{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T23:05:32Z","timestamp":1779318332544,"version":"3.51.4"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T00:00:00Z","timestamp":1777420800000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Lennar Foundation"},{"name":"TGen\u2019s Collaborative Sequencing Center"},{"DOI":"10.13039\/100008308","name":"City of Hope Comprehensive Cancer Center","doi-asserted-by":"publisher","award":["NCI-P30CA033572"],"award-info":[{"award-number":["NCI-P30CA033572"]}],"id":[{"id":"10.13039\/100008308","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Rita Levi Montalcini Award"},{"name":"Italian Ministry of University and Research"},{"name":"AIRC Start-Up","award":["25189"],"award-info":[{"award-number":["25189"]}]},{"name":"Sapienza Excellence"},{"name":"ERC CENTROFUN","award":["101078838"],"award-info":[{"award-number":["101078838"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"United States Government"},{"DOI":"10.13039\/100000016","name":"U.S. Department of Health and Human Services","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000016","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>We present chromosome-level, phased diploid genome assemblies of two widely used human fibroblast cell lines: BJ (46,XY) and IMR-90 (46,XX). Using Oxford Nanopore, PacBio HiFi, and Hi-C sequencing data, we generated assemblies spanning 5.9 and 6.0 Gbp with diploid quality values exceeding QV 60. To validate structural integrity, we developed KaryoScope, an alignment-free tool for generating computational karyograms from k-mer feature databases. We identify &amp;gt;50\u2009000 structural variants relative to T2T-CHM13v2.0, the majority of which are heterozygous and cell-line-specific. Combining reference-based and de novo gene annotation, we uncover a previously unreported 1 Mbp homozygous duplication at the 16p11.2 locus in BJ, demonstrating that even karyotypically normal cell lines can harbor clinically relevant submicroscopic rearrangements. We show that mapping publicly available short-read, RNA-seq, and ChIP-seq data to sample-matched diploid assemblies substantially improves read alignment and enables haplotype phasing of 23%\u201328% of short reads. The BJ and IMR-90 assemblies and associated variant calls are publicly available as a resource for the research community.<\/jats:p>","DOI":"10.1093\/nar\/gkag333","type":"journal-article","created":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T00:06:37Z","timestamp":1777421197000},"source":"Crossref","is-referenced-by-count":1,"title":["Haplotype-resolved genome assemblies of BJ and IMR-90 human fibroblast cell lines reveal extensive structural variation and enable reanalysis of historical sequencing data"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3137-8439","authenticated-orcid":false,"given":"T Rhyker","family":"Ranallo-Benavidez","sequence":"first","affiliation":[{"name":"Translational Genomics Research Institute , Phoenix, AZ, 85004 ,","place":["United 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