{"entity": "publication", "iuid": "bab3243e9eb2426282bc91939f7d7bff", "timestamp": "2026-09-27T17:00:44.513Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bab3243e9eb2426282bc91939f7d7bff.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bab3243e9eb2426282bc91939f7d7bff"}}, "title": "Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation.", "authors": [{"family": "Ten Berk de Boer", "given": "Esmee", "initials": "E"}, {"family": "Ameur", "given": "Adam", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Feuk", "given": "Lars", "initials": "L"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2024-04-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "9000", "issn-l": "2045-2322"}, "abstract": "Long-read genome sequencing (lrGS) is a promising method in genetic diagnostics. Here we investigate the potential of lrGS to detect a disease-associated chromosomal translocation between 17p13 and the 19 centromere. We constructed two sets of phased and non-phased de novo assemblies; (i) based on lrGS only and (ii) hybrid assemblies combining lrGS with optical mapping using lrGS reads with a median coverage of 34X. Variant calling detected both structural variants (SVs) and small variants and the accuracy of the small variant calling was compared with those called with short-read genome sequencing (srGS). The de novo and hybrid assemblies had high quality and contiguity with N50 of 62.85 Mb, enabling a near telomere to telomere assembly with less than a 100 contigs per haplotype. Notably, we successfully identified the centromeric breakpoint of the translocation. A concordance of 92% was observed when comparing small variant calling between srGS and lrGS. In summary, our findings underscore the remarkable potential of lrGS as a comprehensive and accurate solution for the analysis of SVs and small variants. Thus, lrGS could replace a large battery of genetic tests that were used for the diagnosis of a single symptomatic translocation carrier, highlighting the potential of lrGS in the realm of digital karyotyping.", "doi": "10.1038/s41598-024-59683-3", "pmid": "38637641", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11026446"}, {"db": "pii", "key": "10.1038/s41598-024-59683-3"}], "notes": [], "created": "2026-09-23T11:29:26.134Z", "modified": "2026-09-23T11:29:26.169Z"}