Mixed phenotype acute leukaemia (MPAL) is a high-risk subtype of leukaemia with myeloid and lymphoid features, limited genetic characterization, and a lack of consensus regarding appropriate therapy. Here we show that the two principal subtypes of MPAL, T/myeloid (T/M) and B/myeloid (B/M), are genetically distinct. Rearrangement of ZNF384 is common in B/M MPAL, and biallelic WT1 alterations are common in T/M MPAL, which shares genomic features with early T-cell precursor acute lymphoblastic leukaemia. We show that the intratumoral immunophenotypic heterogeneity characteristic of MPAL is independent of somatic genetic variation, that founding lesions arise in primitive haematopoietic progenitors, and that individual phenotypic subpopulations can reconstitute the immunophenotypic diversity in vivo. These findings indicate that the cell of origin and founding lesions, rather than an accumulation of distinct genomic alterations, prime tumour cells for lineage promiscuity. Moreover, these findings position MPAL in the spectrum of immature leukaemias and provide a genetically informed framework for future clinical trials of potential treatments for MPAL.

Aflac Cancer and Blood Disorders Center Children's Healthcare of Atlanta and Emory University School of Medicine Department of Pediatrics Atlanta GA USA

Cancer Therapy Evaluation Program National Cancer Institute Bethesda MD USA

Center for Biomedical Informatics and Information Technology National Cancer Institute Rockville MD USA

Children's Center for Cancer and Blood Disease Children's Hospital Los Angeles Los Angeles CA USA

Children's Oncology Group Arcadia CA USA

Cytogenetics Shared Resource St Jude Children's Research Hospital Memphis TN USA

Department of Biostatistics St Jude Children's Research Hospital Memphis TN USA

Department of Computational Biology St Jude Children's Research Hospital Memphis TN USA

Department of Laboratory Medicine and Pediatrics National Taiwan University Hospital College of Medicine National Taiwan University Taipei Taiwan

Department of Oncology St Jude Children's Research Hospital Memphis TN USA

Department of Paediatric Haematology and Oncology 2nd Faculty of Medicine Charles University and University Hospital Motol Prague Czech Republic

Department of Paediatrics Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore

Department of Pathology St Jude Children's Research Hospital Memphis TN USA

Department of Pediatric Hematology and Oncology Research National Research Institute for Child Health and Development Tokyo Japan

Department of Pediatric Hematology Oncology and Stem Cell Transplantation Ghent University Hospital Ghent Belgium

Department of Pediatric Oncology Erasmus MC Sophia Rotterdam The Netherlands

Department of Pediatrics Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center University of California at San Francisco San Francisco CA USA

Department of Pediatrics Mie University Tsu Japan

Department of Pediatrics University of North Carolina Chapel Hill NC USA

Department of Women and Child Health Hemato Oncology Division University of Padova Padova Italy

Division of Leukemia and Lymphoma Children's Cancer Center National Center for Child Health and Development Tokyo Japan

Division of Oncology and Center for Childhood Cancer Research Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania Philadelphia PA USA

Fred Hutchinson Cancer Research Center Clinical Research Division Seattle WA USA

Johns Hopkins Medical Institutions Baltimore MD USA

Michael Smith Genome Sciences Centre BC Cancer Agency Vancouver British Columbia Canada

Office of Cancer Genomics National Cancer Institute Bethesda MD USA

Pediatric Hematology Oncology Schneider Children's Medical Center Sackler Faculty of Medicine Tel Aviv University Israel

Prinses Maxima Centre Utrecht The Netherlands

The Ohio State University School of Medicine Columbus OH USA

The Tumour Bank CCRU The Kids Research Institute The Children's Hospital at Westmead Westmead New South Wales Australia

The University of Queensland Diamantina Institute and Children's Health Brisbane Queensland Australia

Universitäts Klinikum Essen Germany

University of Alabama at Birmingham Birmingham AL USA

University of Florida Gainesville FL USA

University of Washington Seattle WA USA

Wolfson Childhood Cancer Centre Northern Institute for Cancer Research Newcastle University Newcastle upon Tyne UK

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