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Evaluation of Whole Genome Sequencing Data

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Lymphoma

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1956))

Abstract

Whole genome sequencing (WGS) can provide comprehensive insights into the genetic makeup of lymphomas. Here we describe a selection of methods for the analysis of WGS data, including alignment, identification of different classes of genomic variants, the identification of driver mutations, and the identification of mutational signatures. We further outline design considerations for WGS studies and provide a variety of quality control measures to detect common quality problems in the data.

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Acknowledgments

This work has been supported by the German Ministry of Science and Education (BMBF) in the framework of the ICGC MMML-Seq (01KU1002A-J) and the ICGC DE-MINING (01KU1505E) projects and the Heidelberg Center for Human Bioinformatics (HD-HuB) within the German Network for Bioinformatics Infrastructure (de.NBI) (#031A537A, #031A537C). We are grateful to all present and previous members of the Division of Theoretical Bioinformatics, the DKFZ-HIPO bioinformatics team, the Omics IT and Data Management Core Facility, and the Bioinformatics and Omics Data Analytics group of the German Cancer Research Center (DKFZ, Heidelberg) as well as coworkers in the ICGC MMML-seq and PedBrain projects who were involved in the establishment of the procedures described here.

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  1. Daniel Hübschmann

    Present address: Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany

Authors and Affiliations

  1. Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany

    Daniel Hübschmann

  2. Department of Pediatric Immunology, Hematology and Oncology, University Hospital, Heidelberg, Germany

    Daniel Hübschmann

  3. Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany

    Matthias Schlesner

Authors
  1. Daniel Hübschmann
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  2. Matthias Schlesner
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Correspondence to Matthias Schlesner .

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Editors and Affiliations

  1. Institute of Cell Biology (Cancer Research), Medical School, University of Duisburg-Essen, Nordrhein-Westfalen, Essen, Germany

    Ralf Küppers

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Hübschmann, D., Schlesner, M. (2019). Evaluation of Whole Genome Sequencing Data. In: Küppers, R. (eds) Lymphoma. Methods in Molecular Biology, vol 1956. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9151-8_15

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  • DOI: https://doi.org/10.1007/978-1-4939-9151-8_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9150-1

  • Online ISBN: 978-1-4939-9151-8

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