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Our tumor-normal assembly-based benchmark expands previous multi-technology ensemble benchmark approaches, adding &gt;8,000 somatic small variants altering \u223c40 kbp and 149 somatic SVs altering 939 kbp, including 2,764 small variants and 126 SVs not represented on GRCh38. Additionally, 5,111 somatic small variants change representation because they alter germline variants on GRCh38, impacting mutational signatures. Most source-resolved somatic LINE insertions originate from two non-reference germline LINE insertions with accessible promoter elements. These assemblies demonstrate that centromeric, acrocentric, telomeric, and other polymorphic regions, conventionally excluded from analysis, harbor extensive somatic and epigenetic changes and provide curated paired tumor-normal benchmarks to advance algorithms for repetitive regions of cancer genomes.\n                <\/jats:p>","DOI":"10.64898\/2026.05.01.722316","type":"posted-content","created":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T17:30:20Z","timestamp":1778088620000},"source":"Crossref","is-referenced-by-count":8,"title":["A near-complete human pancreatic cancer genome"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-8903-0504","authenticated-orcid":false,"given":"Justin","family":"Wagner","sequence":"first","affiliation":[{"name":"National Institute of Standards and Technology, Material Measurement Laboratory, 100 Bureau Dr., Gaithersburg, MD 20899, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3934-8587","authenticated-orcid":false,"given":"Ayse G.","family":"Keskus","sequence":"additional","affiliation":[{"name":"National Cancer Institute, Cancer Data Science Laboratory, 9000 Rockville Pike, Bethesda, MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2229-8998","authenticated-orcid":false,"given":"Keisuke K.","family":"Oshima","sequence":"additional","affiliation":[{"name":"University of Pennsylvania, Department of Genetics, Epigenetics Institute, 3400 Civic Center Blvd., Smilow Center for Translational Research, Philadelphia, PA 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3137-8439","authenticated-orcid":false,"given":"T. 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