To characterize the incidence, clinical features and genetics of ETV6-ABL1 leukemias, representing targetable kinase-activating lesions, we analyzed 44 new and published cases of ETV6-ABL1-positive hematologic malignancies [22 cases of acute lymphoblastic leukemia (13 children, 9 adults) and 22 myeloid malignancies (18 myeloproliferative neoplasms, 4 acute myeloid leukemias)]. The presence of the ETV6-ABL1 fusion was ascertained by cytogenetics, fluorescence in-situ hybridization, reverse transcriptase-polymerase chain reaction and RNA sequencing. Genomic and gene expression profiling was performed by single nucleotide polymorphism and expression arrays. Systematic screening of more than 4,500 cases revealed that in acute lymphoblastic leukemia ETV6-ABL1 is rare in childhood (0.17% cases) and slightly more common in adults (0.38%). There is no systematic screening of myeloproliferative neoplasms; however, the number of ETV6-ABL1-positive cases and the relative incidence of acute lymphoblastic leukemia and myeloproliferative neoplasms suggest that in adulthood ETV6-ABL1 is more common in BCR-ABL1-negative chronic myeloid leukemia-like myeloproliferations than in acute lymphoblastic leukemia. The genomic profile of ETV6-ABL1 acute lymphoblastic leukemia resembled that of BCR-ABL1 and BCR-ABL1-like cases with 80% of patients having concurrent CDKN2A/B and IKZF1 deletions. In the gene expression profiling all the ETV6-ABL1-positive samples clustered in close vicinity to BCR-ABL1 cases. All but one of the cases of ETV6-ABL1 acute lymphoblastic leukemia were classified as BCR-ABL1-like by a standardized assay. Over 60% of patients died, irrespectively of the disease or age subgroup examined. In conclusion, ETV6-ABL1 fusion occurs in both lymphoid and myeloid leukemias; the genomic profile and clinical behavior resemble BCR-ABL1-positive malignancies, including the unfavorable prognosis, particularly of acute leukemias. The poor outcome suggests that treatment with tyrosine kinase inhibitors should be considered for patients with this fusion.

Birmingham Children's Hospital NHS Foundation Trust UK

Centro Ricerca Tettamanti Clinica Pediatrica Università di Milano Bicocca Fondazione MBBM Ospedale San Gerardo Monza Italy

CLIP Department of Pediatric Hematology and Oncology 2 Faculty of Medicine Charles University and University Hospital Motol Prague Czech Republic

Department of Cancer Biology Institut Paoli Calmettes Marseille France

Department of Cytogenetics Leicester Royal Infirmary NHS Trust UK

Department of Haematology Our Lady's Children's Hospital Dublin Ireland

Department of Hematology Institut Paoli Calmettes Marseille France

Department of Hematology Leiden University Medical Center The Netherlands

Department of Laboratory Medicine Seoul St Mary's Hospital College of Medicine The Catholic University of Korea Seoul Republic of Korea

Department of Leukemia The University of Texas M D Anderson Cancer Center Houston TX USA

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

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

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

Leukaemia Research Cytogenetics Group Northern Institute for Cancer Research Newcastle University Newcastle upon Tyne UK

Pediatric Hematology and Oncology Hannover Medical School Germany

South Australia Health and Medical Research Institute Adelaide Australia

St Anna Children's Hospital Childrens Cancer Research Institute Vienna Austria

University of New Mexico Cancer Center Albuquerque NM USA

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