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Among 768 patients with prostate, breast, or ovarian cancers, we used mutational signatures to nominate cryptic genomic instability cases lacking a causative biallelic event on short-read sequencing. Long-read nanopore sequencing resolved 32 of 46 cryptic cases (69.6%) through methylation detection, long insertion resolution, and structural variant characterization, confirming\n                  <jats:italic>trans<\/jats:italic>\n                  inactivation in every resolved tumor suppressor case. Analysis of 4,496 MiOncoSeq samples identified 17,519 multi-hit gene pairs, 78.7% of which exceeded the 500 bp short-read phasing limit, and long-read phasing revealed recurrent compound\n                  <jats:italic>cis<\/jats:italic>\n                  alleles in\n                  <jats:italic>NOTCH1<\/jats:italic>\n                  ,\n                  <jats:italic>PIK3CA<\/jats:italic>\n                  ,\n                  <jats:italic>PDGFRB<\/jats:italic>\n                  , and\n                  <jats:italic>KIT<\/jats:italic>\n                  . Haplotype phasing addresses an overlooked gap in cancer variant interpretation and warrants integration into precision oncology.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Statement of Significance<\/jats:title>\n                  <jats:p>\n                    Short-read sequencing cannot resolve whether co-occurring variants within a cancer gene are\n                    <jats:italic>cis<\/jats:italic>\n                    or\n                    <jats:italic>trans<\/jats:italic>\n                    , a distinction critical for clinical interpretation. Long-read nanopore sequencing addresses this gap through haplotype phasing, methylation detection, and structural variant resolution, confirming biallelic tumor suppressor inactivation and revealing compound\n                    <jats:italic>cis<\/jats:italic>\n                    oncogenic alleles with enhanced activity.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.05.05.26351600","type":"posted-content","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T22:05:36Z","timestamp":1778018736000},"source":"Crossref","is-referenced-by-count":0,"title":["Long-Read Haplotype Phasing Resolves Allelic Configuration as a Missing Layer of Precision Oncology"],"prefix":"10.64898","author":[{"given":"Josh N.","family":"Vo","sequence":"first","affiliation":[{"name":"Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA"},{"name":"Department of Pathology, University of Michigan Medical School, Ann 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USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiffany","family":"Pham","sequence":"additional","affiliation":[{"name":"Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA"},{"name":"Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA"},{"name":"Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuhong","family":"Cao","sequence":"additional","affiliation":[{"name":"Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA"},{"name":"Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA"},{"name":"Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, 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