Predicting phenotypes of asthma and eczema with machine learning

• Published in: BMC medical genomics Vol. 7; no. Suppl 1; p. S7
• Main Authors: Prosperi, Mattia CF, Marinho, Susana, Simpson, Angela, Custovic, Adnan, Buchan, Iain E
• Format: Journal Article
• Language: English
• Published: London BioMed Central 2014; Springer Nature B.V
• Subjects: Adult; Allergies; Artificial Intelligence; Asthma; Asthma - diagnosis; Asthma - genetics; Bioinformatics; Biomedical and Life Sciences; Biomedicine; Charitable foundations; Computational Biology - methods; Disease; Dust; Eczema - diagnosis; Eczema - genetics; Environment; Female; Gene Expression; Houses; Human Genetics; Humans; Linear Models; Male; Microarrays; Nonlinear Dynamics; Phenotype; Population; Precision Medicine; Studies; allergen; diagnostics; lung function; wheeze; eczema; model selection; single nucleotide polymorphisms; machine learning; Asthma
• ISSN: 1755-8794; 1755-8794
• DOI: 10.1186/1755-8794-7-S1-S7

Background There is increasing recognition that asthma and eczema are heterogeneous diseases. We investigated the predictive ability of a spectrum of machine learning methods to disambiguate clinical sub-groups of asthma, wheeze and eczema, using a large heterogeneous set of attributes in an unselected population. The aim was to identify to what extent such heterogeneous information can be combined to reveal specific clinical manifestations. Methods The study population comprised a cross-sectional sample of adults, and included representatives of the general population enriched by subjects with asthma. Linear and non-linear machine learning methods, from logistic regression to random forests, were fit on a large attribute set including demographic, clinical and laboratory features, genetic profiles and environmental exposures. Outcome of interest were asthma, wheeze and eczema encoded by different operational definitions. Model validation was performed via bootstrapping. Results The study population included 554 adults, 42% male, 38% previous or current smokers. Proportion of asthma, wheeze, and eczema diagnoses was 16.7%, 12.3%, and 21.7%, respectively. Models were fit on 223 non-genetic variables plus 215 single nucleotide polymorphisms. In general, non-linear models achieved higher sensitivity and specificity than other methods, especially for asthma and wheeze, less for eczema, with areas under receiver operating characteristic curve of 84%, 76% and 64%, respectively. Our findings confirm that allergen sensitisation and lung function characterise asthma better in combination than separately. The predictive ability of genetic markers alone is limited. For eczema, new predictors such as bio-impedance were discovered. Conclusions More usefully-complex modelling is the key to a better understanding of disease mechanisms and personalised healthcare: further advances are likely with the incorporation of more factors/attributes and longitudinal measures.