{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T05:56:39Z","timestamp":1776837399726,"version":"3.51.2"},"reference-count":31,"publisher":"SAGE Publications","issue":"1","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"funder":[{"DOI":"10.13039\/100000143","name":"Division of Computing and Communication Foundations","doi-asserted-by":"crossref","award":["2046488"],"award-info":[{"award-number":["2046488"]}],"id":[{"id":"10.13039\/100000143","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Journal of Computational Biology"],"published-print":{"date-parts":[[2026,1]]},"abstract":"<jats:p>\n                    Cancer arises through an evolutionary process in which somatic mutations, including single-nucleotide variants (SNVs) and copy number aberrations (CNAs), drive the development of a malignant, heterogeneous tumor. Reconstructing this evolutionary history from sequencing data is critical for understanding the order in which mutations are acquired and the dynamic interplay between different types of alterations. Advances in modern whole-genome single-cell sequencing now enable the accurate inference of copy number profiles in individual cells. However, the low sequencing coverage of these low-pass sequencing technologies poses a challenge for reliably inferring the presence or absence of SNVs within tumor cells, limiting the ability to simultaneously study the evolutionary relationships between SNVs and CNAs. In this work, we introduce a novel tumor phylogeny inference method, P\n                    <jats:sc>harming<\/jats:sc>\n                    , that infers the joint evolutionary history of SNVs and CNAs. Our key insight is to leverage the high accuracy of copy number inference methods and the fact that SNVs co-occur in regions with CNAs in order to enable more precise tumor phylogeny reconstruction for both alteration types. We demonstrate via simulations that P\n                    <jats:sc>harming<\/jats:sc>\n                    outperforms state-of-the-art tumor phylogeny inference methods. Additionally, we apply P\n                    <jats:sc>harming<\/jats:sc>\n                    to a triple-negative breast cancer case, achieving high-resolution, joint reconstruction of CNA and SNV evolution, including the de novo detection of a clonal whole-genome duplication event. Thus, P\n                    <jats:sc>harming<\/jats:sc>\n                    offers the potential for more comprehensive and detailed tumor phylogeny inference for high-throughput, low-coverage single-cell DNA sequencing technologies compared with existing approaches.\n                  <\/jats:p>","DOI":"10.1177\/15578666251374694","type":"journal-article","created":{"date-parts":[[2025,9,13]],"date-time":"2025-09-13T10:26:56Z","timestamp":1757759216000},"page":"2-18","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":2,"title":["Pharming: Joint Clonal Tree Reconstruction of Single-Nucleotide Variant and Copy Number Aberration Evolution from Single-Cell DNA Sequencing of Tumors"],"prefix":"10.1177","volume":"33","author":[{"given":"Leah L.","family":"Weber","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Hart","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Idoia","family":"Ochoa","sequence":"additional","affiliation":[{"name":"Department of Electrical &amp; Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, USA."},{"name":"Department of Electrical and Electronics Engineering, Tecnun, University of Navarra, Donostia, Spain."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1468-2407","authenticated-orcid":false,"given":"Mohammed","family":"El-Kebir","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA."},{"name":"Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2026,1,30]]},"reference":[{"key":"e_1_3_4_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03170-5"},{"key":"e_1_3_4_3_1","first-page":"2023.12.07.5707","article-title":"Sc-TUSV-ext: Single-cell clonal lineage inference from single nucleotide variants (SNV), copy number alterations (CNA) and structural variants (SV)","author":"Bristy NA","year":"2023","unstructured":"Bristy NA, , Fu X, , Schwartz R. Sc-TUSV-ext: Single-cell clonal lineage inference from single nucleotide variants (SNV), copy number alterations (CNA) and structural variants (SV). bioRxiv, 2023:2023.12.07.570724.","journal-title":"bioRxiv"},{"key":"e_1_3_4_4_1","doi-asserted-by":"crossref","unstructured":"Chen D Eulenstein O Fern\u00e1ndez-Baca D et al. Supertrees by flipping. In International Computing and Combinatorics Conference. Springer 2002 pp. 391\u2013400.","DOI":"10.1007\/3-540-45655-4_42"},{"key":"e_1_3_4_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msac143"},{"key":"e_1_3_4_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac092"},{"key":"e_1_3_4_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-021-01005-8"},{"key":"e_1_3_4_8_1","first-page":"164","article-title":"Les lois de l\u2019\u00e9volution","volume":"7","author":"Dollo L","year":"1893","unstructured":"Dollo L. Les lois de l\u2019\u00e9volution. Bulletin de la Soci\u00e9t\u00e9 Belge de G\u00e9ologie, de Pal\u00e9ontologie et D\u2019hydrologie, 1893; 7:164\u2013166.","journal-title":"Bulletin de la Soci\u00e9t\u00e9 Belge de G\u00e9ologie, de Pal\u00e9ontologie et D\u2019hydrologie"},{"key":"e_1_3_4_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty589"},{"key":"e_1_3_4_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv261"},{"key":"e_1_3_4_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-05249-0"},{"key":"e_1_3_4_12_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-025-03553-2"},{"key":"e_1_3_4_13_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0936-x"},{"key":"e_1_3_4_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/49.4.725"},{"key":"e_1_3_4_15_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02583-w"},{"key":"e_1_3_4_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.10.026"},{"key":"e_1_3_4_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv003"},{"key":"e_1_3_4_18_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.234435.118"},{"key":"e_1_3_4_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03357-x"},{"key":"e_1_3_4_20_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.959840"},{"key":"e_1_3_4_21_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.232272.117"},{"key":"e_1_3_4_22_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13015-022-00209-9"},{"key":"e_1_3_4_23_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-03106-5"},{"key":"e_1_3_4_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2021.07.006"},{"key":"e_1_3_4_25_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2020.04.001"},{"key":"e_1_3_4_26_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1011590"},{"key":"e_1_3_4_27_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-40378-8"},{"key":"e_1_3_4_28_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1011544"},{"key":"e_1_3_4_29_1","doi-asserted-by":"publisher","DOI":"10.1158\/2643-3230.BCD-21-0092"},{"key":"e_1_3_4_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0661-6"},{"key":"e_1_3_4_31_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.243121.118"},{"key":"e_1_3_4_32_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.277249.122"}],"container-title":["Journal of Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1177\/15578666251374694","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/15578666251374694","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/15578666251374694","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,9]],"date-time":"2026-02-09T05:46:59Z","timestamp":1770616019000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/full\/10.1177\/15578666251374694"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["10.1177\/15578666251374694"],"URL":"https:\/\/doi.org\/10.1177\/15578666251374694","relation":{},"ISSN":["1066-5277","1557-8666"],"issn-type":[{"value":"1066-5277","type":"print"},{"value":"1557-8666","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1]]}}}