title: The hidden genomic landscape of acute myeloid leukemia: subclonal structure revealed by undetected mutations.
abstract: The analyses carried out using 2 different bioinformatics pipelines (SomaticSniper and MuTect) on the same set of genomic data from 133 acute myeloid leukemia (AML) patients, sequenced inside the Cancer Genome Atlas project, gave discrepant results. We subsequently tested these 2 variant-calling pipelines on 20 leukemia samples from our series (19 primary AMLs and 1 secondary AML). By validating many of the predicted somatic variants (variant allele frequencies ranging from 100% to 5%), we observed significantly different calling efficiencies. In particular, despite relatively high specificity, sensitivity was poor in both pipelines resulting in a high rate of false negatives. Our findings raise the possibility that landscapes of AML genomes might be more complex than previously reported and characterized by the presence of hundreds of genes mutated at low variant allele frequency, suggesting that the application of genome sequencing to the clinic requires a careful and critical evaluation. We think that improvements in technology and workflow standardization, through the generation of clear experimental and bioinformatics guidelines, are fundamental to translate the use of next-generation sequencing from research to the clinic and to transform genomic information into better diagnosis and outcomes for the patient.
authors.affiliation: Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy;
authors.forename: Margherita
authors.initials: M
authors.lastname: Bodini
authors.affiliation: Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy;
authors.forename: Chiara
authors.initials: C
authors.lastname: Ronchini
authors.affiliation: Department of Experimental Oncology, European Institute of Oncology, Milan, Italy;
authors.forename: Luciano
authors.initials: L
authors.lastname: Giacò
authors.affiliation: Department of Experimental Oncology, European Institute of Oncology, Milan, Italy;
authors.forename: Anna
authors.initials: A
authors.lastname: Russo
authors.affiliation: Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy;
authors.forename: Giorgio E M
authors.initials: GE
authors.lastname: Melloni
authors.affiliation: Department of Experimental Oncology, European Institute of Oncology, Milan, Italy; IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy;
authors.forename: Lucilla
authors.initials: L
authors.lastname: Luzi
authors.affiliation: IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy; Cogentech, Milan, Italy;
authors.forename: Domenico
authors.initials: D
authors.lastname: Sardella
authors.affiliation: IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy; Cogentech, Milan, Italy;
authors.forename: Sara
authors.initials: S
authors.lastname: Volorio
authors.affiliation: Department of Medical Oncology, Advanced Centre for Treatment, Research & Education in Cancer, Navi Mumbai, India; Department of Biomedicine and Prevention, University of "Rome Tor Vergata," Rome, Italy; Laboratorio di Neuro-Oncoematologia, Fondazione Santa Lucia, Rome, Italy;
authors.forename: Syed K
authors.initials: SK
authors.lastname: Hasan
authors.affiliation: Department of Biomedicine and Prevention, University of "Rome Tor Vergata," Rome, Italy; Laboratorio di Neuro-Oncoematologia, Fondazione Santa Lucia, Rome, Italy;
authors.forename: Tiziana
authors.initials: T
authors.lastname: Ottone
authors.affiliation: Department of Biomedicine and Prevention, University of "Rome Tor Vergata," Rome, Italy; Laboratorio di Neuro-Oncoematologia, Fondazione Santa Lucia, Rome, Italy;
authors.forename: Serena
authors.initials: S
authors.lastname: Lavorgna
authors.affiliation: Department of Biomedicine and Prevention, University of "Rome Tor Vergata," Rome, Italy; Laboratorio di Neuro-Oncoematologia, Fondazione Santa Lucia, Rome, Italy;
authors.forename: Francesco
authors.initials: F
authors.lastname: Lo-Coco
authors.affiliation: Division of Hematology and Bone Marrow Transplantation, University Hospital, Udine, Italy;
authors.forename: Anna
authors.initials: A
authors.lastname: Candoni
authors.affiliation: Division of Hematology and Bone Marrow Transplantation, University Hospital, Udine, Italy;
authors.forename: Renato
authors.initials: R
authors.lastname: Fanin
authors.affiliation: Division of Hematology and Bone Marrow Transplantation, University Hospital, Udine, Italy;
authors.forename: Eleonora
authors.initials: E
authors.lastname: Toffoletti
authors.affiliation: Institute of Hematology "Seràgnoli," Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy;
authors.forename: Ilaria
authors.initials: I
authors.lastname: Iacobucci
authors.affiliation: Institute of Hematology "Seràgnoli," Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy;
authors.forename: Giovanni
authors.initials: G
authors.lastname: Martinelli
authors.affiliation: University Division of Hematology and Cell Therapy, Mauriziano Hospital and University of Torino, Torino, Italy; and.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cignetti
authors.affiliation: University Division of Hematology and Cell Therapy, Mauriziano Hospital and University of Torino, Torino, Italy; and.
authors.forename: Corrado
authors.initials: C
authors.lastname: Tarella
authors.affiliation: Department of Experimental Oncology, European Institute of Oncology, Milan, Italy; Cogentech, Milan, Italy;
authors.forename: Loris
authors.initials: L
authors.lastname: Bernard
authors.affiliation: Department of Experimental Oncology, European Institute of Oncology, Milan, Italy; Dipartimento di Scienze della salute, Università degli Studi di Milano, Milan, Italy.
authors.forename: Pier Giuseppe
authors.initials: PG
authors.lastname: Pelicci
authors.affiliation: Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy;
authors.forename: Laura
authors.initials: L
authors.lastname: Riva
mesh_terms: D019295:Computational Biology / Q000379:methods; D004252:DNA Mutational Analysis / Q000379:methods; D030561:Databases, Nucleic Acid; D005787:Gene Frequency; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics*; D009154:Mutation