Machine learning to improve the interpretation of intercalating dye-based quantitative PCR results

A. Godmer (1, 2) , J. Bigot (3, 2) , Q. Giai Gianetto (4) , Y. Benzerara (2) , N. Veziris (1, 2) , A. Aubry (1, 5) , J. Guitard (3, 2) , C. Hennequin (3, 2)

1 CIMI - Centre d'Immunologie et des Maladies Infectieuses
2 CHU Saint-Antoine [AP-HP]
3 CRSA - Centre de Recherche Saint-Antoine
4 3P5 - Plateforme protéomique 3P5 [Institut Cochin]
5 CHU Pitié-Salpêtrière [AP-HP]

This study aimed to evaluate the contribution of Machine Learning (ML) approach in the interpretation of intercalating dye-based quantitative PCR (IDqPCR) signals applied to the diagnosis of mucormycosis. The ML-based classification approach was applied to 734 results of IDqPCR categorized as positive (n = 74) or negative (n = 660) for mucormycosis after combining "visual reading" of the amplification and denaturation curves with clinical, radiological and microbiological criteria. Fourteen features were calculated to characterize the curves and injected in several pipelines including four ML-algorithms. An initial subset (n = 345) was used for the conception of classifiers. The classifier predictions were combined with majority voting to estimate performances of 48 meta-classifiers on an external dataset (n = 389). The visual reading returned 57 (7.7%), 568 (77.4%) and 109 (14.8%) positive, negative and doubtful results respectively. The Kappa coefficients of all the meta-classifiers were greater than 0.83 for the classification of IDqPCR results on the external dataset. Among these metaclassifiers, 6 exhibited Kappa coefficients at 1. The proposed ML-based approach allows a rigorous interpretation of IDqPCR curves, making the diagnosis of mucormycosis available for non-specialists in molecular diagnosis. A free online application was developed to classify IDqPCR from the raw data of the thermal cycler output (http:// gepamy-sat. asso. st/).

Domaines: Sciences du Vivant [q-bio]; Statistiques [stat]

A. Godmer, J. Bigot, Q. Giai Gianetto, Y. Benzerara, N. Veziris, et al.. Machine learning to improve the interpretation of intercalating dye-based quantitative PCR results. Scientific Reports, 2022, 12 (1), pp.16445. ⟨10.1038/s41598-022-21010-z⟩. ⟨pasteur-04093054⟩