title: Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia.
abstract: In our individualized systems medicine program, personalized treatment options are identified and administered to chemorefractory acute myeloid leukemia (AML) patients based on exome sequencing and ex vivo drug sensitivity and resistance testing data. Here, we analyzed how clonal heterogeneity affects the responses of 13 AML patients to chemotherapy or targeted treatments using ultra-deep (average 68 000 × coverage) amplicon resequencing. Using amplicon resequencing, we identified 16 variants from 4 patients (frequency 0.54-2%) that were not detected previously by exome sequencing. A correlation-based method was developed to detect mutation-specific responses in serial samples across multiple time points. Significant subclone-specific responses were observed for both chemotherapy and targeted therapy. We detected subclonal responses in patients where clinical European LeukemiaNet (ELN) criteria showed no response. Subclonal responses also helped to identify putative mechanisms underlying drug sensitivities, such as sensitivity to azacitidine in DNMT3A mutated cell clones and resistance to cytarabine in a subclone with loss of NF1 gene. In summary, ultra-deep amplicon resequencing method enables sensitive quantification of subclonal variants and their responses to therapies. This approach provides new opportunities for designing combinatorial therapies blocking multiple subclones as well as for real-time assessment of such treatments.
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.
authors: P N
authors: PN
authors: Ojamies
authors: Hematology Research Unit Helsinki, Department of Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
authors: M
authors: M
authors: Kontro
authors: MediSapiens Ltd, Helsinki, Finland.
authors: H
authors: H
authors: Edgren
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.
authors: P
authors: P
authors: Ellonen
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.
authors: S
authors: S
authors: Lagström
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.
authors: H
authors: H
authors: Almusa
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.
authors: T
authors: T
authors: Miettinen
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.
authors: S
authors: 0000-0001-5056-4750
authors: S
authors: Eldfors
authors: Biomedical Genomics Lab, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
authors: D
authors: D
authors: Tamborero
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.
authors: K
authors: K
authors: Wennerberg
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.
authors: C
authors: C
authors: Heckman
authors: Hematology Research Unit Helsinki, Department of Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
authors: K
authors: K
authors: Porkka
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.
authors: M
authors: M
authors: Wolf
authors: Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.|Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden.
authors: O
authors: 0000-0002-3231-0332
authors: O
authors: Kallioniemi
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D001483:Base Sequence; D002999:Clone Cells / Q000187:drug effects*; D016903:Drug Monitoring; D014644:Genetic Variation; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000188:drug therapy* / Q000235:genetics; D058990:Molecular Targeted Therapy; D057285:Precision Medicine
chemical_list: D000970:Antineoplastic Agents