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A Guide to Next Generation Sequence Analysis of Leishmania Genomes

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Leishmania

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1971))

Abstract

Next generation sequencing (NGS) technology transformed Leishmania genome studies and became an indispensable tool for Leishmania researchers. Recent Leishmania genomics analyses facilitated the discovery of various genetic diversities including single nucleotide polymorphisms (SNPs), copy number variations (CNVs), somy variations, and structural variations in detail and provided valuable insights into the complexity of the genome and gene regulation. Many aspects of Leishmania NGS analyses are similar to those of related pathogens like trypanosomes. However, the analyses of Leishmania genomes face a unique challenge because of the presence of frequent aneuploidy. This makes characterization and interpretation of read depth and somy a key part of Leishmania NGS analyses because read depth affects the accuracy of detection of all genetic variations. However, there are no general guidelines on how to explore and interpret the impact of aneuploidy, and this has made it difficult for biologists and bioinformaticians, especially for beginners, to perform their own analyses and interpret results across different analyses. In this guide we discuss a wide range of topics essential for Leishmania NGS analyses, ranging from how to set up a computational environment for genome analyses, to how to characterize genetic variations among Leishmania samples, and we will particularly focus on chromosomal copy number variation and its impact on genome analyses.

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Acknowledgments

We thank Geraldine De Muylder, Bart Cuypers, and Malgorzata Domagalska for their comments on the manuscript.

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Authors and Affiliations

  1. Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium

    Hideo Imamura & Jean-Claude Dujardin

  2. Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium

    Jean-Claude Dujardin

Authors
  1. Hideo Imamura
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  2. Jean-Claude Dujardin
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Corresponding author

Correspondence to Hideo Imamura .

Editor information

Editors and Affiliations

  1. Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany

    Joachim Clos

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Imamura, H., Dujardin, JC. (2019). A Guide to Next Generation Sequence Analysis of Leishmania Genomes. In: Clos, J. (eds) Leishmania. Methods in Molecular Biology, vol 1971. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9210-2_3

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  • DOI: https://doi.org/10.1007/978-1-4939-9210-2_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9209-6

  • Online ISBN: 978-1-4939-9210-2

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