Patient‐tailored analysis of minimal residual disease in acute myeloid leukemia using next‐generation sequencing |
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| Authors: | Anna Rehammar Tore Samuelsson Sofie J. Alm Erik Kristiansson Jonas Abrahamsson Hege Garelius Louise Pettersson Mats Ehinger Lars Palmqvist Linda Fogelstrand |
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| Affiliation: | 1. Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden;2. Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden;3. Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden;4. Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden;5. Department of Medicine, Section of Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden;6. Department of Pathology, Hallands Hospital Halmstad, Halmstad, Sweden;7. Division of Oncology and Pathology, Lund University, Lund, Sweden;8. Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden |
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| Abstract: | Next‐generation sequencing techniques have revealed that leukemic cells in acute myeloid leukemia often are characterized by a limited number of somatic mutations. These mutations can be the basis for the detection of leukemic cells in follow‐up samples. The aim of this study was to identify leukemia‐specific mutations in cells from patients with acute myeloid leukemia and to use these mutations as markers for minimal residual disease. Leukemic cells and normal lymphocytes were simultaneously isolated at diagnosis from 17 patients with acute myeloid leukemia using fluorescence‐activated cell sorting. Exome sequencing of these cells identified 240 leukemia‐specific single nucleotide variations and 22 small insertions and deletions. Based on estimated allele frequencies and their accuracies, 191 of these mutations qualified as candidates for minimal residual disease analysis. Targeted deep sequencing with a significance threshold of 0.027% for single nucleotide variations and 0.006% for NPM1 type A mutation was developed for quantification of minimal residual disease. When tested on follow‐up samples from a patient with acute myeloid leukemia, targeted deep sequencing of single nucleotide variations as well as NPM1 was more sensitive than minimal residual disease quantification with multiparameter flow cytometry. In conclusion, we here describe how exome sequencing can be used for identification of leukemia‐specific mutations in samples already at diagnosis of acute myeloid leukemia. We also show that targeted deep sequencing of such mutations, including single nucleotide variations, can be used for high‐sensitivity quantification of minimal residual disease in a patient‐tailored manner. |
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| Keywords: | acute myeloid leukemia minimal residual disease massively parallel sequencing |
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