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Genomic Variant Annotation: A Comprehensive Review of Tools and Techniques

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Intelligent Systems Design and Applications (ISDA 2021)

Part of the book series: Lecture Notes in Networks and Systems ((LNNS,volume 418))

Abstract

Variant annotation is the process by which variants and mutations in the DNA are assigned functional information and is a crucial process in genomic sequence analysis. The outcomes of such annotation are beneficial because they can directly influence the conclusions arrived at in disease studies. Once genomic sequencing data is processed, and variants are called, it is vital to recognise the functional content of this data and then analyse the data to prioritise these variants. This is an interesting problem in the computational biology field and presents many open challenges that are yet to be addressed. In this paper, a comprehensive review of current work addressing the problem of variant annotation is presented. We detail the various tools and methods that have been developed for variant annotation along with datasets that have been used by these methods. Insights on open challenges and directions for future research are also discussed.

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Acknowledgements

The authors would like to thank Dr. Christopher Antony Cassa, Assistant Professor, Harvard Medical School, for his continued support and ideas for this manuscript.

Author information

Authors and Affiliations

  1. Healthcare Analytics and Language Engineering (HALE) Lab, Department of Information Technology, National Institute of Technology Karnataka, Surathkal, Mangalore, 575025, India

    Prajna Hebbar & S. Kamath Sowmya

Authors
  1. Prajna Hebbar
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  2. S. Kamath Sowmya
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Editor information

Editors and Affiliations

  1. Scientific Network for Innovation and Research Excellence, Machine Intelligence Research Labs (MIR Labs), Auburn, WA, USA

    Ajith Abraham

  2. Scientific Network for Innovation and Research Excellence, Machine Intelligence Research Labs (MIR Labs), Auburn, WA, USA

    Niketa Gandhi

  3. Institut für Wirtschaftsinformatik, Fachhochschule Nordwestschweiz, Olten, Switzerland

    Thomas Hanne

  4. Department of Computer Science and information Engineering, National University of Kaohsiung, Kaohsiung, Taiwan

    Tzung-Pei Hong

  5. Federal University of Bahia, Ondina, Brazil

    Tatiane Nogueira Rios

  6. Nantong University, Nantong Shi, Jiangsu, China

    Weiping Ding

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Hebbar, P., Sowmya, S.K. (2022). Genomic Variant Annotation: A Comprehensive Review of Tools and Techniques. In: Abraham, A., Gandhi, N., Hanne, T., Hong, TP., Nogueira Rios, T., Ding, W. (eds) Intelligent Systems Design and Applications. ISDA 2021. Lecture Notes in Networks and Systems, vol 418. Springer, Cham. https://doi.org/10.1007/978-3-030-96308-8_98

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