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Sandmann S, Behrens YL, Davenport C, Thol F, Heuser M, Dörfel D, Löhr F, Castrup A, Steinemann D, Varghese J, Schlegelberger B, Dugas M, Göhring G. Clonal Evolution at First Sight: A Combined Visualization of Diverse Diagnostic Methods Improves Understanding of Leukemic Progression. Front Oncol 2022; 12:888114. [PMID: 35875134 PMCID: PMC9305660 DOI: 10.3389/fonc.2022.888114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Patients with myeloid neoplasia are classified by the WHO classification systems. Besides clinical and hematological criteria, cytogenetic and molecular genetic alterations highly impact treatment stratification. In routine diagnostics, a combination of methods is used to decipher different types of genetic variants. Eight patients were comprehensively analyzed using karyotyping, fluorescence in situ hybridization, array-CGH and a custom NGS panel. Clonal evolution was reconstructed manually, integrating all mutational information on single nucleotide variants (SNVs), insertions and deletions (indels), structural variants and copy number variants (CNVs). To allow a correct integration, we differentiate between three scenarios: 1) CNV occurring prior to the SNV/indel, but in the same cells. 2) SNV/indel occurring prior to the CNV, but in the same cells. 3) SNV/indel and CNV existing in parallel, independent of each other. Applying this bioinformatics approach, we reconstructed clonal evolution for all patients. This generalizable approach offers the possibility to integrate various data to analyze identification of driver and passenger mutations as well as possible targets for personalized medicine approaches. Furthermore, this model can be used to identify markers to assess the minimal residual disease.
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Affiliation(s)
- Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Yvonne Lisa Behrens
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
- *Correspondence: Yvonne Lisa Behrens,
| | - Claudia Davenport
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Daniela Dörfel
- Department of Hematology, Oncology and Immunology, Klinikum Region Hannover (KRH) Klinikum Siloah, Hannover, Germany
| | - Friederike Löhr
- Department of Hematology and Oncology, Klinikum Braunschweig, Braunschweig, Germany
| | - Agnes Castrup
- Hämato-Onkologische Praxis, Hämato-Onkologische Praxis im Medicum, Bremen, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | | | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
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Kozlov A, Alves JM, Stamatakis A, Posada D. CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data. Genome Biol 2022; 23:37. [PMID: 35081992 PMCID: PMC8790911 DOI: 10.1186/s13059-021-02583-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 12/20/2021] [Indexed: 01/15/2023] Open
Abstract
We introduce CellPhy, a maximum likelihood framework for inferring phylogenetic trees from somatic single-cell single-nucleotide variants. CellPhy leverages a finite-site Markov genotype model with 16 diploid states and considers amplification error and allelic dropout. We implement CellPhy into RAxML-NG, a widely used phylogenetic inference package that provides statistical confidence measurements and scales well on large datasets with hundreds or thousands of cells. Comprehensive simulations suggest that CellPhy is more robust to single-cell genomics errors and outperforms state-of-the-art methods under realistic scenarios, both in accuracy and speed. CellPhy is freely available at https://github.com/amkozlov/cellphy .
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Affiliation(s)
- Alexey Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Joao M. Alves
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
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Sadeqi Azer E, Haghir Ebrahimabadi M, Malikić S, Khardon R, Sahinalp SC. Tumor Phylogeny Topology Inference via Deep Learning. iScience 2020; 23:101655. [PMID: 33117968 PMCID: PMC7582044 DOI: 10.1016/j.isci.2020.101655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/10/2020] [Accepted: 10/02/2020] [Indexed: 01/24/2023] Open
Abstract
Principled computational approaches for tumor phylogeny reconstruction via single-cell sequencing typically aim to build the most likely perfect phylogeny tree from the noisy genotype matrix - which represents genotype calls of single cells. This problem is NP-hard, and as a result, existing approaches aim to solve relatively small instances of it through combinatorial optimization techniques or Bayesian inference. As expected, even when the goal is to infer basic topological features of the tumor phylogeny, rather than reconstructing the topology entirely, these approaches could be prohibitively slow. In this paper, we introduce fast deep learning solutions to the problems of inferring whether the most likely tree has a linear (chain) or branching topology and whether a perfect phylogeny is feasible from a given genotype matrix. We also present a reinforcement learning approach for reconstructing the most likely tumor phylogeny. This preliminary work demonstrates that data-driven approaches can reconstruct key features of tumor evolution.
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Affiliation(s)
- Erfan Sadeqi Azer
- Department of Computer Science, Indiana University, Bloomington, IN 47408, USA
| | - Mohammad Haghir Ebrahimabadi
- Department of Computer Science, Indiana University, Bloomington, IN 47408, USA
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Salem Malikić
- Department of Computer Science, Indiana University, Bloomington, IN 47408, USA
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Roni Khardon
- Department of Computer Science, Indiana University, Bloomington, IN 47408, USA
| | - S. Cenk Sahinalp
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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