856690664f4ffea2336f4325d94ea0.json"}}, {"family": "Dominik", "given": "Natalia", "initials": "N"}, {"family": "Barbier", "given": "Mathieu", "initials": "M", "orcid": "0000-0002-5154-2163", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e1fec79079e4b7c894eefc4bbd5d9d1.json"}}, {"family": "Le Ber", "given": "Isabelle", "initials": "I"}, {"family": "Bassez", "given": "Guillaume", "initials": "G"}, {"family": "Furling", "given": "Denis", "initials": "D", "orcid": "0000-0001-7912-4409", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c5c4cdee0184b6a90cd874cd01e9172.json"}}, {"family": "Delledonne", "given": "Massimo", "initials": "M", "orcid": "0000-0002-7100-4581", "researcher": {"href": "https://publications.scilifelab.se/researcher/f08d60288a2947aa8bbdba30ae4b4e90.json"}}, {"family": "Usdin", "given": "Karen", "initials": "K"}, {"family": "Baulande", "given": "Sylvain", "initials": "S", "orcid": "0000-0003-3104-1684", "researcher": {"href": "https://publications.scilifelab.se/researcher/74e3cd57511542feb8161594ba9947d8.json"}}, {"family": "Gourdon", "given": "Genevi\u00e8ve", "initials": "G"}, {"family": "Sch\u00fcle", "given": "Birgitt", "initials": "B"}, {"family": "Savi\u0107-Pavi\u0107evi\u0107", "given": "Du\u0161anka", "initials": "D", "orcid": "0000-0002-2079-4077", "researcher": {"href": "https://publications.scilifelab.se/researcher/3db2296f13f34758b73867e21697e5f6.json"}}, {"family": "Botta", "given": "Annalisa", "initials": "A", "orcid": "0000-0003-4031-5624", "researcher": {"href": "https://publications.scilifelab.se/researcher/d481de61bb54476083f5fcd66637dd67.json"}}, {"family": "Davidson", "given": "Alice E", "initials": "AE", "orcid": "0000-0002-1816-6151", "researcher": {"href": "https://publications.scilifelab.se/researcher/e22488e94593447d9a1f4bd77df9a992.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Dion", "given": "Vincent", "initials": "V", "orcid": "0000-0003-4953-7637", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe97871375964a1fb5993fb3e7729cd7.json"}}, {"family": "Tom\u00e9", "given": "St\u00e9phanie", "initials": "S", "orcid": "0000-0002-0135-9256", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4a47fbf57d243cc9cf2a0389c5d2912.json"}}, {"family": "LRS-RED Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2026-09-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "58", "issue": "9", "pages": "2087-2103", "issn-l": "1061-4036"}, "abstract": "Repeat-expansion disorders (REDs) are a mechanistically and clinically well-defined subgroup of rare diseases caused by the expansion of short tandem repeats (STRs). These expansions can exceed several kilobases and show complex features, such as noncanonical secondary structures, somatic instability, repeat interruptions and allele-specific methylation. These characteristics are highly relevant for understanding disease mechanisms, clinical variability, prognosis and potentially therapeutic decision-making, but cannot be fully resolved using traditional diagnostic methods or short-read sequencing technologies. By contrast, long-read sequencing (LRS) enables accurate investigation of STR complexity in a single assay, facilitates the discovery of new pathogenic repeat expansions and drives advances in diagnostics, clinical and basic research, which may allow for better patient stratification in future clinical trials. This Perspective discusses recent LRS-driven discoveries, methodological and bioinformatic advances, and emerging diagnostic applications to illustrate the potential of LRS in reshaping both research and clinical practice.", "doi": "10.1038/s41588-026-02694-9", "pmid": "42625059", "labels": {"NGI Long read": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-026-02694-9"}], "notes": [], "created": "2026-09-17T08:43:27.554Z", "modified": "2026-09-17T08:43:29.002Z"}, {"entity": "publication", "iuid": "0a094f348c054d099c58c9b1e242ff44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a094f348c054d099c58c9b1e242ff44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a094f348c054d099c58c9b1e242ff44"}}, "title": "Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR.", "authors": [{"family": "De Coster", "given": "Wouter", "initials": "W", "orcid": "0000-0002-5248-8197", "researcher": {"href": "https://publications.scilifelab.se/researcher/2232314f629841e3ae45eabf32619173.json"}}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "Bruggeman", "given": "Inge", "initials": "I"}, {"family": "D'Hert", "given": "Svenn", "initials": "S", "orcid": "0000-0002-1502-5329", "researcher": {"href": "https://publications.scilifelab.se/researcher/45329364c81c43ce9f545d2289e03d2e.json"}}, {"family": "Melin", "given": "Malin", "initials": "M", "orcid": "0000-0002-6589-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/190c3991975c43ec952a81df72292c9a.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Rademakers", "given": "Rosa", "initials": "R", "orcid": "0000-0002-4049-0863", "researcher": {"href": "https://publications.scilifelab.se/researcher/269957fa02b04958a8d783fa29cf65e2.json"}}], "type": "journal article", "published": "2024-11-20", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "34", "issue": "11", "pages": "2074-2080", "issn-l": "1088-9051"}, "abstract": "The lack of population-scale databases hampers research and diagnostics for medically relevant tandem repeats and repeat expansions. We attempt to fill this gap using our pathSTR web tool, which leverages long-read sequencing of large cohorts to determine repeat length and sequence composition in a healthy population. The current version includes 1040 individuals of The 1000 Genomes Project cohort sequenced on the Oxford Nanopore Technologies PromethION. A comprehensive set of medically relevant tandem repeats has been genotyped using STRdust and LongTR to determine the tandem repeat length and sequence composition. PathSTR provides rich visualizations of this data set and the feature to upload one's data for comparison along the control cohort. We demonstrate the implementation of this application using data from targeted nanopore sequencing of a patient with myotonic dystrophy type 1. This resource will empower the genetics community to get a more complete overview of normal variation in tandem repeat length and sequence composition and, as such, enable a better assessment of rare tandem repeat alleles observed in patients.", "doi": "10.1101/gr.279265.124", "pmid": "39147583", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Technology development", "NGI Long read": "Technology development", "National Genomics Infrastructure": "Technology development", "Clinical Genomics Uppsala": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "gr.279265.124"}], "notes": [], "created": "2024-09-03T12:15:49.306Z", "modified": "2024-11-22T09:46:59.428Z"}, {"entity": "publication", "iuid": "7feac7b384bd4538b6116d30a4f37f9d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7feac7b384bd4538b6116d30a4f37f9d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7feac7b384bd4538b6116d30a4f37f9d"}}, "title": "CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations.", "authors": [{"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "\u00d6stlund", "given": "Rebecka", "initials": "R", "orcid": "0000-0003-4460-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/03b1d5938f74406ebffb5b49ba5b182c.json"}}, {"family": "van Schendel", "given": "Robin", "initials": "R", "orcid": "0000-0001-7068-0679", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aa5a36e5b534bab8a04b4c8f040abb4.json"}}, {"family": "Bozorgpana", "given": "Selma", "initials": "S"}, {"family": "Tijsterman", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8465-9002", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1e816845f6048e2a2c7dc29e9a13cdf.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}], "type": "journal article", "published": "2022-02-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "627"}, "abstract": "CRISPR-Cas9 genome editing has potential to cure diseases without current treatments, but therapies must be safe. Here we show that CRISPR-Cas9 editing can introduce unintended mutations in vivo, which are passed on to the next generation. By editing fertilized zebrafish eggs using four guide RNAs selected for off-target activity in vitro, followed by long-read sequencing of DNA from >1100 larvae, juvenile and adult fish across two generations, we find that structural variants (SVs), i.e., insertions and deletions \u226550 bp, represent 6% of editing outcomes in founder larvae. These SVs occur both at on-target and off-target sites. Our results also illustrate that adult founder zebrafish are mosaic in their germ cells, and that 26% of their offspring carries an off-target mutation and 9% an SV. Hence, pre-testing for off-target activity and SVs using patient material is advisable in clinical applications, to reduce the risk of unanticipated effects with potentially large implications.", "doi": "10.1038/s41467-022-28244-5", "pmid": "35110541", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Technology development", "NGI Long read": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8810904"}, {"db": "pii", "key": "10.1038/s41467-022-28244-5"}], "notes": [], "created": "2022-02-17T14:45:40.515Z", "modified": "2024-01-16T13:48:37.595Z"}, {"entity": "publication", "iuid": "5660b7d3ef2044dca8d30c36ddc899a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5660b7d3ef2044dca8d30c36ddc899a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5660b7d3ef2044dca8d30c36ddc899a1"}}, "title": "Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity.", "authors": [{"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "Johansson", "given": "Josefin", "initials": "J"}, {"family": "Gudmundsson", "given": "Sanna", "initials": "S"}, {"family": "Chin", "given": "Chen-Shan", "initials": "CS"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Wilbe", "given": "Maria", "initials": "M"}, {"family": "den Hoed", "given": "Marcel", "initials": "M"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}], "type": "journal article", "published": "2020-12-01", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "21", "issue": "1", "pages": "290", "issn-l": "1474-7596"}, "abstract": "One ongoing concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target activity is challenging. Here, we present SMRT-OTS and Nano-OTS, two novel, amplification-free, long-read sequencing protocols for detection of gRNA-driven digestion of genomic DNA by Cas9 in vitro.\n\nThe methods are assessed using the human cell line HEK293, re-sequenced at 18x coverage using highly accurate HiFi SMRT reads. SMRT-OTS and Nano-OTS are first applied to three different gRNAs targeting HEK293 genomic DNA, resulting in a set of 55 high-confidence gRNA cleavage sites identified by both methods. Twenty-five of these sites are not reported by off-target prediction software, either because they contain four or more single nucleotide mismatches or insertion/deletion mismatches, as compared with the human reference. Additional experiments reveal that 85% of Cas9 cleavage sites are also found by other in vitro-based methods and that on- and off-target sites are detectable in gene bodies where short-reads fail to uniquely align. Even though SMRT-OTS and Nano-OTS identify several sites with previously validated off-target editing activity in cells, our own CRISPR-Cas9 editing experiments in human fibroblasts do not give rise to detectable off-target mutations at the in vitro-predicted sites. However, indel and structural variation events are enriched at the on-target sites.\n\nAmplification-free long-read sequencing reveals Cas9 cleavage sites in vitro that would have been difficult to predict using computational tools, including in dark genomic regions inaccessible by short-read sequencing.", "doi": "10.1186/s13059-020-02206-w", "pmid": "33261648", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Technology development", "National Genomics Infrastructure": "Technology development", "Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-020-02206-w"}, {"db": "pmc", "key": "PMC7706270"}], "notes": [], "created": "2020-12-03T21:44:41.975Z", "modified": "2024-01-16T13:48:41.187Z"}, {"entity": "publication", "iuid": "16f46fa1ca9d460ab515224b1fdf7084", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16f46fa1ca9d460ab515224b1fdf7084.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16f46fa1ca9d460ab515224b1fdf7084"}}, "title": "Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting.", "authors": [{"family": "Madsen", "given": "Esben B", "initials": "EB", "orcid": "0000-0001-8042-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ba99884e9e84c67b08a6dd0febd0304.json"}}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "Kvist", "given": "Thomas", "initials": "T"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Mikkelsen", "given": "Marie J", "initials": "MJ"}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Hum. Mutat.", "issn": "1098-1004", "volume": "41", "issue": "9", "pages": "1671-1679", "issn-l": "1059-7794"}, "abstract": "Long-read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore are ideal for genome-gap closure, solving structural rearrangements and sequencing through repetitive elements. Here we introduce the Xdrop technology: a novel microfluidic-based system that allows for targeted enrichment of long DNA molecules starting from only a few nanograms of DNA. Xdrop is based on the isolation of long DNA fragments in millions of droplets, where the droplets containing a target sequence of interest are fluorescently labeled and sorted using flow cytometry. The final product from the Xdrop procedure is an enriched population of long DNA molecules that can be investigated by sequencing. To demonstrate the capability of Xdrop, we performed enrichment of the human papilloma virus 18 integrated into the genome of human HeLa cells. Analysis of the sequencing reads resolved three HPV18-chr8 integrations at base-pair resolution, and the captured fragments extended up to 30 kb into the human genome at the integration sites. Further, we enriched the complete TP53 locus in a leukemia cell line and could successfully phase coexisting mutations using PacBio sequencing. In summary, our results show that Xdrop is an efficient enrichment technology for studying complex genomic regions.", "doi": "10.1002/humu.24063", "pmid": "32516842", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7496172"}], "notes": [], "created": "2020-06-16T05:00:02.423Z", "modified": "2024-01-16T13:48:41.796Z"}, {"entity": "publication", "iuid": "3f6c987638d84add91fc127d7dc6af75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f6c987638d84add91fc127d7dc6af75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f6c987638d84add91fc127d7dc6af75"}}, "title": "De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Che", "given": "Huiwen", "initials": "H"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Dahlberg", "given": "Johan", "initials": "J"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2018-10-09", "journal": {"volume": "9", "issn": "2073-4425", "issue": "10", "pages": "486", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we performed a de novo assembly of two Swedish genomes that revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual. Around 6 Mb of these novel sequences (NS) are shared with a Chinese personal genome. The NS are highly repetitive, have an elevated GC-content, and are primarily located in centromeric or telomeric regions. Up to 1 Mb of NS can be assigned to chromosome Y, and large segments are also missing from GRCh38 at chromosomes 14, 17, and 21. Inclusion of NS into the GRCh38 reference radically improves the alignment and variant calling from short-read whole-genome sequencing data at several genomic loci. A re-analysis of a Swedish population-scale sequencing project yields > 75,000 putative novel single nucleotide variants (SNVs) and removes > 10,000 false positive SNV calls per individual, some of which are located in protein coding regions. Our results highlight that the GRCh38 reference is not yet complete and demonstrate that personal genome assemblies from local populations can improve the analysis of short-read whole-genome sequencing data.", "doi": "10.3390/genes9100486", "pmid": "30304863", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "genes9100486"}, {"db": "pmc", "key": "PMC6210158"}], "notes": [], "created": "2018-11-20T14:44:03.808Z", "modified": "2024-01-16T13:48:45.362Z"}, {"entity": "publication", "iuid": "b4d4451c7e4b49bca2ca64e753e5cf5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4d4451c7e4b49bca2ca64e753e5cf5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4d4451c7e4b49bca2ca64e753e5cf5c"}}, "title": "Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing.", "authors": [{"family": "H\u00f6ijer", "given": "Ida", "initials": "I", "orcid": "0000-0002-3915-3384", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba4ce20b1b447ada4fdc8256211436e.json"}}, {"family": "Tsai", "given": "Yu-Chih", "initials": "YC"}, {"family": "Clark", "given": "Tyson A", "initials": "TA"}, {"family": "Kotturi", "given": "Paul", "initials": "P"}, {"family": "Dahl", "given": "Niklas", "initials": "N", "orcid": "0000-0002-8122-0800", "researcher": {"href": "https://publications.scilifelab.se/researcher/689e06ddc001490a8cb891050ba5a732.json"}}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}], "type": "journal article", "published": "2018-09-00", "journal": {"volume": "39", "issn": "1098-1004", "issue": "9", "pages": "1262-1272", "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "Amplification of DNA is required as a mandatory step during library preparation in most targeted sequencing protocols. This can be a critical limitation when targeting regions that are highly repetitive or with extreme guanine-cytosine (GC) content, including repeat expansions associated with human disease. Here, we used an amplification-free protocol for targeted enrichment utilizing the CRISPR/Cas9 system (No-Amp Targeted sequencing) in combination with single molecule, real-time (SMRT) sequencing for studying repeat elements in the huntingtin (HTT) gene, where an expanded CAG repeat is causative for Huntington disease. We also developed a robust data analysis pipeline for repeat element analysis that is independent of alignment of reads to a reference genome. The method was applied to 11 diagnostic blood samples, and for all 22 alleles the resulting CAG repeat count agreed with previous results based on fragment analysis. The amplification-free protocol also allowed for studying somatic variability of repeat elements in our samples, without the interference of PCR stutter. In summary, with No-Amp Targeted sequencing in combination with our analysis pipeline, we could accurately study repeat elements that are difficult to investigate using PCR-based methods.", "doi": "10.1002/humu.23580", "pmid": "29932473", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6175010"}], "notes": [], "created": "2018-10-15T09:36:08.234Z", "modified": "2024-01-16T13:48:45.682Z"}]}