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Computational Methods for Precision Oncology

  • Book
  • © 2022

Overview

Editors:
  1. Alessandro Laganà

    1. Department of Genetics and Genomic Sciences, Department of Oncological Sciences, Mount Sinai Icahn School of Medicine, New York, USA

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  • Provides an overview of the architecture and components of a precision oncology computational workflow
  • Describes each component of workflow in terms of its tasks, illustrates the biological concepts under investigation
  • Discusses current challenges and perspectives, and introduces advanced concepts

Part of the book series: Advances in Experimental Medicine and Biology (AEMB, volume 1361)

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Table of contents (16 chapters)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. The Architecture of a Precision Oncology Platform

    • Alessandro Laganà
    Pages 1-22

  3. Software Workflows and Infrastructures for Precision Oncology

    • Waleed Osman, Alessandro Laganà
    Pages 23-35

  4. Somatic and Germline Variant Calling from Next-Generation Sequencing Data

    • Ti-Cheng Chang, Ke Xu, Zhongshan Cheng, Gang Wu
    Pages 37-54

  5. Identification of Copy Number Alterations from Next-Generation Sequencing Data

    • Sheida Nabavi, Fatima Zare
    Pages 55-74

  6. Assessment of Microsatellite Instability from Next-Generation Sequencing Data

    • Victor Renault, Emmanuel Tubacher, Alexandre How-Kit
    Pages 75-100

  7. Computational Approaches for the Investigation of Intra-tumor Heterogeneity and Clonal Evolution from Bulk Sequencing Data in Precision Oncology Applications

    • Alessandro Laganà
    Pages 101-118

  8. Computational Methods for Drug Repurposing

    • Rosaria Valentina Rapicavoli, Salvatore Alaimo, Alfredo Ferro, Alfredo Pulvirenti
    Pages 119-141

  9. Pathway Analysis for Cancer Research and Precision Oncology Applications

    • Alessandro La Ferlita, Salvatore Alaimo, Alfredo Ferro, Alfredo Pulvirenti
    Pages 143-161

  10. RNA-seq Fusion Detection in Clinical Oncology

    • Dale J. Hedges
    Pages 163-175

  11. Computational Resources for the Interpretation of Variations in Cancer

    • Grete Francesca Privitera, Salvatore Alaimo, Alfredo Ferro, Alfredo Pulvirenti
    Pages 177-198

  12. Network Approaches for Precision Oncology

    • Shraddha Pai
    Pages 199-213

  13. Patient-Derived In Vitro and In Vivo Models of Cancer

    • Sally E. Claridge, Julie-Ann Cavallo, Benjamin D. Hopkins
    Pages 215-233

  14. Molecular Profiling of Liquid Biopsies for Precision Oncology

    • Edgar E. Gonzalez-Kozlova
    Pages 235-247

  15. Artificial Intelligence for Precision Oncology

    • Sherry Bhalla, Alessandro Laganà
    Pages 249-268

  16. Single-Cell Sequencing Technologies in Precision Oncology

    • David T. Melnekoff, Alessandro Laganà
    Pages 269-282

  17. Multi-Omics Profiling of the Tumor Microenvironment

    • Oliver Van Oekelen, Alessandro Laganà
    Pages 283-326

  18. Back Matter

    Pages 327-336
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Keywords

About this book

Precision medicine holds great promise for the treatment of cancer and represents a unique opportunity for accelerated development and application of novel and repurposed therapeutic approaches. Current studies and clinical trials demonstrate the benefits of genomic profiling for patients whose cancer is driven by specific, targetable alterations. However, precision oncologists continue to be challenged by the widespread heterogeneity of cancer genomes and drug responses in designing personalized treatments. Chapters provide a comprehensive overview of the computational approaches, methods, and tools that enable precision oncology, as well as related biological concepts. Covered topics include genome sequencing, the architecture of a precision oncology workflow, and introduces cutting-edge research topics in the field of precision oncology. This book is intended for computational biologists, bioinformaticians, biostatisticians and computational pathologists working in precision oncology and related fields, including cancer genomics, systems biology, and immuno-oncology.

Editors and Affiliations

  • Department of Genetics and Genomic Sciences, Department of Oncological Sciences, Mount Sinai Icahn School of Medicine, New York, USA

    Alessandro Laganà

About the editor

Alessandro Laganà is Assistant Professor of Oncological Sciences at the Icahn School of Medicine at Mount Sinai, NY. Dr. Laganà's main research interests are integrative cancer genomics, cancer network biology and precision oncology. His current research is focused on the treatment of Multiple Myeloma (malignancy of bone marrow plasma cells). He received both his M.Sc. and Ph.D. from the University of Catania in Catania, Italy. He is also the author of the Humana Press title MicroRNA Target Identification: Methods and Protocols (2019).

Bibliographic Information

  • Book Title: Computational Methods for Precision Oncology

  • Editors: Alessandro Laganà

  • Series Title: Advances in Experimental Medicine and Biology

  • DOI: https://doi.org/10.1007/978-3-030-91836-1

  • Publisher: Springer Cham

  • eBook Packages: Biomedical and Life Sciences, Biomedical and Life Sciences (R0)

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2022

  • Hardcover ISBN: 978-3-030-91835-4Published: 02 March 2022

  • eBook ISBN: 978-3-030-91836-1Published: 01 March 2022

  • Series ISSN: 0065-2598

  • Series E-ISSN: 2214-8019

  • Edition Number: 1

  • Number of Pages: XIV, 336

  • Number of Illustrations: 10 b/w illustrations, 26 illustrations in colour

  • Topics: Cancer Research, Oncology, Bioinformatics

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