{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:50:10Z","timestamp":1787010610791,"version":"build-2736575974"},"posted":{"date-parts":[[2025,3,19]]},"group-title":"Cancer Biology","reference-count":40,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T00:00:00Z","timestamp":1742342400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,11,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Approximately 15-20% of children with acute lymphoblastic leukemia (pALL) are not cured despite years of treatment with more than ten chemotherapeutic agents, yet bulk sequencing reveals minimal somatic variation that could explain genetic treatment resistance. Using error-corrected bulk sequencing, and primary template-directed amplification (PTA)-enabled single-cell exome and whole-genome sequencing, we discovered much more genetic diversity in pALL. Individual leukemic cells harbor 3.7-fold more mutations (mean 3,553) than detected in bulk samples (mean 965). Many ETV6-RUNX1 patients harbor multiple independent ras-mutated clones, and we also identified convergent evolution of\n                  <jats:italic>JAK2<\/jats:italic>\n                  mutations as well as copy number alterations. PTA-based phylogenetic analysis of over 150 single-cell genomes linked heritable phenotypes to specific genetic alterations and identified low-frequency clones harboring mutations in treatment resistance-associated genes (\n                  <jats:italic>ITGA9<\/jats:italic>\n                  ,\n                  <jats:italic>NTRK3<\/jats:italic>\n                  ,\n                  <jats:italic>SULF2<\/jats:italic>\n                  ) that increased in frequency during treatment. These findings reveal extensive hidden genetic diversity in pALL while providing a framework for the early detection of high-risk leukemic populations.\n                <\/jats:p>","DOI":"10.1101\/2025.03.19.644196","type":"posted-content","created":{"date-parts":[[2025,3,21]],"date-time":"2025-03-21T23:02:34Z","timestamp":1742598154000},"source":"Crossref","is-referenced-by-count":3,"title":["Single-Cell Sequencing Reveals Extensive Genetic Diversity Underlying Pediatric ALL Treatment Complexity"],"prefix":"10.64898","author":[{"given":"Yakun","family":"Pang","sequence":"first","affiliation":[{"name":"Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tamara","family":"Prieto","sequence":"additional","affiliation":[{"name":"Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA"},{"name":"Sandra and Edward Meyer Cancer Center, Weill Cornell 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Weill Cornell Medicine, New York, NY, USA"},{"name":"Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA"},{"name":"New York Genome Center, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathaniel D.","family":"Omans","sequence":"additional","affiliation":[{"name":"Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA"},{"name":"Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA"},{"name":"New York Genome Center, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Potenski","sequence":"additional","affiliation":[{"name":"Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA"},{"name":"Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA"},{"name":"New York Genome Center, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Klein","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"MacKay","sequence":"additional","affiliation":[{"name":"Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, US"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iwijn","family":"De Vlaminck","sequence":"additional","affiliation":[{"name":"Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, US"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Easton","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, St. Jude Children\u2019s Research Hospital, Memphis, TN, 38105, 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