Machine learning application for development of a data-driven predictive model able to investigate quality of life scores in a rare disease

• Published in: Orphanet journal of rare diseases Vol. 15; no. 1; p. 46
• Main Authors: Spiga, Ottavia, Cicaloni, Vittoria, Fiorini, Cosimo, Trezza, Alfonso, Visibelli, Anna, Millucci, Lia, Bernardini, Giulia, Bernini, Andrea, Marzocchi, Barbara, Braconi, Daniela, Prischi, Filippo, Santucci, Annalisa
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 12.02.2020; BioMed Central; BMC
• Subjects: Algorithms; Alkaptonuria; Amyloid; Amyloidosis; Arthritis; Biological markers; Biomarkers; Body mass index; Care and treatment; Diseases; Genes; Health; Homogentisate 1,2-dioxygenase; Inflammation; Investigations; Learning algorithms; Lung diseases; Machine learning; Management science; Medical research; Mental health; Mutation; Neural networks; Osteoarthritis; Oxidation-reduction reactions; Oxidative stress; Pain; Patient monitoring equipment; Patient satisfaction; Patients; Plasma; Precision medicine; Prediction models; Proteins; QoL scores; Quality of life; Rare disease; Rare diseases; Regression analysis; Statistical analysis; Variables; Precision medicine; Alkaptonuria; QoL scores; Rare disease; Machine learning
• ISSN: 1750-1172; 1750-1172
• DOI: 10.1186/s13023-020-1305-0

Alkaptonuria (AKU) is an ultra-rare autosomal recessive disease caused by a mutation in the homogentisate 1,2-dioxygenase (HGD) gene. One of the main obstacles in studying AKU, and other ultra-rare diseases, is the lack of a standardized methodology to assess disease severity or response to treatment. Quality of Life scores (QoL) are a reliable way to monitor patients' clinical condition and health status. QoL scores allow to monitor the evolution of diseases and assess the suitability of treatments by taking into account patients' symptoms, general health status and care satisfaction. However, more comprehensive tools to study a complex and multi-systemic disease like AKU are needed. In this study, a Machine Learning (ML) approach was implemented with the aim to perform a prediction of QoL scores based on clinical data deposited in the ApreciseKUre, an AKU- dedicated database. Data derived from 129 AKU patients have been firstly examined through a preliminary statistical analysis (Pearson correlation coefficient) to measure the linear correlation between 11 QoL scores. The variable importance in QoL scores prediction of 110 ApreciseKUre biomarkers has been then calculated using XGBoost, with K-nearest neighbours algorithm (k-NN) approach. Due to the limited number of data available, this model has been validated using surrogate data analysis. We identified a direct correlation of 6 (age, Serum Amyloid A, Chitotriosidase, Advanced Oxidation Protein Products, S-thiolated proteins and Body Mass Index) out of 110 biomarkers with the QoL health status, in particular with the KOOS (Knee injury and Osteoarthritis Outcome Score) symptoms (Relative Absolute Error (RAE) 0.25). The error distribution of surrogate-model (RAE 0.38) was unequivocally higher than the true-model one (RAE of 0.25), confirming the consistency of our dataset. Our data showed that inflammation, oxidative stress, amyloidosis and lifestyle of patients correlates with the QoL scores for physical status, while no correlation between the biomarkers and patients' mental health was present (RAE 1.1). This proof of principle study for rare diseases confirms the importance of database, allowing data management and analysis, which can be used to predict more effective treatments.