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Patients may respond to initial therapy, but often relapse, underscoring an evolving disease. Next generation sequencing technologies are being applied to AML for risk stratification and monitoring treatment response. We aimed to evaluate the efficiency of whole exome sequencing (WES) and single-cell DNA sequencing (scDNA-seq) for determining clonal heterogeneity and evolution in AML induced by treatment, assessing strengths and limitations of each technology<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec sec-type=\"materials-methods\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We conducted WES and scDNA-seq on samples from 6 patients with AML, including sequential samples from four patients. We identified somatic variants, clonal composition and phylogeny using both technologies and compared the results.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec sec-type=\"results\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>WES detected more variants and clones due to broader coverage, while scDNA-seq provided clonality results for targeted genes revealing zygosity and rare clones. Both techniques missed clinically important variants, posing challenges for clinical application. However, they identified similar founding clones and strong correlation of variant allele frequencies and clonal prevalences.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec sec-type=\"conclusion\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>As both technologies can overlook variants, multiple technologies should be utilized to understand clonality in heterogeneous diseases such as AML. Careful scDNA-seq target panel planning, utilizing knowledge obtained from bulk sequencing, can offer more information on clonal heterogeneity. One limitation of our study is the small sample size which may limit the generalizability of the conclusions.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1016\/j.csbj.2025.11.066","type":"journal-article","created":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T16:17:23Z","timestamp":1764692243000},"page":"5549-5560","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"title":["Whole exome sequencing and single-cell DNA sequencing for assessment of clonal heterogeneity and evolution in acute myeloid leukemia"],"prefix":"10.34133","volume":"27","author":[{"given":"Sadiksha","family":"Adhikari","sequence":"first","affiliation":[{"name":"Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuli","family":"Eldfors","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland"},{"name":"Massachusetts General Hospital Cancer Center, Charlestown, MA, USA"},{"name":"Department of Medicine, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esa","family":"Pitk\u00e4nen","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland"},{"name":"Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"V\u00e4h\u00e4-Koskela","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline A.","family":"Heckman","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","published-online":{"date-parts":[[2025,12,5]]},"reference":[{"key":"e_1_3_6_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-018-0081-z"},{"key":"e_1_3_6_3_2","doi-asserted-by":"publisher","DOI":"10.1182\/blood.2019004397"},{"key":"e_1_3_6_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2864-x"},{"key":"e_1_3_6_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature10738"},{"key":"e_1_3_6_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-01819-x"},{"key":"e_1_3_6_7_2","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1038\/s41375-024-02211-z","article-title":"Mutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity","volume":"38","author":"Schwede M.","year":"2024","unstructured":"Schwede M., Jahn K., Kuipers J., Miles L.A., Bowman R.L., Robinson T. et al: Mutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity. 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