Acute promyelocytic leukemia with torque teno mini virus (TTMV)::RARA fusion: an approach to screening and diagnosis

Acute promyelocytic leukemia (APL) with variant RARA translocation is linked to over 15 partner genes. Recent publications encompassing six cases have expanded the spectrum of RARA partners to torque teno mini virus (TTMV). This entity is likely under-recognized due to lack of clinician and pathologist familiarity, inability to detect the fusion using routine testing modalities, and informatic challenges in its recognition within next-generation sequencing (NGS) data. We describe a clinicopathologic approach and provide necessary tools to screen and diagnose APL with TTMV::RARA using existing clinical DNA or RNA-based NGS assays, which led to identification of four cases, all without other known cytogenetic/molecular drivers. One was identified prospectively and three retrospectively, including two from custom automated screening of multiple data sets (50,257 cases of hematopoietic malignancy, including 4809 acute myeloid leukemia (AML)/myeloid sarcoma/APL cases). Two cases presented as myeloid sarcoma, including one with multiple relapses after AML-type chemotherapy and hematopoietic stem cell transplant (HSCT). Two cases presented as leukemia, had a poor response to induction chemotherapy, but achieved remission upon re-induction (including all-trans retinoic acid (ATRA) in one case) and subsequent HSCT. Neoplastic cells demonstrated features of APL including frequent azurophilic granules and dim/absent CD34 and HLA-DR expression. RARA rearrangement was not detected by karyotype or FISH. Custom analysis of NGS fusion panel data identified TTMV::RARA rearrangements, and in the prospectively identified case, facilitated monitoring in sequential bone marrow samples. APL with TTMV::RARA is a rare leukemia with a high rate of treatment failure in described cases. The diagnosis should be considered in leukemias with features of APL that lack detectable RARA fusions and other drivers, and may be confirmed by appropriate NGS tests with custom informatics. Incorporation of ATRA may have a role in treatment but requires accurate recognition of the fusion for appropriate classification as APL. ### Competing Interest Statement MM: Employee of Foundation Medicine, Inc. and shareholder of Roche Holding AG. EAW: Employee of Foundation Medicine, Inc. ### Funding Statement Funding for fusion analysis performed at BCH was through intra-departmental funds. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Institutional Review Board of Boston Children's Hospital gave ethical approval for this work (Protocol #IRB-P00012434 entitled "Targeted Molecular Analysis of Pediatric Solid Tumor and Hematologic Malignancy Samples"). The Institutional Review Board of Mass General Brigham gave ethical approval for this work (Protocol #2014P000940 entitled "Molecular characterization of hematological malignancies and solid tumors"). The Western Institutional Review Board (Protocol No. 20152817) approved the inclusion of the Foundation Medicine Inc samples in this study, including a waiver of informed consent and the Health Insurance Portability and Accountability Act (HIPAA) waiver of authorization. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Code for the automated custom TTMV::RARA analysis described in this paper is available at: github.com/ht50/ttmv\_rara\_SR. For other data please contact the corresponding author. [https://github.com/ht50/ttmv\_rara\_SR][1] [1]: https://github.com/ht50/ttmv_rara_SR