Detecting gene-gene interactions for complex quantitative traits using generalized fuzzy classification.

Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

Original Publication: [London] : BioMed Central, 2000-

Epistasis, Genetic* ; Fuzzy Logic* ; Phenotype*; Computational Biology/*methods; Animals ; Female ; Genetic Markers/genetics ; Humans ; Mice ; Models, Genetic ; Polymorphism, Single Nucleotide

Background: Quantitative traits or continuous outcomes related to complex diseases can provide more information and therefore more accurate analysis for identifying gene-gene and gene- environment interactions associated with complex diseases. Multifactor Dimensionality Reduction (MDR) is originally proposed to identify gene-gene and gene- environment interactions associated with binary status of complex diseases. Some efforts have been made to extend it to quantitative traits (QTs) and ordinal traits. However these and other methods are still not computationally efficient or effective.
Results: Generalized Fuzzy Quantitative trait MDR (GFQMDR) is proposed in this paper to strengthen identification of gene-gene interactions associated with a quantitative trait by first transforming it to an ordinal trait and then selecting best sets of genetic markers, mainly single nucleotide polymorphisms (SNPs) or simple sequence length polymorphic markers (SSLPs), as having strong association with the trait through generalized fuzzy classification using extended member functions. Experimental results on simulated datasets and real datasets show that our algorithm has better success rate, classification accuracy and consistency in identifying gene-gene interactions associated with QTs.
Conclusion: The proposed algorithm provides a more effective way to identify gene-gene interactions associated with quantitative traits.

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Keywords: Fuzzy accuracy; Gene-gene interactions; Multifactor dimensionality reduction; Ordinal traits; Quantitative traits

0 (Genetic Markers)

Date Created: 20180920 Date Completed: 20181018 Latest Revision: 20230928

20250114

PMC6145205

10.1186/s12859-018-2361-5

30227829