A Framework for Efficient N-Way Interaction Testing in Case/Control Studies With Categorical Data.

Journal: IEEE open journal of engineering in medicine and biology
Published Date: Jul 27, 2021

Abstract

Most common diseases are influenced by multiple gene interactions and interactions with the environment. Performing an exhaustive search to identify such interactions is computationally expensive and needs to address the multiple testing problem. A four-step framework is proposed for the efficient identification of n-Way interactions. The framework was applied on a Multiple Sclerosis dataset with 725 subjects and 147 tagging SNPs. The first two steps of the framework are quality control and feature selection. The next step uses clustering and binary encodes the features. The final step performs the n-Way interaction testing. The feature space was reduced to 7 SNPs and using the proposed binary encoding, more 2-SNP and 3-SNP interactions were identified compared to using the initial encoding. The framework selects informative features and with the proposed binary encoding it is able to identify more n-way interactions by increasing the power of the statistical analysis.

Authors

  • Aristos Aristodimou
    Department of Computer ScienceUniversity of Cyprus Nicosia 1678 Cyprus.
  • Athos Antoniades
    Stremble Ventures Ltd. Limassol 59 4042 Cyprus.
  • Efthimios Dardiotis
    Department of Neurology, Faculty of MedicineUniversity of Thessaly Volos 38221 Greece.
  • Eleni Loizidou
    Department of Hygiene and EpidemiologyUniversity of Ioannina Ioannina 451 10 Greece.
  • George Spyrou
    Bioinformatics Department and Cyprus School of Molecular MedicineCyprus Institute of Neurology and Genetics Nicosia 2371 Cyprus.
  • Christina Votsi
    Neurogenetics Department and Cyprus School of Molecular MedicineCyprus Institute of Neurology and Genetics Nicosia 2371 Cyprus.
  • Christodoulou Kyproula
    Neurogenetics Department and Cyprus School of Molecular MedicineCyprus Institute of Neurology and Genetics Nicosia 2371 Cyprus.
  • Marios Pantzaris
    Department of Neurology and Cyprus School of Molecular MedicineCyprus Institute of Neurology and Genetics Nicosia 2371 Cyprus.
  • Nikolaos Grigoriadis
    Department of Neurology IIAristotle University of Thessaloniki Thessaloniki 541 24 Greece.
  • Georgios Hadjigeorgiou
    Medical SchoolUniversity of Cyprus Nicosia 1678 Cyprus.
  • Theodoros Kyriakides
    Department of Basic and Clinical SciencesMedical School University of Nicosia Nicosia 1678 Cyprus.
  • Constantinos Pattichi
    Department of Computer ScienceUniversity of Cyprus Nicosia 1678 Cyprus.

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