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      The mutational oncoprint of recurrent cytogenetic abnormalities in adult patients with de novo acute myeloid leukemia

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          Abstract

          Recurrent chromosomal abnormalities and gene mutations detected at the time of diagnosis of acute myeloid leukemia (AML) are associated with particular disease features, treatment response and survival of AML patients, and are used to denote specific disease entities in the World Health Organization classification of myeloid neoplasms and acute leukemia. However, large studies that integrate cytogenetic and comprehensive mutational information are scarce. We created a comprehensive oncoprint of mutations associated with recurrent cytogenetic findings by combining the information on mutational patterns of 80 cancer- and leukemia-associated genes with cytogenetic findings in 1603 adult patients with de novo AML. We show unique differences in the mutational profiles among major cytogenetic subsets, identify novel associations between recurrent cytogenetic abnormalities and both specific gene mutations and gene functional groups, and reveal differences in cytogenetic and mutational features between patients younger than 60 years and those aged 60 years or older. The identified associations between cytogenetic and molecular genetic data may help guide mutation testing in AML, and result in more focused application of targeted therapy in patients with de novo AML.

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          Most cited references37

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          Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

          The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.
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            TP53 alterations in acute myeloid leukemia with complex karyotype correlate with specific copy number alterations, monosomal karyotype, and dismal outcome.

            To assess the frequency of TP53 alterations and their correlation with other genetic changes and outcome in acute myeloid leukemia with complex karyotype (CK-AML), we performed integrative analysis using TP53 mutational screening and array-based genomic profiling in 234 CK-AMLs. TP53 mutations were found in 141 of 234 (60%) and TP53 losses were identified in 94 of 234 (40%) CK-AMLs; in total, 164 of 234 (70%) cases had TP53 alterations. TP53-altered CK-AML were characterized by a higher degree of genomic complexity (aberrations per case, 14.30 vs 6.16; P < .0001) and by a higher frequency of specific copy number alterations, such as -5/5q-, -7/7q-, -16/16q-, -18/18q-, +1/+1p, and +11/+11q/amp11q13∼25; among CK-AMLs, TP53-altered more frequently exhibited a monosomal karyotype (MK). Patients with TP53 alterations were older and had significantly lower complete remission rates, inferior event-free, relapse-free, and overall survival. In multivariable analysis for overall survival, TP53 alterations, white blood cell counts, and age were the only significant factors. In conclusion, TP53 is the most frequently known altered gene in CK-AML. TP53 alterations are associated with older age, genomic complexity, specific DNA copy number alterations, MK, and dismal outcome. In multivariable analysis, TP53 alteration is the most important prognostic factor in CK-AML, outweighing all other variables, including the MK category.
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              Spectrum and prognostic relevance of driver gene mutations in acute myeloid leukemia.

              The clinical and prognostic relevance of many recently identified driver gene mutations in adult acute myeloid leukemia (AML) is poorly defined. We sequenced the coding regions or hotspot areas of 68 recurrently mutated genes in a cohort of 664 patients aged 18 to 86 years treated on 2 phase 3 trials of the German AML Cooperative Group (AMLCG). The median number of 4 mutations per patient varied according to cytogenetic subgroup, age, and history of previous hematologic disorder or antineoplastic therapy. We found patterns of significantly comutated driver genes suggesting functional synergism. Conversely, we identified 8 virtually nonoverlapping patient subgroups, jointly comprising 78% of AML patients, that are defined by mutually exclusive genetic alterations. These subgroups, likely representing distinct underlying pathways of leukemogenesis, show widely divergent outcomes. Furthermore, we provide detailed information on associations between gene mutations, clinical patient characteristics, and therapeutic outcomes in this large cohort of uniformly treated AML patients. In multivariate analyses including a comprehensive set of molecular and clinical variables, we identified DNMT3A and RUNX1 mutations as important predictors of shorter overall survival (OS) in AML patients <60 years, and particularly in those with intermediate-risk cytogenetics. NPM1 mutations in the absence of FLT3-ITD, mutated TP53, and biallelic CEBPA mutations were identified as important molecular prognosticators of OS irrespective of patient age. In summary, our study provides a comprehensive overview of the spectrum, clinical associations, and prognostic relevance of recurrent driver gene mutations in a large cohort representing a broad spectrum and age range of intensively treated AML patients.
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                Author and article information

                Journal
                Leukemia
                Leukemia
                Leukemia
                Nature Publishing Group
                0887-6924
                1476-5551
                October 2017
                24 March 2017
                18 April 2017
                : 31
                : 10
                : 2211-2218
                Affiliations
                [1 ]The Ohio State University Comprehensive Cancer Center , Columbus, OH, USA
                [2 ]Alliance Statistics and Data Center, Mayo Clinic , Rochester, MN, USA
                [3 ]Division of Hematology, Department of Internal Medicine, The Ohio State University, Comprehensive Cancer Center , Columbus, OH, USA
                [4 ]Department of Genetics, University of Alabama at Birmingham , Birmingham, AL, USA
                [5 ]Monter Cancer Center, Hofstra North Shore-Long Island Jewish School of Medicine , Lake Success, NY, USA
                [6 ]Comprehensive Cancer Center of Wake Forest University , Winston-Salem, NC, USA
                [7 ]Department of Medicine, Roswell Park Cancer Institute , Buffalo, NY, USA
                [8 ]Department of Medical Oncology, Dana-Farber/Partners CancerCare , Boston, MA, USA
                Author notes
                [* ]The Ohio State University Comprehensive Cancer Center , 460 West 12th Avenue, Room 850, Columbus, OH 43210-1228, USA E-mail: ann-kathrin.eisfeld@ 123456osumc.edu
                [* ]The Ohio State University Comprehensive Cancer Center , 370A Tzagournis Medical Research Facility, 420 West 12th Avenue, Columbus, OH 43210-1228, USA E-mail: krzysztof.mrozek@ 123456osumc.edu
                [* ]The Ohio State University Comprehensive Cancer Center , C933 James Cancer Hospital, 460 West 10th Avenue, Columbus, OH 43210-1228, USA. E-mail: clara.bloomfield@ 123456osumc.edu
                [9]

                These authors contributed equally to this work.

                [10]

                These senior authors contributed equally to this work.

                Article
                leu201786
                10.1038/leu.2017.86
                5628133
                28321123
                59484a13-3df3-43ff-8de3-f898b72ceccb
                Copyright © 2017 Macmillan Publishers Limited, part of Springer Nature.
                History
                : 02 November 2016
                : 17 January 2017
                : 16 February 2017
                Categories
                Original Article

                Oncology & Radiotherapy
                Oncology & Radiotherapy

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